diff --git a/apollo_sv-base.json b/apollo_sv-base.json index 31ca33c..4e47885 100644 --- a/apollo_sv-base.json +++ b/apollo_sv-base.json @@ -52,9 +52,9 @@ "val" : "2023-01-10" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-06-02" + "val" : "2024-02-23" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2023-06-02/apollo_sv-base.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-02-23/apollo_sv-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", @@ -8334,7 +8334,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000480", - "lbl" : "geographical migration of organism", + "lbl" : "geographical movement of organism", "type" : "CLASS", "meta" : { "definition" : { @@ -11135,6 +11135,279 @@ "val" : "William R. Hogan" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000622", + "lbl" : "cumulative epidemic case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic." + }, + "comments" : [ "The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of cases from the beginning of the epidemic until recently." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000623", + "lbl" : "incident epidemic case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic." + }, + "comments" : [ "Incident case counts are measured according to regular intervals, typically day or week.", "The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624", + "lbl" : "count of events occurring in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of processes in which a population and/or its members participate during a given temporal region." + }, + "comments" : [ "As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625", + "lbl" : "count of deaths in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of death events that occurred in a population in a given temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population death count" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626", + "lbl" : "count of vaccinations in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccination events that occurred in a population during a temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population vaccination count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of vaccinations in a population during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627", + "lbl" : "count of hospital stays in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospital stays in a population during a temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population hospitalization count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of hospitalizations in a population during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628", + "lbl" : "count of infections in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections (process) that occurred in a population in a given temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population infection count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of infections in a population during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000629", + "lbl" : "cumulative epidemic infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000630", + "lbl" : "incident epidemic infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000631", + "lbl" : "cumulative epidemic death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000632", + "lbl" : "incident epidemic death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000633", + "lbl" : "cumulative epidemic hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000634", + "lbl" : "incident epidemic hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000635", + "lbl" : "cumulative epidemic vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000636", + "lbl" : "incident epidemic vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000637", + "lbl" : "intent to be vaccinated", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An intent to be vaccinated in the future." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000638", + "lbl" : "intent to vaccinate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An intention to give a vaccine to someone or an animal." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000639", + "lbl" : "vaccination with nirsevimab", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -31399,6 +31672,78 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000621", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000229" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000622", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000498" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000623", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000498" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000629", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000630", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000631", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000632", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000633", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000634", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000635", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000636", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000637", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/MF_0000073" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000638", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/MF_0000073" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000639", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000142" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "pred" : "is_a", diff --git a/apollo_sv-base.obo b/apollo_sv-base.obo index 0173acd..8a28910 100644 --- a/apollo_sv-base.obo +++ b/apollo_sv-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: apollo_sv/releases/2023-06-02/apollo_sv-base.owl +data-version: apollo_sv/releases/2024-02-23/apollo_sv-base.owl remark: 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). ontology: apollo_sv/apollo_sv-base property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string @@ -15,7 +15,7 @@ property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string property_value: owl:versionInfo "2023-01-10" xsd:string -property_value: owl:versionInfo "2023-06-02" xsd:string +property_value: owl:versionInfo "2024-02-23" xsd:string property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -4158,7 +4158,7 @@ property_value: IAO:0000600 "A predicted data item that is the maximum value of [Term] id: APOLLO_SV:00000480 -name: geographical migration of organism +name: geographical movement of organism def: "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." [] is_a: GO:0007610 ! behavior property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -4632,7 +4632,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string 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 migration of organism +is_a: APOLLO_SV:00000480 ! geographical movement of organism property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5487,6 +5487,148 @@ is_a: APOLLO_SV:00000229 ! place closure control strategy property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string +[Term] +id: APOLLO_SV:00000622 +name: cumulative epidemic case count +def: "A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic." [] +comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. +is_a: APOLLO_SV:00000498 ! count of cases in an epidemic +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "A count of cases from the beginning of the epidemic until recently." xsd:string + +[Term] +id: APOLLO_SV:00000623 +name: incident epidemic case count +def: "A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic." [] +comment: Incident case counts are measured according to regular intervals, typically day or week. +comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. +is_a: APOLLO_SV:00000498 ! count of cases in an epidemic +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week." xsd:string + +[Term] +id: APOLLO_SV:00000624 +name: count of events occurring in a population +def: "A count of processes in which a population and/or its members participate during a given temporal region." [] +comment: As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time. +is_a: APOLLO_SV:00000032 ! count +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000625 +name: count of deaths in a population +def: "A count of death events that occurred in a population in a given temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population death count" xsd:string + +[Term] +id: APOLLO_SV:00000626 +name: count of vaccinations in a population +def: "A count of vaccination events that occurred in a population during a temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population vaccination count" xsd:string +property_value: IAO:0000600 "A count of vaccinations in a population during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000627 +name: count of hospital stays in a population +def: "A count of hospital stays in a population during a temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population hospitalization count" xsd:string +property_value: IAO:0000600 "A count of hospitalizations in a population during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000628 +name: count of infections in a population +def: "A count of infections (process) that occurred in a population in a given temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population infection count" xsd:string +property_value: IAO:0000600 "A count of infections in a population during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000629 +name: cumulative epidemic infection count +def: "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000630 +name: incident epidemic infection count +def: "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000631 +name: cumulative epidemic death count +def: "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000632 +name: incident epidemic death count +def: "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000633 +name: cumulative epidemic hospitalization count +def: "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000627 ! count of hospital stays in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000634 +name: incident epidemic hospitalization count +def: "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000627 ! count of hospital stays in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000635 +name: cumulative epidemic vaccination count +def: "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000636 +name: incident epidemic vaccination count +def: "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000637 +name: intent to be vaccinated +def: "An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization." [] +is_a: MF:0000073 +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "An intent to be vaccinated in the future." xsd:string + +[Term] +id: APOLLO_SV:00000638 +name: intent to vaccinate +def: "An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system." [] +is_a: MF:0000073 +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "An intention to give a vaccine to someone or an animal." xsd:string + +[Term] +id: APOLLO_SV:00000639 +name: vaccination with nirsevimab +def: "A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab." [] +is_a: APOLLO_SV:00000142 ! vaccination +property_value: IAO:0000117 "William R. Hogan" xsd:string + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification @@ -5968,8 +6110,8 @@ name: eclose name: eclosion namespace: biological_process def: "The emergence of an adult insect from a pupa case." [] -xref: _:genid2147485523 -xref: _:genid2147485524 +xref: _:genid2147485547 +xref: _:genid2147485548 is_a: GO:0071684 ! organism emergence from protective structure property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -6001,10 +6143,10 @@ name: aging namespace: biological_process alt_id: GO:0016280 subset: goslim_generic -synonym: "_:genid2147485525" EXACT [] -synonym: "_:genid2147485526" EXACT [] -xref: _:genid2147485527 -xref: _:genid2147485528 +synonym: "_:genid2147485549" EXACT [] +synonym: "_:genid2147485550" EXACT [] +xref: _:genid2147485551 +xref: _:genid2147485552 is_a: GO:0032502 ! developmental process property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -6063,12 +6205,12 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0018991 name: oviposition namespace: biological_process -synonym: "_:genid2147485517" BROAD [] -synonym: "_:genid2147485518" BROAD [] -synonym: "_:genid2147485519" BROAD [] -synonym: "_:genid2147485520" BROAD [] -xref: _:genid2147485521 -xref: _:genid2147485522 +synonym: "_:genid2147485541" BROAD [] +synonym: "_:genid2147485542" BROAD [] +synonym: "_:genid2147485543" BROAD [] +synonym: "_:genid2147485544" BROAD [] +xref: _:genid2147485545 +xref: _:genid2147485546 is_a: GO:0019098 ! reproductive behavior property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -6126,8 +6268,8 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0019098 name: reproductive behavior namespace: biological_process -synonym: "_:genid2147485531" EXACT [] -synonym: "_:genid2147485532" EXACT [] +synonym: "_:genid2147485555" EXACT [] +synonym: "_:genid2147485556" EXACT [] is_a: GO:0007610 ! behavior is_a: GO:0048609 ! multicellular organismal reproductive process property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -6148,8 +6290,8 @@ namespace: biological_process subset: goslim_aspergillus subset: goslim_pir subset: gosubset_prok -synonym: "_:genid2147485529" NARROW [] -synonym: "_:genid2147485530" NARROW [] +synonym: "_:genid2147485553" NARROW [] +synonym: "_:genid2147485554" NARROW [] is_a: GO:0008150 ! biological process property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -6165,8 +6307,8 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0033057 name: multicellular organismal reproductive behavior namespace: biological_process -synonym: "_:genid2147485515" EXACT [] -synonym: "_:genid2147485516" EXACT [] +synonym: "_:genid2147485539" EXACT [] +synonym: "_:genid2147485540" EXACT [] is_a: GO:0019098 ! reproductive behavior property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string diff --git a/apollo_sv-base.owl b/apollo_sv-base.owl index 7d18b5e..d5acd97 100644 --- a/apollo_sv-base.owl +++ b/apollo_sv-base.owl @@ -9,6 +9,7 @@ xmlns:www="http://www.referent-tracking.com/" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" @@ -20,9 +21,10 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:apollo_sv="http://purl.obolibrary.org/obo/apollo_sv.owl/" - xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> + xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" + xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -39,7 +41,7 @@ 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). 2023-01-10 - 2023-06-02 + 2024-02-23 @@ -10850,7 +10852,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s Matthew Diller William R. Hogan 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. - geographical migration of organism + geographical movement of organism @@ -13055,6 +13057,304 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic. + William R. Hogan + A count of cases from the beginning of the epidemic until recently. + The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. + cumulative epidemic case count + + + + + + + + + A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic. + William R. Hogan + A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week. + Incident case counts are measured according to regular intervals, typically day or week. + The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. + incident epidemic case count + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of processes in which a population and/or its members participate during a given temporal region. + William R. Hogan + A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time. + As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time. + count of events occurring in a population + + + + + + + + + A count of death events that occurred in a population in a given temporal region. + William R. Hogan + population death count + count of deaths in a population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of vaccination events that occurred in a population during a temporal region. + William R. Hogan + population vaccination count + A count of vaccinations in a population during a particular time. + count of vaccinations in a population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of hospital stays in a population during a temporal region. + William R. Hogan + population hospitalization count + A count of hospitalizations in a population during a particular time. + count of hospital stays in a population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of infections (process) that occurred in a population in a given temporal region. + William R. Hogan + population infection count + A count of infections in a population during a particular time. + count of infections in a population + + + + + + + + + A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic infection count + + + + + + + + + A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic infection count + + + + + + + + + A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic death count + + + + + + + + + A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic death count + + + + + + + + + A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic hospitalization count + + + + + + + + + A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic hospitalization count + + + + + + + + + A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic vaccination count + + + + + + + + + A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic vaccination count + + + + + + + + + An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization. + William R. Hogan + An intent to be vaccinated in the future. + intent to be vaccinated + + + + + + + + + An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system. + William R. Hogan + An intention to give a vaccine to someone or an animal. + intent to vaccinate + + + + + + + + + A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. + William R. Hogan + vaccination with nirsevimab + + + + @@ -15117,6 +15417,12 @@ concretized and realized by an actor" with alternative term "instruct + + + + + + @@ -27516,5 +27822,5 @@ np.average(range(1,11), weights=range(10,0,-1)) - + diff --git a/apollo_sv-full.json b/apollo_sv-full.json index 74a8154..9272a70 100644 --- a/apollo_sv-full.json +++ b/apollo_sv-full.json @@ -49,9 +49,9 @@ "val" : "2023-01-10" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-06-02" + "val" : "2024-02-23" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2023-06-02/apollo_sv-full.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-02-23/apollo_sv-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", @@ -197,6 +197,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" } ] } }, { @@ -245,7 +248,7 @@ "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + "val" : "term created to ease viewing/sort terms for development purpose, and will not be included in a release" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -263,6 +266,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ready for release" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { @@ -302,6 +308,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "pending final vetting" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { @@ -364,12 +373,21 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -386,9 +404,18 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Barry Smith, Werner Ceusters" @@ -408,6 +435,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" @@ -427,6 +460,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" @@ -462,6 +501,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "requires discussion" + }, { + "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" : "Alan Ruttenberg" @@ -8785,7 +8827,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000480", - "lbl" : "geographical migration of organism", + "lbl" : "geographical movement of organism", "type" : "CLASS", "meta" : { "definition" : { @@ -11599,6 +11641,279 @@ "val" : "William R. Hogan" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000622", + "lbl" : "cumulative epidemic case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic." + }, + "comments" : [ "The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of cases from the beginning of the epidemic until recently." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000623", + "lbl" : "incident epidemic case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic." + }, + "comments" : [ "Incident case counts are measured according to regular intervals, typically day or week.", "The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624", + "lbl" : "count of events occurring in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of processes in which a population and/or its members participate during a given temporal region." + }, + "comments" : [ "As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625", + "lbl" : "count of deaths in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of death events that occurred in a population in a given temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population death count" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626", + "lbl" : "count of vaccinations in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccination events that occurred in a population during a temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population vaccination count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of vaccinations in a population during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627", + "lbl" : "count of hospital stays in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospital stays in a population during a temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population hospitalization count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of hospitalizations in a population during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628", + "lbl" : "count of infections in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections (process) that occurred in a population in a given temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population infection count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of infections in a population during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000629", + "lbl" : "cumulative epidemic infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000630", + "lbl" : "incident epidemic infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000631", + "lbl" : "cumulative epidemic death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000632", + "lbl" : "incident epidemic death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000633", + "lbl" : "cumulative epidemic hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000634", + "lbl" : "incident epidemic hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000635", + "lbl" : "cumulative epidemic vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000636", + "lbl" : "incident epidemic vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000637", + "lbl" : "intent to be vaccinated", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An intent to be vaccinated in the future." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000638", + "lbl" : "intent to vaccinate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An intention to give a vaccine to someone or an animal." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000639", + "lbl" : "vaccination with nirsevimab", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -11870,6 +12185,7 @@ "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])" }, + "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" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "ic" @@ -12091,6 +12407,7 @@ "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])" }, + "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "process" @@ -12294,6 +12611,7 @@ "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])" }, + "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" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "sdc" @@ -12336,12 +12654,21 @@ }, { "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " }, { "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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/OBOFoundry/COB/issues/65" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -12399,6 +12726,9 @@ "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "fiat-object" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "fiat-object-part" }, { @@ -12708,6 +13038,7 @@ "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])" }, + "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" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "gdc" @@ -12936,6 +13267,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." @@ -12975,6 +13309,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -13004,6 +13341,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." @@ -13025,6 +13365,15 @@ }, "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000054" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000054s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000054ed" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obsolete_is_realized_by" }, { @@ -13093,6 +13442,15 @@ "meta" : { "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000055" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000055s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000055ed" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "realizes" }, { @@ -13139,6 +13497,9 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } }, { @@ -13192,6 +13553,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { @@ -13298,6 +13662,15 @@ "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://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000110" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000110s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000110ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "c-has-part_at" }, { @@ -13329,6 +13702,15 @@ "val" : "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001" }, "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000111" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000111s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000111ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "c-has-ppart_at" }, { @@ -13388,6 +13770,15 @@ "val" : "b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" }, "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000117" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000117s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000117ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "o-has-part" }, { @@ -13431,6 +13822,15 @@ "val" : "b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" }, "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000118" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000118s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000118ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "o-has-ppart" }, { @@ -13506,6 +13906,15 @@ "val" : "[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" }, "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000132" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000132s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000132ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "o-part-of" }, { @@ -13981,6 +14390,22 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000157", "lbl" : "during which exists", "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000167", + "lbl" : "has participant at all times", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000167" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000167s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000167ed" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000169", "lbl" : "specifically depends on at some time", @@ -15541,10 +15966,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." + "val" : "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." }, "subsets" : [ "http://purl.org/obo/owl/obo#goslim_generic", "http://purl.org/obo/owl/obo#goslim_pir", "http://purl.org/obo/owl/obo#goslim_plant", "http://purl.org/obo/owl/obo#gosubset_prok" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -15570,10 +15998,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", + "val" : "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.", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecular function" @@ -15664,6 +16092,19 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006955", + "lbl" : "immune response", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0007562", "lbl" : "eclosion", @@ -15773,6 +16214,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", "val" : "Behavior" @@ -15799,6 +16243,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -15812,7 +16259,7 @@ "definition" : { "val" : "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." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological process" @@ -15832,6 +16279,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "biological_process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ido.owl" @@ -15900,7 +16350,13 @@ "lbl" : "oviposition", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water." + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -16034,7 +16490,13 @@ "lbl" : "reproductive behavior", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "The specific behavior of an organism that is associated with reproduction." + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -16064,8 +16526,14 @@ "lbl" : "developmental process", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." + }, "subsets" : [ "http://purl.org/obo/owl/obo#goslim_aspergillus", "http://purl.org/obo/owl/obo#goslim_pir", "http://purl.org/obo/owl/obo#gosubset_prok" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -16124,6 +16592,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -16240,7 +16711,11 @@ "meta" : { "definition" : { "val" : "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." - } + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044419", @@ -16306,6 +16781,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "janelomax" @@ -16317,6 +16795,19 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045297", + "lbl" : "post-mating behavior", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The specific behavior of an organism following mating." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0048609", "lbl" : "multicellular organismal reproductive process", @@ -16424,6 +16915,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "establishment of localization" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "Gene Ontology: http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ido.owl" @@ -16453,7 +16950,11 @@ "meta" : { "definition" : { "val" : "A biological process which involves another organism of the same or different species." - } + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051705", @@ -16489,6 +16990,9 @@ "val" : "GOC:mah" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go/releases/2019-07-01/go.owl" }, { @@ -16855,7 +17359,13 @@ "lbl" : "post-mating oviposition", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "The deposition of eggs, either fertilized or not, upon a surface or into a medium, following mating." + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -16879,6 +17389,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -18359,7 +18872,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Data about an ontology part is a data item about a part of an ontology, for example a term" + "val" : "data about an ontology part is a data item about a part of an ontology, for example a term" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -18367,6 +18880,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" } ] } }, { @@ -18519,6 +19035,9 @@ "val" : "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." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "example of usage" }, { @@ -18571,6 +19090,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000281" } ] } }, { @@ -18618,6 +19140,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" @@ -18660,12 +19185,15 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like." + "val" : "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)" }, "comments" : [ "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)." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "alternative label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -18678,6 +19206,9 @@ }, { "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" } ] } }, { @@ -18686,7 +19217,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "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" + "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -18700,6 +19231,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" @@ -20632,6 +21166,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" } ] } }, { @@ -21150,6 +21687,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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 ." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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 ." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" @@ -23919,6 +24459,782 @@ "val" : "EL++ ontology module" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000406", + "lbl" : "opportunistic infectious disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition to become part of a disorder only in organisms whose defenses are compromised." + }, + "comments" : [ "The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.", "This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "opportunitistic pathogenic disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000407", + "lbl" : "primary infectious disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition to become part of a disorder in organisms that have intact defenses." + }, + "comments" : [ "A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.", "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.\"" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000450", + "lbl" : "pathogenic disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disposition to initiate processes that result in a disorder." + }, + "comments" : [ "A pathogenic disposition is realized in processes that create a disorder.", "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pathogenicity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000452", + "lbl" : "infectious disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000453", + "lbl" : "zoonotic disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host." + }, + "comments" : [ "An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000454", + "lbl" : "reverse zoonotic disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host." + }, + "comments" : [ "An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000457", + "lbl" : "immunocompetent organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organism that has immunocompetence." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000463", + "lbl" : "infectious agent transmissibility", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process." + }, + "comments" : [ "The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000464", + "lbl" : "infectivity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "This quality is measured by the proportion of exposed who become infected." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000466", + "lbl" : "virulence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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. " + }, + "comments" : [ "This quality is measured by the proportion of clinically apparent cases that are severe or fatal." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000467", + "lbl" : "susceptibility", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality that inheres in an entity and is the degree to which it can be harmed by another entity." + }, + "comments" : [ "Low susceptibility is often referred to as resistance. In this sense, resistance is a quality." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000479", + "lbl" : "infectious disease incidence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000480", + "lbl" : "infection incidence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000481", + "lbl" : "infectious disease incidence proportion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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. " + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "cumulative incidence of infectious disease" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000482", + "lbl" : "infection incidence proportion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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. " + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "cumulative incidence of infection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000483", + "lbl" : "infectious disease incidence rate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000484", + "lbl" : "infection incidence rate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality that inheres in an organism population and is the infection incidence proportion per unit time." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000485", + "lbl" : "infectious disease prevalence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000486", + "lbl" : "infection prevalence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000487", + "lbl" : "infectious disease lifetime prevalence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000488", + "lbl" : "infectious agent seroprevalence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000489", + "lbl" : "infectious disease mortality rate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000490", + "lbl" : "infectious disease endemicity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000494", + "lbl" : "infectious disease sporadicity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "Sporadic quality of infectious disease is relational to previous prevalence of the disease." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000509", + "lbl" : "organism population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An aggregate of organisms of the same Species." + }, + "comments" : [ "The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000528", + "lbl" : "pathogen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity with a pathogenic disposition." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000530", + "lbl" : "primary pathogen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious agent with a primary infectious disposition." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "principal pathogen" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000531", + "lbl" : "host", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organism bearing a host role." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000596", + "lbl" : "infectious agent", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organism that has an infectious disposition." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000610", + "lbl" : "immunosuppression", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that attenuates an immune response." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000618", + "lbl" : "immunocompetence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disposition that is the ability to mount a normal immune response." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000623", + "lbl" : "communicability", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission." + }, + "comments" : [ "The disposition is realized in a direct, horizontal transmission process between members of the same Species." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000625", + "lbl" : "establishment of localization in host", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Requested addition of this term to the GO." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000626", + "lbl" : "appearance of disorder", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process by which a disorder comes into existence." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000629", + "lbl" : "host role", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000654", + "lbl" : "opportunistic pathogen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious agent with an opportunistic infectious disposition." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alex Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "opportunist" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000656", + "lbl" : "horizontal pathogen transmission process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000660", + "lbl" : "results_in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/MF_0000073", + "lbl" : "intentionality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/MF_0000074", + "lbl" : "bodily quality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A bodily quality is a quality that inheres in some extended organism." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/MF_0000075", + "lbl" : "mental quality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning." + } + } }, { "id" : "http://purl.obolibrary.org/obo/NBO_0000034", "lbl" : "sexual activity", @@ -23959,8 +25275,14 @@ } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", - "lbl" : "Virus", - "type" : "CLASS" + "lbl" : "Viruses", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10240", "lbl" : "Poxviridae", @@ -27575,7 +28897,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2", "lbl" : "Bacteria", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_201174", "lbl" : "Actinobacteria ", @@ -27741,6 +29069,16 @@ "val" : "Mirela L Vasconcelos" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2157", + "lbl" : "Archaea", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_223472", "lbl" : "Psoroptidia", @@ -27932,7 +29270,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", "lbl" : "Eukaryota", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_27592", "lbl" : "Bovinae", @@ -34507,7 +35851,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A device is a processed material which is designed to perform some function or functions" + "val" : "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." }, "comments" : [ "would include reagents" ], "basicPropertyValues" : [ { @@ -34516,9 +35860,18 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A voltmeter is a measurement device which is intended to perform some measure function." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." + }, { + "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" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "food should not classify as a device - counter example for using manufacturer and not device. macroscopic only" @@ -34534,6 +35887,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI Vancouver workshop 2010" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI development call 2012-12-17." } ] } }, { @@ -35062,6 +36418,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000121" + }, { + "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" : "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" @@ -35074,6 +36433,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://en.wikipedia.org/wiki/Organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", "val" : "Individual" @@ -35517,6 +36879,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "creation date: 2009-06-23T11:21:20Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ogms.owl" }, { "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", "val" : "disease" @@ -35573,6 +36938,23 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ogms.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ogms.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OGMS_0000060", + "lbl" : "bodily process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process in which at least one bodily component of an organsim participates." + }, + "comments" : [ "From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.jbiomedsem.com/content/1/1/10" } ] } }, { @@ -35595,6 +36977,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "creation date: 2009-06-23T11:55:44Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ogms.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ido.owl" @@ -35611,6 +36996,7 @@ "definition" : { "val" : "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." }, + "comments" : [ "From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Albert Goldfain" @@ -35623,6 +37009,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ogms.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ogms.owl" } ] } }, { @@ -36778,7 +38167,7 @@ "subsets" : [ "http://purl.org/obo/owl/obo#attribute_slim" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147486889" + "val" : "_:genid2147487112" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" @@ -36999,22 +38388,31 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", + "lbl" : "inheres in", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + "val" : "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" }, "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility inheres in this vase" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color inheres in this apple" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A dependent inheres in its bearer at all times for which the dependent exists." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inheres_in" @@ -37029,7 +38427,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -37058,6 +38456,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -37123,6 +38524,9 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } }, { @@ -37388,49 +38792,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "location_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001018", - "lbl" : "contained in", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "contained in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " + "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contained_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001019", - "lbl" : "contains", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "contains" + "val" : "location_of" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -37460,6 +38827,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "located_in" @@ -37469,6 +38839,12 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" } ] } }, { @@ -37482,6 +38858,9 @@ "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://xmlns.com/foaf/0.1/page", + "val" : "https://github.com/oborel/obo-relations/wiki/ROAndTime" } ] } }, { @@ -37564,7 +38943,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -37581,7 +38960,7 @@ "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -37598,7 +38977,7 @@ "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -37612,7 +38991,7 @@ "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -37628,7 +39007,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -37642,7 +39021,7 @@ "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -37655,11 +39034,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -37672,11 +39051,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -37689,12 +39068,12 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -37909,10 +39288,16 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + "val" : "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" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-7476-6306" }, { @@ -37921,6 +39306,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Hill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Tanya Berardini" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" @@ -38319,6 +39713,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "consumes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -38356,7 +39753,32 @@ "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "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" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" } ] } }, { @@ -38375,6 +39797,9 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -38392,6 +39817,9 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -38506,6 +39934,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -38559,7 +39990,7 @@ "val" : "enables part of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -38574,6 +40005,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -38747,6 +40181,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -38766,6 +40203,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -38938,7 +40378,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -38954,6 +40394,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes activity in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -39419,6 +40862,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -39439,6 +40885,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -39490,7 +40939,7 @@ "val" : "2018-01-26T23:49:30Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -39508,6 +40957,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:51Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -39530,7 +40982,7 @@ "val" : "2018-01-26T23:53:14Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -39553,7 +41005,7 @@ "val" : "2018-01-26T23:53:22Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -39570,6 +41022,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -39586,6 +41041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -39614,7 +41072,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -39719,7 +41177,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -39735,7 +41193,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -40138,18 +41596,45 @@ "val" : "https://github.com/ISA-tools/stato/issues/59" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/TRANS_0000000", + "lbl" : "transmission process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Suggested label: pathogen transmission process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/trans.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000061", "lbl" : "anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome." + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.", + "xrefs" : [ "CARO:0000003" ] }, - "subsets" : [ "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" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological structure" + }, { + "pred" : "hasExactSynonym", + "val" : "connected biological structure", + "xrefs" : [ "CARO:0000003" ] } ], "xrefs" : [ { "val" : "AAO:0010825" @@ -40165,6 +41650,8 @@ "val" : "EMAPA:0" }, { "val" : "FBbt:00007001" + }, { + "val" : "FMA:305751" }, { "val" : "FMA:67135" }, { @@ -40175,6 +41662,8 @@ "val" : "MA:0003000" }, { "val" : "MESH:A13" + }, { + "val" : "MESH:D000825" }, { "val" : "SCTID:362889002" }, { @@ -40195,6 +41684,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/uberon.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -40206,9 +41701,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that has mass." + "val" : "Anatomical entity that has mass.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "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" ], "xrefs" : [ { "val" : "AAO:0010264" }, { @@ -40235,6 +41731,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/uberon.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -40449,6 +41951,59 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "lbl" : "anatomical entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.", + "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "AAO:0010841" + }, { + "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" + }, { + "val" : "BILA:0000000" + }, { + "val" : "BIRNLEX:6" + }, { + "val" : "CARO:0000000" + }, { + "val" : "EHDAA2:0002229" + }, { + "val" : "FMA:62955" + }, { + "val" : "HAO:0000000" + }, { + "val" : "MA:0000001" + }, { + "val" : "NCIT:C12219" + }, { + "val" : "TAO:0100000" + }, { + "val" : "TGMA:0001822" + }, { + "val" : "UMLS:C1515976" + }, { + "val" : "WBbt:0000100" + }, { + "val" : "XAO:0000000" + }, { + "val" : "ZFA:0100000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0002405", "lbl" : "immune system", @@ -40507,12 +42062,14 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure that has more than one cell as a part." + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] }, - "subsets" : [ "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" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "multicellular structure" + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] } ], "xrefs" : [ { "val" : "CARO:0010000" @@ -40522,6 +42079,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/uberon.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -40571,6 +42134,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/uberon.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/uberon.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -41056,7 +42622,7 @@ "val" : "http://www.geneontology.org/formats/oboInOwl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147486870" + "val" : "_:genid2147487093" } ] } }, { @@ -41200,6 +42766,7 @@ "type" : "PROPERTY" }, { "id" : "http://www.w3.org/2002/07/owl#topObjectProperty", + "type" : "PROPERTY", "meta" 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"http://purl.obolibrary.org/obo/IDO_0000654", + "pred" : "http://purl.obolibrary.org/obo/RO_0000091", + "obj" : "http://purl.obolibrary.org/obo/IDO_0000406" + }, { + "sub" : "http://purl.obolibrary.org/obo/IDO_0000656", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/TRANS_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/MF_0000073", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/MF_0000075" + }, { + "sub" : "http://purl.obolibrary.org/obo/MF_0000074", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "sub" : "http://purl.obolibrary.org/obo/MF_0000075", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/MF_0000074" }, { "sub" : "http://purl.obolibrary.org/obo/NBO_0000034", "pred" : "is_a", @@ -46627,6 +48566,10 @@ "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_213849", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_29547" + }, { + "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2157", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_223472", "pred" : "is_a", @@ -48131,6 +50074,14 @@ "sub" : "http://purl.obolibrary.org/obo/OGMS_0000045", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OGMS_0000060", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/OGMS_0000060", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000167", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000087" }, { "sub" : "http://purl.obolibrary.org/obo/OGMS_0000063", "pred" : "is_a", @@ -48475,6 +50426,10 @@ "sub" : "http://purl.obolibrary.org/obo/STATO_0000398", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000679" + }, { + "sub" : "http://purl.obolibrary.org/obo/TRANS_0000000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000061", "pred" : "is_a", @@ -48483,6 +50438,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000467", "pred" : "is_a", @@ -48495,6 +50454,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000480", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002405", "pred" : "is_a", @@ -48587,6 +50550,10 @@ "sub" : "http://www.ebi.ac.uk/efo/EFO_0004600", "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://www.geneontology.org/formats/oboInOwl#Subset", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", "pred" : "type", @@ -48715,6 +50682,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000051", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000051", + "pred" : "subPropertyOf", + "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", "pred" : "subPropertyOf", @@ -49179,6 +51150,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002264", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002297", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/IDO_0000660" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002304", "pred" : "subPropertyOf", @@ -49607,6 +51582,10 @@ "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", @@ -49663,10 +51642,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0001015", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001025" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0001018", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001019" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002000", "pred" : "inverseOf", @@ -50288,6 +52263,55 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020000" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000457", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000618" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000528", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000450" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000530", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000407" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000531", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000629" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000596", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000452" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000610", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0006955" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000654", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000406" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0000679", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000027" ], @@ -50334,6 +52358,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50351,6 +52379,13 @@ "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000312", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], @@ -50388,7 +52423,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000083", @@ -50468,7 +52503,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", @@ -50493,10 +52528,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -50662,9 +52693,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/apollo_sv-full.obo b/apollo_sv-full.obo index 33e424c..4d03cd8 100644 --- a/apollo_sv-full.obo +++ b/apollo_sv-full.obo @@ -1,6 +1,7 @@ format-version: 1.2 -data-version: apollo_sv/releases/2023-06-02/apollo_sv-full.owl +data-version: apollo_sv/releases/2024-02-23/apollo_sv-full.owl subsetdef: attribute_slim "" +subsetdef: common_anatomy "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -10,6 +11,7 @@ subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" subsetdef: unit_group_slim "" +subsetdef: upper_level "" remark: 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). ontology: apollo_sv/apollo_sv-full property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string @@ -24,7 +26,7 @@ property_value: http://purl.org/dc/elements/1.1/title "Apollo Structured Vocabul property_value: http://purl.org/dc/terms/description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string property_value: owl:versionInfo "2023-01-10" xsd:string -property_value: owl:versionInfo "2023-06-02" xsd:string +property_value: owl:versionInfo "2024-02-23" xsd:string property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -1164,7 +1166,7 @@ name: disposition to become contaminated with a pathogen is_a: BFO:0000016 ! disposition intersection_of: BFO:0000016 ! disposition intersection_of: BFO:0000054 APOLLO_SV:00000167 {all_some="true", all_only="true"} ! is realized by contamination acquisition -relationship: RO:0000052 BFO:0000040 ! characteristic of material entity +relationship: RO:0000052 BFO:0000040 ! inheres in material entity property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -3471,8 +3473,8 @@ comment: The disposition of Influenza A virus H3N2 subtype to infect human being is_a: BFO:0000016 ! disposition intersection_of: BFO:0000016 ! disposition intersection_of: BFO:0000054 APOLLO_SV:00000114 {all_only="true"} ! is realized by infection -intersection_of: RO:0000052 OBI:0100026 ! characteristic of organism -relationship: RO:0000052 OBI:0100026 ! characteristic of organism +intersection_of: RO:0000052 OBI:0100026 ! inheres in organism +relationship: RO:0000052 OBI:0100026 ! inheres in organism property_value: IAO:0000111 "infectious disposition" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "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." xsd:string @@ -4231,7 +4233,7 @@ property_value: IAO:0000600 "A predicted data item that is the maximum value of [Term] id: APOLLO_SV:00000480 -name: geographical migration of organism +name: geographical movement of organism def: "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." [] is_a: GO:0007610 ! behavior property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -4711,7 +4713,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string 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 migration of organism +is_a: APOLLO_SV:00000480 ! geographical movement of organism property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5520,8 +5522,8 @@ def: "A monkeypox disease inhering in a human being." [] comment: requested by MIDAS CC is_a: DOID:3292 ! monkeypox intersection_of: DOID:3292 ! monkeypox -intersection_of: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens -relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens +intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens +relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens property_value: http://purl.org/dc/elements/1.1/date "2022-09-18T18:51:00" xsd:dateTime property_value: IAO:0000111 "monkeypox disease inhering in a human being" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5577,6 +5579,148 @@ is_a: APOLLO_SV:00000229 ! place closure control strategy property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string +[Term] +id: APOLLO_SV:00000622 +name: cumulative epidemic case count +def: "A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic." [] +comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. +is_a: APOLLO_SV:00000498 ! count of cases in an epidemic +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "A count of cases from the beginning of the epidemic until recently." xsd:string + +[Term] +id: APOLLO_SV:00000623 +name: incident epidemic case count +def: "A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic." [] +comment: Incident case counts are measured according to regular intervals, typically day or week. +comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. +is_a: APOLLO_SV:00000498 ! count of cases in an epidemic +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week." xsd:string + +[Term] +id: APOLLO_SV:00000624 +name: count of events occurring in a population +def: "A count of processes in which a population and/or its members participate during a given temporal region." [] +comment: As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time. +is_a: APOLLO_SV:00000032 ! count +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000625 +name: count of deaths in a population +def: "A count of death events that occurred in a population in a given temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population death count" xsd:string + +[Term] +id: APOLLO_SV:00000626 +name: count of vaccinations in a population +def: "A count of vaccination events that occurred in a population during a temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population vaccination count" xsd:string +property_value: IAO:0000600 "A count of vaccinations in a population during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000627 +name: count of hospital stays in a population +def: "A count of hospital stays in a population during a temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population hospitalization count" xsd:string +property_value: IAO:0000600 "A count of hospitalizations in a population during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000628 +name: count of infections in a population +def: "A count of infections (process) that occurred in a population in a given temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population infection count" xsd:string +property_value: IAO:0000600 "A count of infections in a population during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000629 +name: cumulative epidemic infection count +def: "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000630 +name: incident epidemic infection count +def: "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000631 +name: cumulative epidemic death count +def: "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000632 +name: incident epidemic death count +def: "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000633 +name: cumulative epidemic hospitalization count +def: "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000627 ! count of hospital stays in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000634 +name: incident epidemic hospitalization count +def: "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000627 ! count of hospital stays in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000635 +name: cumulative epidemic vaccination count +def: "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000636 +name: incident epidemic vaccination count +def: "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000637 +name: intent to be vaccinated +def: "An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization." [] +is_a: MF:0000073 ! intentionality +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "An intent to be vaccinated in the future." xsd:string + +[Term] +id: APOLLO_SV:00000638 +name: intent to vaccinate +def: "An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system." [] +is_a: MF:0000073 ! intentionality +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "An intention to give a vaccine to someone or an animal." xsd:string + +[Term] +id: APOLLO_SV:00000639 +name: vaccination with nirsevimab +def: "A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab." [] +is_a: APOLLO_SV:00000142 ! vaccination +property_value: IAO:0000117 "William R. Hogan" xsd:string + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification @@ -5693,8 +5837,8 @@ property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string property_value: IAO:0000116 "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" xsd:string -property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} -property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: IAO:0000116 "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" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5707,15 +5851,15 @@ relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part_of continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: IAO:0000116 "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" xsd:string -property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} -property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} -property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000116 "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" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5728,22 +5872,24 @@ property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} -property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} -property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} -property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} -property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000020 ! characteristic +disjoint_from: BFO:0000020 ! characteristic disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part_of independent continuant property_value: BFO:0000179 "ic" xsd:string @@ -5758,11 +5904,11 @@ property_value: IAO:0000112 "an orchestra." xsd:string property_value: IAO:0000112 "an organism" xsd:string property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string property_value: IAO:0000112 "the interior of your mouth" xsd:string -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} -property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} -property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5770,15 +5916,16 @@ id: BFO:0000006 name: spatial region is_a: BFO:0000141 ! immaterial entity disjoint_from: BFO:0000029 ! site +disjoint_from: BFO:0000029 ! site disjoint_from: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "s-region" xsd:string property_value: BFO:0000180 "SpatialRegion" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Spatial regions do not participate in processes." xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} -property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} -property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} +property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} +property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5786,17 +5933,18 @@ id: BFO:0000008 name: temporal region is_a: BFO:0000003 ! occurrent disjoint_from: BFO:0000011 ! spatiotemporal region +disjoint_from: BFO:0000011 ! spatiotemporal region disjoint_from: BFO:0000015 ! process disjoint_from: BFO:0000035 ! process boundary property_value: BFO:0000179 "t-region" xsd:string property_value: BFO:0000180 "TemporalRegion" xsd:string -property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} -property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} -property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} -property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} -property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} +property_value: IAO:0000116 "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" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} +property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} +property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} +property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} +property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5808,8 +5956,8 @@ property_value: BFO:0000179 "2d-s-region" xsd:string property_value: BFO:0000180 "TwoDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an infinitely thin plane in space." xsd:string property_value: IAO:0000112 "the surface of a sphere-shaped part of space" xsd:string -property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} -property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} +property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} +property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5821,25 +5969,27 @@ property_value: BFO:0000180 "SpatiotemporalRegion" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a human life" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a process of cellular meiosis." xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by the development of a cancer tumor" xsd:string -property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} -property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} -property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} -property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} +property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} +property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} +property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} +property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} property_value: IAO:0000601 "Every spatiotemporal region occupies_spatiotemporal_region itself." xsd:string -property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} -property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} -property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} -property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} +property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} +property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} +property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} +property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000015 {all_only="true"} ! part_of process property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string @@ -5850,7 +6000,7 @@ property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string property_value: IAO:0000116 "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)" xsd:string -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5865,17 +6015,18 @@ property_value: IAO:0000112 "certain people have a predisposition to colon cance property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 +name: realizable name: realizable entity def: "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." [] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic disjoint_from: BFO:0000019 ! quality relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part_of realizable entity property_value: BFO:0000179 "realizable" xsd:string @@ -5885,10 +6036,10 @@ property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:str property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5898,14 +6049,14 @@ is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "0d-s-region" xsd:string property_value: BFO:0000180 "ZeroDimensionalSpatialRegion" xsd:string -property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} -property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} +property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} +property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part_of quality property_value: BFO:0000179 "quality" xsd:string property_value: BFO:0000180 "Quality" xsd:string @@ -5915,20 +6066,24 @@ property_value: IAO:0000112 "the length of the circumference of your waist" xsd: property_value: IAO:0000112 "the mass of this piece of gold." xsd:string property_value: IAO:0000112 "the shape of your nose" xsd:string property_value: IAO:0000112 "the shape of your nostril" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 +name: characteristic name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part_of specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part_of characteristic +relationship: BFO:0000051 BFO:0000020 {all_only="true"} ! has part characteristic property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string @@ -5942,9 +6097,12 @@ property_value: IAO:0000112 "the pink color of a medium rare piece of grilled fi property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string [Term] id: BFO:0000023 @@ -5961,14 +6119,16 @@ property_value: IAO:0000112 "the role of a stone in marking a property boundary" property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000024 +name: fiat object name: fiat object part is_a: BFO:0000040 ! material entity +property_value: BFO:0000179 "fiat-object" xsd:string property_value: BFO:0000179 "fiat-object-part" xsd:string property_value: BFO:0000180 "FiatObjectPart" xsd:string property_value: IAO:0000112 "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" xsd:string @@ -5979,8 +6139,8 @@ property_value: IAO:0000112 "the FMA:regional parts of an intact human body." xs property_value: IAO:0000112 "the upper and lower lobes of the left lung" xsd:string property_value: IAO:0000112 "the Western hemisphere of the Earth" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5991,8 +6151,8 @@ disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "1d-s-region" xsd:string property_value: BFO:0000180 "OneDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an edge of a cube-shaped portion of space." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} -property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} +property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6018,12 +6178,12 @@ 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 {http://purl.obolibrary.org/obo/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 {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +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"} 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 {http://purl.obolibrary.org/obo/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 {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +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"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6034,8 +6194,8 @@ property_value: BFO:0000179 "3d-s-region" xsd:string property_value: BFO:0000180 "ThreeDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "a cube-shaped region of space" xsd:string property_value: IAO:0000112 "a sphere-shaped region of space," xsd:string -property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} -property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} +property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} +property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6059,8 +6219,8 @@ property_value: IAO:0000112 "the interior of your refrigerator" xsd:string property_value: IAO:0000112 "the lumen of your gut" xsd:string property_value: IAO:0000112 "the Piazza San Marco" xsd:string property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} -property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6085,14 +6245,15 @@ property_value: IAO:0000116 "BFO 2 Reference: BFO rests on the presupposition th property_value: IAO:0000116 "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)." xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant def: "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." [] -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +comment: 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. is_a: BFO:0000002 ! continuant relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part_of generically dependent continuant property_value: BFO:0000179 "gdc" xsd:string @@ -6100,7 +6261,7 @@ property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string -property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6113,21 +6274,21 @@ property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:str property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000035 name: process boundary -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "p-boundary" xsd:string property_value: BFO:0000180 "ProcessBoundary" xsd:string property_value: IAO:0000112 "the boundary between the 2nd and 3rd year of your life." xsd:string -property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} -property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} -property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} +property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} +property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} +property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6140,8 +6301,8 @@ property_value: BFO:0000179 "1d-t-region" xsd:string property_value: BFO:0000180 "OneDimensionalTemporalRegion" xsd:string property_value: IAO:0000112 "the temporal region during which a process occurs." xsd:string property_value: IAO:0000116 "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)." xsd:string -property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} -property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} +property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} +property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6167,26 +6328,26 @@ property_value: IAO:0000112 "the undetached arm of a human being" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000140 name: continuant fiat boundary -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} is_a: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "cf-boundary" xsd:string property_value: BFO:0000180 "ContinuantFiatBoundary" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"} property_value: IAO:0000601 "Every continuant fiat boundary is located at some spatial region at every time at which it exists" xsd:string -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6211,14 +6372,14 @@ property_value: IAO:0000112 "all lines of latitude and longitude" xsd:string property_value: IAO:0000112 "The Equator" xsd:string property_value: IAO:0000112 "the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin." xsd:string property_value: IAO:0000112 "the median sulcus of your tongue" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} -property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} +property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000144 name: process profile -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} is_a: BFO:0000015 ! process disjoint_from: BFO:0000182 ! history property_value: BFO:0000179 "process-profile" xsd:string @@ -6226,21 +6387,21 @@ property_value: BFO:0000180 "ProcessProfile" xsd:string property_value: IAO:0000112 "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" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000112 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} -property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} +property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000145 name: relational quality -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} is_a: BFO:0000019 ! quality property_value: BFO:0000179 "r-quality" xsd:string property_value: BFO:0000180 "RelationalQuality" xsd:string property_value: IAO:0000112 "a marriage bond, an instance of requited love, an obligation between one person and another." xsd:string property_value: IAO:0000112 "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." xsd:string -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6249,8 +6410,8 @@ name: two-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "2d-cf-boundary" xsd:string property_value: BFO:0000180 "TwoDimensionalContinuantFiatBoundary" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} -property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} +property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6262,9 +6423,9 @@ property_value: BFO:0000180 "ZeroDimensionalContinuantFiatBoundary" xsd:string property_value: IAO:0000112 "the geographic North Pole" xsd:string property_value: IAO:0000112 "the point of origin of some spatial coordinate system." xsd:string property_value: IAO:0000112 "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet" xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", http://www.w3.org/2000/01/rdf-schema#seeAlso="ZDRnpiIi:TUJ"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} -property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", seeAlso="ZDRnpiIi:TUJ"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} +property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6279,8 +6440,8 @@ property_value: IAO:0000112 "the moment at which a child is born" xsd:string property_value: IAO:0000112 "the moment at which a finger is detached in an industrial accident" xsd:string property_value: IAO:0000112 "the moment of death." xsd:string property_value: IAO:0000118 "temporal instant." xsd:string -property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} -property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} +property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} +property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6290,7 +6451,7 @@ is_a: BFO:0000015 ! process property_value: BFO:0000179 "history" xsd:string property_value: BFO:0000180 "History" xsd:string property_value: IAO:0000600 "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. " xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6941,21 +7102,27 @@ namespace: biological_process alt_id: GO:0019952 alt_id: GO:0050876 def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [] +def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok is_a: GO:0008150 ! biological_process property_value: APOLLO_SV:0000040 "Reproduction" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string property_value: IAO:0000600 "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." xsd:string [Term] id: GO:0003674 +name: gene product or complex activity name: molecular_function -def: "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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt] +def: "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." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +comment: This is the same as GO molecular function synonym: "molecular function" EXACT [] +is_a: BFO:0000015 ! process +disjoint_from: GO:0008150 ! biological_process [Term] id: GO:0006950 @@ -7002,14 +7169,21 @@ xref: Wikipedia:Inflammation is_a: GO:0006952 ! defense response property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string +[Term] +id: GO:0006955 +name: immune response +def: "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." [] +is_a: GO:0008150 ! biological_process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0007562 name: eclose name: eclosion namespace: biological_process def: "The emergence of an adult insect from a pupa case." [] -xref: _:genid2147486879 -xref: _:genid2147486880 +xref: _:genid2147487102 +xref: _:genid2147487103 is_a: GO:0071684 ! organism emergence from protective structure property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -7041,10 +7215,10 @@ name: aging namespace: biological_process alt_id: GO:0016280 subset: goslim_generic -synonym: "_:genid2147486881" EXACT [] -synonym: "_:genid2147486882" EXACT [] -xref: _:genid2147486883 -xref: _:genid2147486884 +synonym: "_:genid2147487104" EXACT [] +synonym: "_:genid2147487105" EXACT [] +xref: _:genid2147487106 +xref: _:genid2147487107 is_a: GO:0032502 ! developmental process property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -7052,6 +7226,7 @@ property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string id: GO:0007610 name: behavior namespace: biological_process +def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [] def: "The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate @@ -7062,8 +7237,10 @@ synonym: "behaviour" EXACT [] synonym: "behavioural response to stimulus" EXACT [] xref: Wikipedia:Behavior is_a: GO:0008150 ! biological_process +is_a: OGMS:0000060 ! bodily process property_value: APOLLO_SV:0000040 "Behavior" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007617 @@ -7074,13 +7251,16 @@ synonym: "mating behaviour" EXACT [] xref: Wikipedia:Mating_behaviour is_a: GO:0044705 ! multi-organism reproductive behavior property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008150 name: biological process name: biological_process -def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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." [GOC:pdt] +def: "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." [GOC:pdt] +def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." [] def: "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." [] +comment: A biological process is an evolved process comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] @@ -7088,7 +7268,9 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process +relationship: BFO:0000051 GO:0003674 ! has part molecular_function property_value: IAO:0000111 "biological_process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -7123,13 +7305,15 @@ is_a: GO:0003674 ! molecular_function id: GO:0018991 name: oviposition namespace: biological_process -synonym: "_:genid2147486871" BROAD [] -synonym: "_:genid2147486872" BROAD [] -synonym: "_:genid2147486873" BROAD [] -synonym: "_:genid2147486874" BROAD [] -xref: _:genid2147486875 -xref: _:genid2147486876 +def: "The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water." [] +synonym: "_:genid2147487094" BROAD [] +synonym: "_:genid2147487095" BROAD [] +synonym: "_:genid2147487096" BROAD [] +synonym: "_:genid2147487097" BROAD [] +xref: _:genid2147487098 +xref: _:genid2147487099 is_a: GO:0019098 ! reproductive behavior +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string [Term] @@ -7186,10 +7370,12 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0019098 name: reproductive behavior namespace: biological_process -synonym: "_:genid2147486887" EXACT [] -synonym: "_:genid2147486888" EXACT [] +def: "The specific behavior of an organism that is associated with reproduction." [] +synonym: "_:genid2147487110" EXACT [] +synonym: "_:genid2147487111" EXACT [] is_a: GO:0007610 ! behavior is_a: GO:0048609 ! multicellular organismal reproductive process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string [Term] @@ -7205,12 +7391,14 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0032502 name: developmental process namespace: biological_process +def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [] subset: goslim_aspergillus subset: goslim_pir subset: gosubset_prok -synonym: "_:genid2147486885" NARROW [] -synonym: "_:genid2147486886" NARROW [] +synonym: "_:genid2147487108" NARROW [] +synonym: "_:genid2147487109" NARROW [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string [Term] @@ -7225,8 +7413,8 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0033057 name: multicellular organismal reproductive behavior namespace: biological_process -synonym: "_:genid2147486877" EXACT [] -synonym: "_:genid2147486878" EXACT [] +synonym: "_:genid2147487100" EXACT [] +synonym: "_:genid2147487101" EXACT [] is_a: GO:0019098 ! reproductive behavior property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -7240,7 +7428,9 @@ synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior is_a: GO:0044419 ! interspecies interaction between organisms +is_a: GO:0051705 ! multi-organism behavior property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035821 @@ -7291,7 +7481,8 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0044409 name: entry into host def: "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." [] -is_a: GO:0008150 ! biological_process +is_a: GO:0051704 ! multi-organism process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044419 @@ -7325,10 +7516,19 @@ name: multi-organism reproductive behavior namespace: biological_process def: "The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species." [] is_a: GO:0019098 ! reproductive behavior +is_a: GO:0051705 ! multi-organism behavior property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl created_by: janelomax creation_date: 2012-09-19T16:02:12Z +[Term] +id: GO:0045297 +name: post-mating behavior +def: "The specific behavior of an organism following mating." [] +is_a: GO:0019098 ! reproductive behavior +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0048609 name: multicellular organismal reproductive process @@ -7380,9 +7580,12 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string [Term] id: GO:0051234 name: establishment of localization +def: "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [] def: "The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location." [] is_a: GO:0008150 ! biological_process property_value: IAO:0000111 "establishment of localization" xsd:string +property_value: IAO:0000412 "Gene Ontology: http://purl.obolibrary.org/obo/go.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string [Term] @@ -7399,6 +7602,7 @@ id: GO:0051704 name: multi-organism process def: "A biological process which involves another organism of the same or different species." [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051705 @@ -7417,6 +7621,7 @@ synonym: "behavioural interaction with other organism" EXACT [] xref: GOC:ai xref: GOC:mah is_a: GO:0007610 ! behavior +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go/releases/2019-07-01/go.owl" xsd:string [Term] @@ -7563,7 +7768,10 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0060403 name: post-mating oviposition namespace: biological_process +def: "The deposition of eggs, either fertilized or not, upon a surface or into a medium, following mating." [] is_a: GO:0018991 ! oviposition +is_a: GO:0045297 ! post-mating behavior +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string [Term] @@ -7575,6 +7783,7 @@ subset: goslim_pir subset: gosubset_prok synonym: "regulation" BROAD [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string [Term] @@ -8215,9 +8424,11 @@ 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" [] +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 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 [Term] id: IAO:0000104 @@ -8899,8 +9110,11 @@ def: "A denotator type indicates how a term should be interpreted from an ontolo is_a: IAO:0000102 ! data about an ontology part property_value: IAO:0000111 "denotator type" xsd:string property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string [Term] id: IAO:0000414 @@ -10259,6 +10473,440 @@ name: EL++ ontology module is_a: IAO:8000019 ! ontology module subsetted by OWL profile property_value: IAO:0000111 "EL++ ontology module" xsd:string +[Term] +id: IDO:0000406 +name: opportunistic infectious disposition +def: "An infectious disposition to become part of a disorder only in organisms whose defenses are compromised." [] +comment: The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host. +comment: This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin). +is_a: IDO:0000452 ! infectious disposition +disjoint_from: IDO:0000407 ! primary infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "opportunitistic pathogenic disposition" xsd:string + +[Term] +id: IDO:0000407 +name: primary infectious disposition +def: "An infectious disposition to become part of a disorder in organisms that have intact defenses." [] +comment: A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. +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." +is_a: IDO:0000452 ! infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000450 +name: pathogenic disposition +def: "A disposition to initiate processes that result in a disorder." [] +comment: A pathogenic disposition is realized in processes that create a disorder. +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. +is_a: BFO:0000016 ! disposition +disjoint_from: IDO:0000618 ! immunocompetence +disjoint_from: OGMS:0000031 ! disease +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "pathogenicity" xsd:string + +[Term] +id: IDO:0000452 +name: infectious disposition +def: "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." [] +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. +is_a: IDO:0000450 ! pathogenic disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000453 +name: zoonotic disposition +def: "An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host." [] +comment: An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis. +is_a: IDO:0000452 ! infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000454 +name: reverse zoonotic disposition +def: "An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host." [] +comment: An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. +is_a: IDO:0000452 ! infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000457 +name: immunocompetent organism +def: "An organism that has immunocompetence." [] +is_a: OBI:0100026 ! organism +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000091 IDO:0000618 ! has disposition immunocompetence +relationship: RO:0000091 IDO:0000618 ! has disposition immunocompetence +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000463 +name: infectious agent transmissibility +def: "A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process." [] +comment: The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. +is_a: BFO:0000019 ! quality +disjoint_from: IDO:0000464 ! infectivity +relationship: RO:0000052 IDO:0000596 ! inheres in infectious agent +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000464 +name: infectivity +def: "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." [] +comment: This quality is measured by the proportion of exposed who become infected. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000466 +name: virulence +def: "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. " [] +comment: This quality is measured by the proportion of clinically apparent cases that are severe or fatal. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000596 ! inheres in infectious agent +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000467 +name: susceptibility +def: "A quality that inheres in an entity and is the degree to which it can be harmed by another entity." [] +comment: Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 BFO:0000040 ! inheres in material entity +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000479 +name: infectious disease incidence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000480 +name: infection incidence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000481 +name: infectious disease incidence proportion +def: "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. " [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "cumulative incidence of infectious disease" xsd:string + +[Term] +id: IDO:0000482 +name: infection incidence proportion +def: "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. " [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "cumulative incidence of infection" xsd:string + +[Term] +id: IDO:0000483 +name: infectious disease incidence rate +def: "A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000484 +name: infection incidence rate +def: "A quality that inheres in an organism population and is the infection incidence proportion per unit time." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000485 +name: infectious disease prevalence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000486 +name: infection prevalence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000487 +name: infectious disease lifetime prevalence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000488 +name: infectious agent seroprevalence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000489 +name: infectious disease mortality rate +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000490 +name: infectious disease endemicity +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000494 +name: infectious disease sporadicity +def: "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." [] +comment: Sporadic quality of infectious disease is relational to previous prevalence of the disease. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000509 +name: organism population +def: "An aggregate of organisms of the same Species." [] +comment: The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. +is_a: BFO:0000027 ! object aggregate +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000528 +name: pathogen +def: "A material entity with a pathogenic disposition." [] +is_a: BFO:0000040 ! material entity +intersection_of: BFO:0000040 ! material entity +intersection_of: RO:0000091 IDO:0000450 ! has disposition pathogenic disposition +relationship: RO:0000091 IDO:0000450 ! has disposition pathogenic disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000530 +name: primary pathogen +def: "An infectious agent with a primary infectious disposition." [] +is_a: IDO:0000596 ! infectious agent +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000091 IDO:0000407 ! has disposition primary infectious disposition +relationship: RO:0000091 IDO:0000407 ! has disposition primary infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "principal pathogen" xsd:string + +[Term] +id: IDO:0000531 +name: host +def: "An organism bearing a host role." [] +is_a: OBI:0100026 ! organism +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000087 IDO:0000629 ! has role host role +relationship: RO:0000087 IDO:0000629 ! has role host role +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000596 +name: infectious agent +def: "An organism that has an infectious disposition." [] +is_a: IDO:0000528 ! pathogen +is_a: OBI:0100026 ! organism +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000091 IDO:0000452 ! has disposition infectious disposition +relationship: RO:0000091 IDO:0000452 ! has disposition infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000610 +name: immunosuppression +def: "A process that attenuates an immune response." [] +is_a: BFO:0000015 ! process +intersection_of: BFO:0000015 ! process +intersection_of: RO:0002212 GO:0006955 ! negatively regulates immune response +relationship: RO:0002212 GO:0006955 ! negatively regulates immune response +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000618 +name: immunocompetence +def: "A disposition that is the ability to mount a normal immune response." [] +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. +is_a: BFO:0000016 ! disposition +disjoint_from: OGMS:0000031 ! disease +relationship: BFO:0000054 GO:0006955 ! is realized by immune response +relationship: RO:0000052 OBI:0100026 ! inheres in organism +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000623 +name: communicability +def: "An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission." [] +comment: The disposition is realized in a direct, horizontal transmission process between members of the same Species. +is_a: IDO:0000452 ! infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000625 +name: establishment of localization in host +def: "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." [] +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. +is_a: GO:0051234 ! establishment of localization +relationship: BFO:0000066 IDO:0000531 ! occurs in host +property_value: IAO:0000116 "Requested addition of this term to the GO." xsd:string +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000626 +name: appearance of disorder +def: "A process by which a disorder comes into existence." [] +is_a: BFO:0000015 ! process +relationship: results_in_formation_of OGMS:0000045 ! disorder +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000629 +name: host role +def: "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism." [] +is_a: BFO:0000023 ! role +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000654 +name: opportunistic pathogen +def: "An infectious agent with an opportunistic infectious disposition." [] +is_a: IDO:0000596 ! infectious agent +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000091 IDO:0000406 ! has disposition opportunistic infectious disposition +relationship: RO:0000091 IDO:0000406 ! has disposition opportunistic infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alex Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "opportunist" xsd:string + +[Term] +id: IDO:0000656 +name: horizontal pathogen transmission process +def: "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." [] +is_a: TRANS:0000000 ! transmission process +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: MF:0000073 +name: intentionality +def: "Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something." [] +is_a: MF:0000075 ! mental quality + +[Term] +id: MF:0000074 +name: bodily quality +def: "A bodily quality is a quality that inheres in some extended organism." [] +is_a: BFO:0000019 ! quality + +[Term] +id: MF:0000075 +name: mental quality +def: "A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning." [] +is_a: MF:0000074 ! bodily quality + [Term] id: NBO:0000034 name: sexual activity @@ -10280,7 +10928,9 @@ property_value: IAO:0000118 "House mouse" xsd:string [Term] id: NCBITaxon:10239 name: Virus +name: Viruses is_a: OBI:0100026 ! organism +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:10240 @@ -12030,6 +12680,7 @@ property_value: has_rank NCBITaxon:species id: NCBITaxon:2 name: Bacteria is_a: OBI:0100026 ! organism +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:201174 @@ -12112,6 +12763,12 @@ name: Campylobacterales is_a: NCBITaxon:29547 ! Epsilonproteobacteria property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string +[Term] +id: NCBITaxon:2157 +name: Archaea +is_a: OBI:0100026 ! organism +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl + [Term] id: NCBITaxon:223472 name: Psoroptidia @@ -12203,6 +12860,7 @@ property_value: has_rank NCBITaxon:family id: NCBITaxon:2759 name: Eukaryota is_a: OBI:0100026 ! organism +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:27592 @@ -15153,15 +15811,20 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: OBI:0000968 name: device def: "A device is a processed material which is designed to perform some function or functions" [] +def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [] comment: would include reagents is_a: OBI:0000047 ! processed material property_value: IAO:0000111 "device" xsd:string property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string +property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string +property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." xsd:string property_value: IAO:0000116 "food should not classify as a device - counter example for using manufacturer and not device. macroscopic only" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string property_value: IAO:0000118 "instrument" xsd:string +property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string property_value: IAO:0000119 "OBI Vancouver workshop 2010" xsd:string [Term] @@ -15368,6 +16031,11 @@ id: OBI:0100026 name: organism def: "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." [] is_a: BFO:0000040 ! material entity +union_of: NCBITaxon:10239 ! Virus +union_of: NCBITaxon:2 ! Bacteria +union_of: NCBITaxon:2157 ! Archaea +union_of: NCBITaxon:2759 ! Eukaryota +disjoint_from: OGMS:0000045 ! disorder property_value: APOLLO_SV:0000040 "Individual" xsd:string property_value: IAO:0000111 "organism" xsd:string property_value: IAO:0000112 "animal" xsd:string @@ -15375,10 +16043,12 @@ property_value: IAO:0000112 "fungus" xsd:string property_value: IAO:0000112 "plant" xsd:string property_value: IAO:0000112 "virus" xsd:string property_value: IAO:0000114 IAO:0000121 +property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" xsd:string property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0200000 @@ -15573,6 +16243,7 @@ property_value: APOLLO_SV:0000040 "disease" xsd:string property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:21:20Z" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl [Term] id: OGMS:0000032 @@ -15595,8 +16266,18 @@ is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:39:44Z" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string +[Term] +id: OGMS:0000060 +name: bodily process +def: "A process in which at least one bodily component of an organsim participates." [] +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:0000119 "http://www.jbiomedsem.com/content/1/1/10" xsd:string + [Term] id: OGMS:0000063 name: disease course @@ -15607,17 +16288,20 @@ property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:55:44Z" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string [Term] id: OGMS:0000087 name: extended organism def: "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." [] +comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087 is_a: BFO:0000027 ! object aggregate property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=3" xsd:string property_value: IAO:0000232 "creation date: 2010-01-25T04:51:11Z" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl [Term] id: OGMS:0000090 @@ -15725,7 +16409,7 @@ id: OMRSE:00000001 name: human social role def: "A social role inhering in a human being." [] is_a: OMRSE:00000026 ! organism social role -relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens +relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens property_value: IAO:0000117 "Mathias Brochhausen\n" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string @@ -15827,7 +16511,7 @@ comment: Defined class that we will ultimately move to an application ontology. comment: Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. comment: Previous definition: A role in human social processes played by an organism. is_a: BFO:0000023 ! role -relationship: RO:0000052 OBI:0100026 ! characteristic of organism +relationship: RO:0000052 OBI:0100026 ! inheres in organism property_value: IAO:0000117 "William R. Hogan\nMathias Brochhausen" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string @@ -16056,7 +16740,7 @@ property_value: IAO:0000412 "http://www.geneontology.org/formats/oboInOwl" xsd:s id: PATO:0000001 name: quality def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic [Term] id: PATO:0000040 @@ -16412,13 +17096,30 @@ property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Weighted_arithmetic_m property_value: STATO:0000041 "" xsd:string property_value: STATO:0000391 "https://docs.scipy.org/doc/numpy/reference/generated/numpy.average.html\n\nnp.average(range(1,11), weights=range(10,0,-1))" xsd:string +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: TRANS:0000000 +name: transmission process +def: "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." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000116 "Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species." xsd:string +property_value: IAO:0000116 "Suggested label: pathogen transmission process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/trans.owl +property_value: IAO:0000412 "Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl" xsd:string + [Term] id: UBERON:0000061 name: anatomical structure namespace: uberon def: "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome." [] +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003] +subset: common_anatomy subset: upper_level synonym: "biological structure" EXACT [] +synonym: "connected biological structure" EXACT [CARO:0000003] xref: AAO:0010825 xref: AEO:0000003 xref: BILA:0000003 @@ -16426,12 +17127,14 @@ xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 xref: FBbt:00007001 +xref: FMA:305751 xref: FMA:67135 xref: GAID:781 xref: HAO:0000003 xref: http://dbpedia.org/ontology/AnatomicalStructure xref: MA:0003000 xref: MESH:A13 +xref: MESH:D000825 xref: SCTID:362889002 xref: TAO:0000037 xref: TGMA:0001823 @@ -16441,12 +17144,15 @@ xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 name: material anatomical entity namespace: uberon -def: "Anatomical entity that has mass." [] +def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy subset: upper_level xref: AAO:0010264 xref: AEO:0000006 @@ -16460,7 +17166,10 @@ xref: TAO:0001836 xref: TGMA:0001826 xref: VHOG:0001721 is_a: BFO:0000040 ! material entity +is_a: UBERON:0001062 ! anatomical entity property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -16562,6 +17271,33 @@ xref: ZFA:0001512 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +[Term] +id: UBERON:0001062 +name: anatomical entity +def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy +subset: upper_level +xref: AAO:0010841 +xref: AEO:0000000 +xref: BFO:0000004 +xref: BILA:0000000 +xref: BIRNLEX:6 +xref: CARO:0000000 +xref: EHDAA2:0002229 +xref: FMA:62955 +xref: HAO:0000000 +xref: MA:0000001 +xref: NCIT:C12219 +xref: TAO:0100000 +xref: TGMA:0001822 +xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} +xref: WBbt:0000100 +xref: XAO:0000000 +xref: ZFA:0100000 +is_a: BFO:0000004 ! independent continuant +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + [Term] id: UBERON:0002405 name: immune system @@ -16593,13 +17329,16 @@ property_value: UBPROP:0000003 "The antibody-based immune system defined by the id: UBERON:0010000 name: multicellular anatomical structure namespace: uberon -def: "An anatomical structure that has more than one cell as a part." [] +def: "An anatomical structure that has more than one cell as a part." [CARO:0010000] +subset: common_anatomy subset: upper_level -synonym: "multicellular structure" EXACT [] +synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 xref: FBbt:00100313 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0035943 @@ -16622,6 +17361,7 @@ synonym: "moment of death" EXACT [] synonym: "time of death" EXACT [] is_a: UBERON:0035943 ! life cycle temporal boundary property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UO:0000000 @@ -16830,6 +17570,7 @@ property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 @@ -16843,6 +17584,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_reflexive: true is_transitive: true is_a: RO:0002131 ! overlaps @@ -16861,6 +17603,7 @@ property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant p property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 @@ -16894,6 +17637,9 @@ property_value: IAO:0000231 IAO:0000228 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: TV_pl "BFO_0000054" xsd:string +property_value: TV_sg "BFO_0000054s" xsd:string +property_value: TV_vbg "BFO_0000054ed" xsd:string domain: BFO:0000017 ! realizable entity range: BFO:0000015 ! process inverse_of: BFO:0000055 ! realizes @@ -16908,6 +17654,9 @@ property_value: IAO:0000112 "this investigation realizes this investigator role" property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +property_value: TV_pl "BFO_0000055" xsd:string +property_value: TV_sg "BFO_0000055s" xsd:string +property_value: TV_vbg "BFO_0000055ed" xsd:string domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity @@ -16917,6 +17666,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -16960,7 +17710,9 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process @@ -17023,6 +17775,10 @@ property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a tern 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 +property_value: TV_pl "BFO_0000110" xsd:string +property_value: TV_sg "BFO_0000110s" xsd:string +property_value: TV_vbg "BFO_0000110ed" xsd:string +is_transitive: true [Typedef] id: BFO:0000111 @@ -17033,6 +17789,10 @@ 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 +property_value: TV_pl "BFO_0000111" xsd:string +property_value: TV_sg "BFO_0000111s" xsd:string +property_value: TV_vbg "BFO_0000111ed" xsd:string +is_transitive: true is_a: BFO:0000110 ! has continuant part at all times [Typedef] @@ -17063,6 +17823,11 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string property_value: IAO:0000600 "[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])" xsd:string property_value: IAO:0000602 "(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] " xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: TV_pl "BFO_0000117" xsd:string +property_value: TV_sg "BFO_0000117s" xsd:string +property_value: TV_vbg "BFO_0000117ed" xsd:string +is_transitive: true +inverse_of: BFO:0000132 ! part of occurrent [Typedef] id: BFO:0000118 @@ -17073,6 +17838,10 @@ property_value: BFO:0000179 "o-has-ppart" xsd:string property_value: BFO:0000180 "hasProperOccurrentPart" 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 +property_value: TV_pl "BFO_0000118" xsd:string +property_value: TV_sg "BFO_0000118s" xsd:string +property_value: TV_vbg "BFO_0000118ed" xsd:string +is_transitive: true is_a: BFO:0000117 ! has occurrent part [Typedef] @@ -17124,6 +17893,10 @@ property_value: IAO:0000602 "(forall (x y t) (if (exists (v) (and (occurrentPart property_value: IAO:0000602 "(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] " xsd:string property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] " xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: TV_pl "BFO_0000132" xsd:string +property_value: TV_sg "BFO_0000132s" xsd:string +property_value: TV_vbg "BFO_0000132ed" xsd:string +is_transitive: true [Typedef] id: BFO:0000136 @@ -17207,6 +17980,13 @@ is_a: BFO:0000157 ! during which exists id: BFO:0000157 name: during which exists +[Typedef] +id: BFO:0000167 +name: has participant at all times +property_value: TV_pl "BFO_0000167" xsd:string +property_value: TV_sg "BFO_0000167s" xsd:string +property_value: TV_vbg "BFO_0000167ed" xsd:string + [Typedef] id: BFO:0000169 name: specifically depends on at some time @@ -17295,7 +18075,7 @@ id: BFO:0000184 name: history of domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: BFO:0000066 ! unfolds_in +is_a: BFO:0000066 ! occurs in [Typedef] id: BFO:0000185 @@ -17559,6 +18339,10 @@ is_a: ObsoleteProperty ! ObsoleteProperty is_obsolete: true is_asymmetric: true +[Typedef] +id: IDO:0000660 +name: results_in + [Typedef] id: OBI:0000293 name: has_specified_input @@ -17675,11 +18459,16 @@ name: ObsoleteProperty [Typedef] id: RO:0000052 name: characteristic of +name: inheres in def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 is_functional: true @@ -17688,9 +18477,11 @@ inverse_of: RO:0000053 ! is bearer of [Typedef] id: RO:0000053 +name: bearer of name: bearer_of name: has characteristic name: is bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] def: "Inverse of characteristic_of" [] property_value: IAO:0000111 "bearer of" xsd:string property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string @@ -17701,7 +18492,8 @@ property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string +range: BFO:0000020 ! characteristic is_inverse_functional: true [Typedef] @@ -17724,6 +18516,7 @@ name: has participant name: has_participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000111 "has_participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string @@ -17733,6 +18526,7 @@ property_value: IAO:0000116 "Has_participant is a primitive instance-level relat property_value: IAO:0000118 "has_participant" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -17745,7 +18539,7 @@ property_value: IAO:0000112 "A journal article is an information artifact that i property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string domain: BFO:0000031 ! generically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic inverse_of: RO:0000059 ! concretizes [Typedef] @@ -17757,7 +18551,7 @@ property_value: IAO:0000111 "is_concretization_of" xsd:string property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -domain: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic range: BFO:0000031 ! generically dependent continuant [Typedef] @@ -17770,7 +18564,7 @@ property_value: IAO:0000116 "A function inheres in its bearer at all times for w property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function -is_a: RO:0000052 ! characteristic of +is_a: RO:0000052 ! inheres in inverse_of: RO:0000085 ! has function [Typedef] @@ -17782,7 +18576,7 @@ property_value: IAO:0000112 "this red color is a quality of this apple" xsd:stri property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string -is_a: RO:0000052 ! characteristic of +is_a: RO:0000052 ! inheres in inverse_of: RO:0000086 ! has quality [Typedef] @@ -17794,7 +18588,7 @@ property_value: IAO:0000112 "this investigator role is a role of this person" xs property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string -is_a: RO:0000052 ! characteristic of +is_a: RO:0000052 ! inheres in inverse_of: RO:0000087 ! has role [Typedef] @@ -17844,7 +18638,7 @@ name: disposition of def: "inverse of has disposition" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. subset: RO:0002259 -is_a: RO:0000052 ! characteristic of +is_a: RO:0000052 ! inheres in [Typedef] id: RO:0001000 @@ -17875,48 +18669,30 @@ property_value: IAO:0000111 "is location of" xsd:string property_value: IAO:0000112 "my head is the location of my brain" xsd:string property_value: IAO:0000112 "this cage is the location of this rat" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000118 "location_of" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true inverse_of: RO:0001025 ! located in -[Typedef] -id: RO:0001018 -name: contained in -subset: ro-eco -property_value: IAO:0000111 "contained in" xsd:string -property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string -property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string -property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string -property_value: IAO:0000118 "contained_in" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000004 ! independent continuant -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains - -[Typedef] -id: RO:0001019 -name: contains -subset: ro-eco -property_value: IAO:0000111 "contains" xsd:string -property_value: RO:0001900 RO:0001901 - [Typedef] id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {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."} ! independent continuant +range: BFO:0000004 {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."} ! independent continuant is_transitive: true transitive_over: BFO:0000050 ! part_of @@ -17953,7 +18729,7 @@ name: has regulatory component activity def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] is_a: RO:0002017 ! has component activity is_a: RO:0002334 ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -17963,7 +18739,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002335 ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -17973,7 +18749,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -17981,7 +18757,7 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -17991,44 +18767,44 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002180 ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -18084,7 +18860,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -18125,12 +18901,18 @@ is_a: BFO:0000051 ! has part id: RO:0002211 name: regulates def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] +def: "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" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -18206,7 +18988,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -18235,7 +19017,7 @@ def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -18360,6 +19142,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: RO:0002224 RO:0002233 is_a: RO:0000057 ! has_participant @@ -18382,7 +19165,7 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -18395,6 +19178,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -18406,6 +19190,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -18419,7 +19204,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part_of @@ -18460,6 +19245,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -18478,7 +19264,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -18488,7 +19274,7 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -18500,6 +19286,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: RO:0000057 ! has_participant is_a: RO:0002328 ! functionally related to @@ -18599,6 +19386,7 @@ def: "p indirectly positively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 @@ -18614,6 +19402,7 @@ def: "p indirectly negatively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true @@ -18720,12 +19509,13 @@ is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -18815,7 +19605,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002481 @@ -18975,6 +19765,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates @@ -18988,6 +19779,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -19016,7 +19808,7 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -19027,6 +19819,7 @@ id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -19038,7 +19831,7 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect @@ -19051,7 +19844,7 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect @@ -19062,6 +19855,7 @@ creation_date: 2018-01-26T23:53:22Z id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -19070,6 +19864,7 @@ creation_date: 2018-03-13T23:55:05Z id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -19089,7 +19884,7 @@ is_obsolete: true id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 @@ -19145,7 +19940,7 @@ id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: RO:0002411 ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -19154,7 +19949,7 @@ name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -19279,3 +20074,13 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string is_a: ObsoleteProperty ! ObsoleteProperty is_obsolete: true +[Typedef] +id: results_in_formation_of +name: results in formation of +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string +is_a: IDO:0000660 ! results_in + diff --git a/apollo_sv-full.owl b/apollo_sv-full.owl index 5c3f37c..e923d0e 100644 --- a/apollo_sv-full.owl +++ b/apollo_sv-full.owl @@ -9,6 +9,7 @@ xmlns:www="http://www.referent-tracking.com/" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" @@ -22,9 +23,10 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:apollo_sv="http://purl.obolibrary.org/obo/apollo_sv.owl/" - xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> + xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" + xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -40,7 +42,7 @@ 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). 2023-01-10 - 2023-06-02 + 2024-02-23 @@ -56,6 +58,24 @@ + + + + + + + + + + + + + + + + + + @@ -322,6 +342,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. + example example of usage 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. @@ -353,6 +374,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot + OBI_0000281 has curation status has curation status @@ -364,6 +386,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. definition + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -402,6 +425,7 @@ We also have the outstanding issue of how to aim different definitions to differ 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. PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note @@ -432,12 +456,15 @@ We also have the outstanding issue of how to aim different definitions to differ alternative label + alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee 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 alternative term @@ -451,7 +478,9 @@ We also have the outstanding issue of how to aim different definitions to differ definition source 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 + 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 PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -552,6 +581,7 @@ 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)" 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 + Chris Mungall Chris Mungall expand expression to @@ -602,6 +632,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. + 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 . 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 . PERSON:Alan Ruttenberg PERSON:Bjoern Peters @@ -810,6 +841,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] term replaced by + Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg @@ -883,10 +915,17 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] temporal interpretation temporal interpretation + https://github.com/oborel/obo-relations/wiki/ROAndTime + + + + + + @@ -1095,6 +1134,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1245,6 +1312,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -1393,6 +1466,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -1604,6 +1683,7 @@ For example, the disposition of a piece of glass to bend light and the lattice s a core relation that holds between a part and its whole 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. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 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'. @@ -1620,11 +1700,13 @@ A continuant cannot be part of an occurrent: use 'participates in'. An + part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -1633,6 +1715,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An + has part @@ -1642,6 +1725,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An a core relation that holds between a whole and its part 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. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 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'. @@ -1650,6 +1734,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has part has part @@ -1662,6 +1747,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. + BFO_0000054 + BFO_0000054s + BFO_0000054ed obsolete_is_realized_by realized in this disease is realized in this disease course @@ -1695,6 +1783,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. + BFO_0000055 + BFO_0000055s + BFO_0000055ed realizes this disease course realizes this disease this investigation realizes this investigator role @@ -1727,6 +1818,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. preceded_by http://purl.obolibrary.org/obo/ro.owl http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1759,6 +1851,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -1782,8 +1875,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + occurs in occurs in unfolds_in + https://wiki.geneontology.org/Occurs_in @@ -1855,6 +1950,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + BFO_0000110 + BFO_0000110s + BFO_0000110ed 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) @@ -1873,6 +1972,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + BFO_0000111 + BFO_0000111s + BFO_0000111ed c-has-ppart_at hasProperContinuantPartAt b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001 @@ -1906,6 +2009,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + BFO_0000117 + BFO_0000117s + BFO_0000117ed o-has-part hasOccurrentPart [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life @@ -1927,6 +2035,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + BFO_0000118 + BFO_0000118s + BFO_0000118ed o-has-ppart hasProperOccurrentPart [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) @@ -1975,6 +2087,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + BFO_0000132 + BFO_0000132s + BFO_0000132ed o-part-of occurrentPartOf Mary’s 5th birthday occurrent_part_of Mary’s life @@ -2112,6 +2228,17 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + BFO_0000167 + BFO_0000167s + BFO_0000167ed + has participant at all times + + + + @@ -2705,6 +2832,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + + + + results_in + + + + @@ -2883,13 +3018,18 @@ Werner suggests a solution based on "Magnitudes" a proposal for which inheres in + this fragility inheres in this vase this fragility is a characteristic of this vase + this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + 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 + A dependent inheres in its bearer at all times for which the dependent exists. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of + inheres in @@ -2904,15 +3044,19 @@ Werner suggests a solution based on "Magnitudes" a proposal for which this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of + 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 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. bearer of bearer_of is bearer of http://purl.obolibrary.org/obo/omrse.owl + bearer of bearer_of + has characteristic has characteristic is bearer of + https://github.com/oborel/obo-relations/pull/284 @@ -2941,6 +3085,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + @@ -2961,6 +3106,8 @@ Werner suggests a solution based on "Magnitudes" a proposal for which 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 has participant has_participant has_participant @@ -3159,6 +3306,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location 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/ + 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 location_of location of @@ -3166,42 +3314,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - - - - - contained in - Containment is location not involving parthood, and arises only where some immaterial continuant is involved. - Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - - contained_in - - - contained in - - - - - - - - contains - - - contains - - - - @@ -3238,11 +3350,14 @@ range: spatial region or site (immaterial continuant) a relation between two independent continuants, the target and the location, in which the target is entirely within the location 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 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/ + 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 located_in http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in + https://wiki.geneontology.org/Located_in @@ -3300,7 +3415,7 @@ range: spatial region or site (immaterial continuant) A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z has regulatory component activity @@ -3313,7 +3428,7 @@ range: spatial region or site (immaterial continuant) A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -3327,7 +3442,7 @@ range: spatial region or site (immaterial continuant) A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -3339,7 +3454,7 @@ range: spatial region or site (immaterial continuant) - dos + 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -3354,7 +3469,7 @@ range: spatial region or site (immaterial continuant) w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z has component process @@ -3366,7 +3481,7 @@ range: spatial region or site (immaterial continuant) - dos + 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -3375,7 +3490,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -3386,7 +3501,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z directly negatively regulated by @@ -3394,7 +3509,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -3405,7 +3520,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z directly positively regulated by @@ -3413,7 +3528,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -3424,7 +3539,7 @@ range: spatial region or site (immaterial continuant) A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -3433,7 +3548,7 @@ range: spatial region or site (immaterial continuant) A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -3634,10 +3749,16 @@ range: spatial region or site (immaterial continuant) + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. + 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 + 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 + Chris Mungall + David Hill + Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -3963,6 +4084,7 @@ range: spatial region or site (immaterial continuant) has input + https://wiki.geneontology.org/Has_input @@ -3997,7 +4119,22 @@ range: spatial region or site (immaterial continuant) affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within + + + + + + + + + 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. + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + Chris Mungall + GOC:mtg_berkeley_2013 + results_in_formation_of + results in formation of @@ -4014,6 +4151,7 @@ range: spatial region or site (immaterial continuant) 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 causally upstream of, positive effect + @@ -4029,6 +4167,7 @@ range: spatial region or site (immaterial continuant) causally upstream of, negative effect + @@ -4123,6 +4262,7 @@ range: spatial region or site (immaterial continuant) This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables + https://wiki.geneontology.org/Enables @@ -4181,7 +4321,7 @@ range: spatial region or site (immaterial continuant) actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -4194,7 +4334,9 @@ range: spatial region or site (immaterial continuant) inverse of enables + enabled by enabled by + https://wiki.geneontology.org/Enabled_by @@ -4358,6 +4500,7 @@ range: spatial region or site (immaterial continuant) indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4385,6 +4528,7 @@ range: spatial region or site (immaterial continuant) indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4575,6 +4719,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different enables activity in is active in + https://wiki.geneontology.org/Is_active_in @@ -4589,8 +4734,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -4994,6 +5139,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -5011,6 +5157,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -5062,7 +5209,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -5080,6 +5227,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -5099,7 +5247,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -5119,7 +5267,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -5132,6 +5280,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -5144,6 +5293,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -5193,7 +5343,7 @@ For example, A and B may be gene products and binding of B by A positively regul triggered by process - RO:cjm + @@ -5258,7 +5408,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -5271,7 +5421,7 @@ For example, A and B may be gene products and binding of B by A positively regul p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -5291,7 +5441,7 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -5456,10 +5606,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a. A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl - + @@ -16002,7 +16152,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s Matthew Diller William R. Hogan 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. - geographical migration of organism + geographical movement of organism @@ -18409,6 +18559,304 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic. + William R. Hogan + A count of cases from the beginning of the epidemic until recently. + The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. + cumulative epidemic case count + + + + + + + + + A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic. + William R. Hogan + A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week. + Incident case counts are measured according to regular intervals, typically day or week. + The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. + incident epidemic case count + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of processes in which a population and/or its members participate during a given temporal region. + William R. Hogan + A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time. + As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time. + count of events occurring in a population + + + + + + + + + A count of death events that occurred in a population in a given temporal region. + William R. Hogan + population death count + count of deaths in a population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of vaccination events that occurred in a population during a temporal region. + William R. Hogan + population vaccination count + A count of vaccinations in a population during a particular time. + count of vaccinations in a population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of hospital stays in a population during a temporal region. + William R. Hogan + population hospitalization count + A count of hospitalizations in a population during a particular time. + count of hospital stays in a population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of infections (process) that occurred in a population in a given temporal region. + William R. Hogan + population infection count + A count of infections in a population during a particular time. + count of infections in a population + + + + + + + + + A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic infection count + + + + + + + + + A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic infection count + + + + + + + + + A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic death count + + + + + + + + + A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic death count + + + + + + + + + A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic hospitalization count + + + + + + + + + A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic hospitalization count + + + + + + + + + A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic vaccination count + + + + + + + + + A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic vaccination count + + + + + + + + + An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization. + William R. Hogan + An intent to be vaccinated in the future. + intent to be vaccinated + + + + + + + + + An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system. + William R. Hogan + An intention to give a vaccine to someone or an animal. + intent to vaccinate + + + + + + + + + A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. + William R. Hogan + vaccination with nirsevimab + + + + @@ -18780,6 +19228,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (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] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -19057,6 +19506,12 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + process Process a process of cell-division, \ a beating of the heart @@ -19070,6 +19525,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si 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]) 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) (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] + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -19158,6 +19614,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si (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] (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] + realizable realizable entity @@ -19276,6 +19733,12 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + sdc SpecificallyDependentContinuant @@ -19291,12 +19754,24 @@ By "similar vaccines" we typically mean same pathogen, but could be si the shape of this hole. the smell of this portion of mozzarella 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. + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) 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]) 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. + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (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] + 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. + characteristic specifically dependent continuant + https://github.com/OBOFoundry/COB/issues/65 + https://github.com/oborel/obo-relations/pull/284 + + + + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + + @@ -19310,6 +19785,12 @@ By "similar vaccines" we typically mean same pathogen, but could be si per discussion with Barry Smith + + + + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + + @@ -19358,6 +19839,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si + fiat-object fiat-object-part FiatObjectPart 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 @@ -19371,6 +19853,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si 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]) (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] + fiat object fiat object part @@ -19602,6 +20085,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si 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. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + 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. generically dependent continuant @@ -21260,6 +21744,8 @@ Date accessed: 2015-04-13 The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. + The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. + http://purl.org/obo/owl/gene_ontology The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. Reproduction @@ -21270,6 +21756,7 @@ Date accessed: 2015-04-13 + reproduction reproduction @@ -21278,16 +21765,20 @@ Date accessed: 2015-04-13 - 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + + + 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. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + This is the same as GO molecular function + gene product or complex activity molecular_function - 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + 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. GOC:pdt @@ -21353,6 +21844,17 @@ Date accessed: 2015-04-13 + + + + + Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. + + immune response + + + + @@ -21433,7 +21935,10 @@ Date accessed: 2015-04-13 + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. + http://purl.obolibrary.org/obo/go.owl Behavior Wikipedia:Behavior @@ -21456,6 +21961,7 @@ Date accessed: 2015-04-13 The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. + http://purl.obolibrary.org/obo/go.owl Wikipedia:Mating_behaviour mating behaviour @@ -21470,9 +21976,18 @@ Date accessed: 2015-04-13 + + + + + + biological_process - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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. + 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. + A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. + 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. 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. + http://purl.obolibrary.org/obo/ido.owl jl 2012-09-19T15:05:24Z @@ -21482,6 +21997,7 @@ Date accessed: 2015-04-13 single organism process single-organism process GO:0008150 + A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological process biological_process @@ -21489,7 +22005,7 @@ Date accessed: 2015-04-13 - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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. + 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. GOC:pdt @@ -21564,6 +22080,8 @@ Date accessed: 2015-04-13 + The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water. + http://purl.org/obo/owl/gene_ontology @@ -21584,6 +22102,7 @@ Date accessed: 2015-04-13 biological_process + oviposition oviposition @@ -21659,6 +22178,8 @@ Date accessed: 2015-04-13 + The specific behavior of an organism that is associated with reproduction. + http://purl.org/obo/owl/gene_ontology @@ -21667,6 +22188,7 @@ Date accessed: 2015-04-13 biological_process + reproductive behavior reproductive behavior @@ -21690,6 +22212,8 @@ Date accessed: 2015-04-13 + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. + http://purl.org/obo/owl/gene_ontology @@ -21701,6 +22225,7 @@ Date accessed: 2015-04-13 + developmental process developmental process @@ -21740,7 +22265,9 @@ Date accessed: 2015-04-13 + Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + http://purl.obolibrary.org/obo/go.owl Wikipedia:Social_behavior social behaviour @@ -21821,8 +22348,10 @@ Date accessed: 2015-04-13 - + 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. + + entry into host entry into host @@ -21872,7 +22401,9 @@ Date accessed: 2015-04-13 + The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species. + http://purl.obolibrary.org/obo/go.owl janelomax 2012-09-19T16:02:12Z @@ -21883,6 +22414,17 @@ Date accessed: 2015-04-13 + + + + + The specific behavior of an organism following mating. + + post-mating behavior + + + + @@ -21956,7 +22498,10 @@ Date accessed: 2015-04-13 establishment of localization + Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. + + Gene Ontology: http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/ido.owl establishment of localization establishment of localization @@ -21983,6 +22528,8 @@ Date accessed: 2015-04-13 A biological process which involves another organism of the same or different species. + + multi-organism process multi-organism process @@ -21993,6 +22540,7 @@ Date accessed: 2015-04-13 Any process in which an organism has a behavioral effect on another organism of the same or different species. + http://purl.obolibrary.org/obo/go/releases/2019-07-01/go.owl GO:0023032 GO:0044709 @@ -22196,8 +22744,12 @@ Date accessed: 2015-04-13 + + The deposition of eggs, either fertilized or not, upon a surface or into a medium, following mating. + http://purl.org/obo/owl/gene_ontology biological_process + post-mating oviposition post-mating oviposition @@ -22208,6 +22760,7 @@ Date accessed: 2015-04-13 Any process that modulates a measurable attribute of any biological process, quality or function. + http://purl.obolibrary.org/obo/go.owl regulation biological_process @@ -23132,6 +23685,8 @@ XML document; The instructions in a XSD file" data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg Person:Alan Ruttenberg data about an ontology part @@ -23541,6 +24096,17 @@ clustering algorithm. + + + + + + + + + + + @@ -24331,10 +24897,15 @@ GO gene ontology denotator type + 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. 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. + A denotator type indicates how a term should be interpreted from an ontological perspective. A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg Alan Ruttenberg + Barry Smith, Werner Ceusters Barry Smith, Werner Ceusters + denotator type denotator type @@ -26672,6 +27243,1011 @@ No imports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious disposition to become part of a disorder only in organisms whose defenses are compromised. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + opportunitistic pathogenic disposition + The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host. + This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin). + opportunistic infectious disposition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious disposition to become part of a disorder in organisms that have intact defenses. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. + 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." + primary infectious disposition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A disposition to initiate processes that result in a disorder. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + pathogenicity + A pathogenic disposition is realized in processes that create a disorder. + 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. + pathogenic disposition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disposition + + + + + + + + + An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis. + zoonotic disposition + + + + + + + + + An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. + reverse zoonotic disposition + + + + + + + + + + + + + + + + + + + + + + + + + + An organism that has immunocompetence. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + immunocompetent organism + + + + + + + + + + + + + + + A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. + infectious agent transmissibility + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + This quality is measured by the proportion of exposed who become infected. + infectivity + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + This quality is measured by the proportion of clinically apparent cases that are severe or fatal. + virulence + + + + + + + + + + + + + + + A quality that inheres in an entity and is the degree to which it can be harmed by another entity. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. + susceptibility + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease incidence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infection incidence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + cumulative incidence of infectious disease + 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. + infectious disease incidence proportion + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + cumulative incidence of infection + 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. + infection incidence proportion + + + + + + + + + + + + + + + A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease incidence rate + + + + + + + + + + + + + + + A quality that inheres in an organism population and is the infection incidence proportion per unit time. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infection incidence rate + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease prevalence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infection prevalence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease lifetime prevalence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious agent seroprevalence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease mortality rate + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease endemicity + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + Sporadic quality of infectious disease is relational to previous prevalence of the disease. + infectious disease sporadicity + + + + + + + + + An aggregate of organisms of the same Species. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. + organism population + + + + + + + + + + + + + + + + + + + + + + + + + + A material entity with a pathogenic disposition. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + pathogen + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious agent with a primary infectious disposition. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + principal pathogen + primary pathogen + + + + + + + + + + + + + + + + + + + + + + + + + + An organism bearing a host role. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + host + + + + + + + + + + + + + + + + + + + + + + + + + + + An organism that has an infectious disposition. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + infectious agent + + + + + + + + + + + + + + + + + + + + + + + + + + A process that attenuates an immune response. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + immunosuppression + + + + + + + + + + + + + + + + + + + + + + + + A disposition that is the ability to mount a normal immune response. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + immunocompetence + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + The disposition is realized in a direct, horizontal transmission process between members of the same Species. + communicability + + + + + + + + + + + + + + + + + + + + + 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. + Requested addition of this term to the GO. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + establishment of localization in host + + + + + + + + + + + + + + + + + + + + + A process by which a disorder comes into existence. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + appearance of disorder + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + host role + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious agent with an opportunistic infectious disposition. + Albert Goldfain + Alex Diehl + Lindsay Cowell + opportunist + opportunistic pathogen + + + + + + + + + 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. + Lindsay Cowell + horizontal pathogen transmission process + + + + + + + + + Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something. + intentionality + + + + + + + + + A bodily quality is a quality that inheres in some extended organism. + bodily quality + + + + + + + + + A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning. + mental quality + + + + @@ -26702,7 +28278,9 @@ No imports + Virus + Viruses @@ -30271,6 +31849,8 @@ No imports + + Bacteria Bacteria @@ -30421,6 +32001,16 @@ No imports + + + + + + Archaea + + + + @@ -30606,6 +32196,8 @@ No imports + + Eukaryota Eukaryota @@ -35926,6 +37518,7 @@ No imports Homo sapiens human being + Homo sapiens Homo sapiens @@ -36826,13 +38419,28 @@ for now. device A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + A device is a processed material which is designed to perform some function or functions + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + +2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: + +(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. + +(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. + +(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. + +In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. food should not classify as a device - counter example for using manufacturer and not device. macroscopic only 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. PERSON: Helen Parkinson instrument OBI Vancouver workshop 2010 + OBI development call 2012-12-17. would include reagents device @@ -37168,13 +38776,25 @@ https://www.doi.org/ + + + + + + + + + + + organism animal fungus plant virus + 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. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: @@ -37182,6 +38802,7 @@ OBI doesn't take position as to when an organism starts or ends being an o This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism + Individual organism @@ -37459,6 +39080,7 @@ This issue is outside the scope of OBI. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:21:20Z + disease disease @@ -37492,12 +39114,31 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:39:44Z + http://purl.obolibrary.org/obo/ogms.owl disorder + + + + + + + + + + + A process in which at least one bodily component of an organsim participates. + http://www.jbiomedsem.com/content/1/1/10 + From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060 + bodily process + + + + @@ -37507,6 +39148,7 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z + http://purl.obolibrary.org/obo/ido.owl http://purl.obolibrary.org/obo/ogms.owl disease course @@ -37522,7 +39164,9 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z + http://purl.obolibrary.org/obo/ogms.owl + From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087 extended organism @@ -38751,12 +40395,29 @@ np.average(range(1,11), weights=range(10,0,-1)) + + + + + 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. + Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species. + Suggested label: pathogen transmission process + + Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl + transmission process + + + + Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. http://purl.obolibrary.org/obo/uberon.owl + + AAO:0010825 AEO:0000003 BILA:0000003 @@ -38764,11 +40425,13 @@ np.average(range(1,11), weights=range(10,0,-1)) EHDAA2:0003003 EMAPA:0 FBbt:00007001 + FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:A13 + MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 @@ -38778,11 +40441,25 @@ np.average(range(1,11), weights=range(10,0,-1)) ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure + connected biological structure uberon UBERON:0000061 + anatomical structure + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + + + + + connected biological structure + CARO:0000003 + @@ -38790,8 +40467,11 @@ np.average(range(1,11), weights=range(10,0,-1)) + Anatomical entity that has mass. http://purl.obolibrary.org/obo/uberon.owl + + AAO:0010264 AEO:0000006 BILA:0000006 @@ -38805,9 +40485,16 @@ np.average(range(1,11), weights=range(10,0,-1)) VHOG:0001721 uberon UBERON:0000465 + material anatomical entity + + + + Anatomical entity that has mass. + http://orcid.org/0000-0001-9114-8737 + @@ -38926,6 +40613,51 @@ np.average(range(1,11), weights=range(10,0,-1)) + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + AAO:0010841 + AEO:0000000 + BFO:0000004 + BILA:0000000 + BIRNLEX:6 + CARO:0000000 + EHDAA2:0002229 + FMA:62955 + HAO:0000000 + MA:0000001 + NCIT:C12219 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + WBbt:0000100 + XAO:0000000 + ZFA:0100000 + UBERON:0001062 + + + anatomical entity + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + FMA:62955 + http://orcid.org/0000-0001-9114-8737 + + + + + UMLS:C1515976 + ncithesaurus:Anatomic_Structure_System_or_Substance + + + + @@ -38964,14 +40696,29 @@ np.average(range(1,11), weights=range(10,0,-1)) An anatomical structure that has more than one cell as a part. http://purl.obolibrary.org/obo/uberon.owl + + CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 + multicellular anatomical structure + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + + + + + multicellular structure + FBbt:00100313 + @@ -38994,6 +40741,7 @@ np.average(range(1,11), weights=range(10,0,-1)) A life cycle temporal boundary that marks the end of the life cycle of the organism. + http://purl.obolibrary.org/obo/uberon.owl end of life cycle moment of death @@ -39332,12 +41080,28 @@ np.average(range(1,11), weights=range(10,0,-1)) + Obsolete Class Obsolete Class obsolete_class + + + + + + + + + + + + + + + + + +## Elucidation + +This is used when the statement/axiom is assumed to hold true 'eternally' + +## How to interpret (informal) + +First the "atemporal" FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + + ## Elucidation This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; @@ -39741,6 +41554,63 @@ This interpretation is *not* the same as an at-all-times relation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -39774,10 +41644,10 @@ This interpretation is *not* the same as an at-all-times relation - + - + @@ -39795,66 +41665,54 @@ This interpretation is *not* the same as an at-all-times relation - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -39867,8 +41725,8 @@ This interpretation is *not* the same as an at-all-times relation - - + + @@ -39878,7 +41736,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -39888,7 +41746,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -39905,8 +41763,8 @@ This interpretation is *not* the same as an at-all-times relation - - + + @@ -40168,7 +42026,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40178,8 +42036,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40189,8 +42047,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40207,8 +42065,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40227,7 +42085,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40237,8 +42095,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40248,8 +42106,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40266,8 +42124,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40283,8 +42141,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40294,7 +42152,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40304,8 +42162,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40315,8 +42173,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40335,8 +42193,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40354,8 +42212,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40365,8 +42223,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40376,8 +42234,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40394,8 +42252,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40412,8 +42270,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40423,8 +42281,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40434,8 +42292,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40452,8 +42310,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40470,8 +42328,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40481,8 +42339,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40492,8 +42350,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40510,8 +42368,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40527,9 +42385,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40538,9 +42396,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40555,8 +42413,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40572,9 +42430,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40583,9 +42441,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40600,8 +42458,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40617,9 +42475,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40628,9 +42486,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40645,8 +42503,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40662,9 +42520,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40673,9 +42531,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40690,8 +42548,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40707,9 +42565,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40718,9 +42576,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40735,8 +42593,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40752,9 +42610,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40763,9 +42621,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40780,7 +42638,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40790,7 +42648,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40808,9 +42666,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40819,9 +42677,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40836,7 +42694,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40846,7 +42704,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40863,7 +42721,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40874,7 +42732,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40907,9 +42765,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40918,9 +42776,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40935,8 +42793,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40951,9 +42809,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40962,9 +42820,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40978,9 +42836,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40995,7 +42853,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -41006,7 +42864,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -41022,7 +42880,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -41039,9 +42897,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -41050,9 +42908,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -41084,8 +42942,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -41095,8 +42953,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -41123,5 +42981,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/apollo_sv.json b/apollo_sv.json index 8a3045d..6dbc268 100644 --- a/apollo_sv.json +++ b/apollo_sv.json @@ -49,9 +49,9 @@ "val" : "2023-01-10" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-06-02" + "val" : "2024-02-23" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2023-06-02/apollo_sv.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-02-23/apollo_sv.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", @@ -197,6 +197,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" } ] } }, { @@ -245,7 +248,7 @@ "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + "val" : "term created to ease viewing/sort terms for development purpose, and will not be included in a release" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -263,6 +266,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ready for release" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { @@ -302,6 +308,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "pending final vetting" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { @@ -364,12 +373,21 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -386,9 +404,18 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Barry Smith, Werner Ceusters" @@ -408,6 +435,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" @@ -427,6 +460,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" @@ -462,6 +501,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "requires discussion" + }, { + "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" : "Alan Ruttenberg" @@ -8785,7 +8827,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000480", - "lbl" : "geographical migration of organism", + "lbl" : "geographical movement of organism", "type" : "CLASS", "meta" : { "definition" : { @@ -11599,6 +11641,279 @@ "val" : "William R. Hogan" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000622", + "lbl" : "cumulative epidemic case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic." + }, + "comments" : [ "The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of cases from the beginning of the epidemic until recently." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000623", + "lbl" : "incident epidemic case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic." + }, + "comments" : [ "Incident case counts are measured according to regular intervals, typically day or week.", "The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624", + "lbl" : "count of events occurring in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of processes in which a population and/or its members participate during a given temporal region." + }, + "comments" : [ "As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625", + "lbl" : "count of deaths in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of death events that occurred in a population in a given temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population death count" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626", + "lbl" : "count of vaccinations in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccination events that occurred in a population during a temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population vaccination count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of vaccinations in a population during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627", + "lbl" : "count of hospital stays in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospital stays in a population during a temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population hospitalization count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of hospitalizations in a population during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628", + "lbl" : "count of infections in a population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections (process) that occurred in a population in a given temporal region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "population infection count" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A count of infections in a population during a particular time." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000629", + "lbl" : "cumulative epidemic infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000630", + "lbl" : "incident epidemic infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000631", + "lbl" : "cumulative epidemic death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000632", + "lbl" : "incident epidemic death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000633", + "lbl" : "cumulative epidemic hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000634", + "lbl" : "incident epidemic hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000635", + "lbl" : "cumulative epidemic vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000636", + "lbl" : "incident epidemic vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000637", + "lbl" : "intent to be vaccinated", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An intent to be vaccinated in the future." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000638", + "lbl" : "intent to vaccinate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An intention to give a vaccine to someone or an animal." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000639", + "lbl" : "vaccination with nirsevimab", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -11870,6 +12185,7 @@ "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])" }, + "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" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "ic" @@ -12091,6 +12407,7 @@ "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])" }, + "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "process" @@ -12294,6 +12611,7 @@ "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])" }, + "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" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "sdc" @@ -12336,12 +12654,21 @@ }, { "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " }, { "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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/OBOFoundry/COB/issues/65" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -12399,6 +12726,9 @@ "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "fiat-object" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "fiat-object-part" }, { @@ -12708,6 +13038,7 @@ "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])" }, + "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" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "gdc" @@ -12936,6 +13267,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." @@ -12975,6 +13309,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -13004,6 +13341,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." @@ -13025,6 +13365,15 @@ }, "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000054" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000054s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000054ed" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obsolete_is_realized_by" }, { @@ -13093,6 +13442,15 @@ "meta" : { "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000055" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000055s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000055ed" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "realizes" }, { @@ -13139,6 +13497,9 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } }, { @@ -13192,6 +13553,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { @@ -13298,6 +13662,15 @@ "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://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000110" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000110s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000110ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "c-has-part_at" }, { @@ -13329,6 +13702,15 @@ "val" : "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001" }, "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000111" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000111s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000111ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "c-has-ppart_at" }, { @@ -13388,6 +13770,15 @@ "val" : "b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" }, "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000117" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000117s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000117ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "o-has-part" }, { @@ -13431,6 +13822,15 @@ "val" : "b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" }, "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000118" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000118s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000118ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "o-has-ppart" }, { @@ -13506,6 +13906,15 @@ "val" : "[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" }, "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000132" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000132s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000132ed" + }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "o-part-of" }, { @@ -13981,6 +14390,22 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000157", "lbl" : "during which exists", "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000167", + "lbl" : "has participant at all times", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_pl", + "val" : "BFO_0000167" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_sg", + "val" : "BFO_0000167s" + }, { + "pred" : "http://attempto.ifi.uzh.ch/ace_lexicon#TV_vbg", + "val" : "BFO_0000167ed" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000169", "lbl" : "specifically depends on at some time", @@ -15541,10 +15966,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." + "val" : "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." }, "subsets" : [ "http://purl.org/obo/owl/obo#goslim_generic", "http://purl.org/obo/owl/obo#goslim_pir", "http://purl.org/obo/owl/obo#goslim_plant", "http://purl.org/obo/owl/obo#gosubset_prok" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -15570,10 +15998,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", + "val" : "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.", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecular function" @@ -15664,6 +16092,19 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006955", + "lbl" : "immune response", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0007562", "lbl" : "eclosion", @@ -15773,6 +16214,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", "val" : "Behavior" @@ -15799,6 +16243,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -15812,7 +16259,7 @@ "definition" : { "val" : "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." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological process" @@ -15832,6 +16279,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "biological_process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ido.owl" @@ -15900,7 +16350,13 @@ "lbl" : "oviposition", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water." + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -16034,7 +16490,13 @@ "lbl" : "reproductive behavior", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "The specific behavior of an organism that is associated with reproduction." + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -16064,8 +16526,14 @@ "lbl" : "developmental process", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." + }, "subsets" : [ "http://purl.org/obo/owl/obo#goslim_aspergillus", "http://purl.org/obo/owl/obo#goslim_pir", "http://purl.org/obo/owl/obo#gosubset_prok" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -16124,6 +16592,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -16240,7 +16711,11 @@ "meta" : { "definition" : { "val" : "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." - } + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044419", @@ -16306,6 +16781,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "janelomax" @@ -16317,6 +16795,19 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045297", + "lbl" : "post-mating behavior", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The specific behavior of an organism following mating." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0048609", "lbl" : "multicellular organismal reproductive process", @@ -16424,6 +16915,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "establishment of localization" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "Gene Ontology: http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ido.owl" @@ -16453,7 +16950,11 @@ "meta" : { "definition" : { "val" : "A biological process which involves another organism of the same or different species." - } + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/GO_0051705", @@ -16489,6 +16990,9 @@ "val" : "GOC:mah" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go/releases/2019-07-01/go.owl" }, { @@ -16855,7 +17359,13 @@ "lbl" : "post-mating oviposition", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "The deposition of eggs, either fertilized or not, upon a surface or into a medium, following mating." + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.org/obo/owl/gene_ontology" }, { @@ -16879,6 +17389,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/go.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -18359,7 +18872,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Data about an ontology part is a data item about a part of an ontology, for example a term" + "val" : "data about an ontology part is a data item about a part of an ontology, for example a term" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -18367,6 +18880,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" } ] } }, { @@ -18519,6 +19035,9 @@ "val" : "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." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "example of usage" }, { @@ -18571,6 +19090,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000281" } ] } }, { @@ -18618,6 +19140,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" @@ -18660,12 +19185,15 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like." + "val" : "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)" }, "comments" : [ "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)." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "alternative label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -18678,6 +19206,9 @@ }, { "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" } ] } }, { @@ -18686,7 +19217,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "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" + "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -18700,6 +19231,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" @@ -20632,6 +21166,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" } ] } }, { @@ -21150,6 +21687,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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 ." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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 ." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" @@ -23919,6 +24459,782 @@ "val" : "EL++ ontology module" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000406", + "lbl" : "opportunistic infectious disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition to become part of a disorder only in organisms whose defenses are compromised." + }, + "comments" : [ "The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.", "This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "opportunitistic pathogenic disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000407", + "lbl" : "primary infectious disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition to become part of a disorder in organisms that have intact defenses." + }, + "comments" : [ "A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.", "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.\"" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000450", + "lbl" : "pathogenic disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disposition to initiate processes that result in a disorder." + }, + "comments" : [ "A pathogenic disposition is realized in processes that create a disorder.", "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pathogenicity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000452", + "lbl" : "infectious disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000453", + "lbl" : "zoonotic disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host." + }, + "comments" : [ "An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000454", + "lbl" : "reverse zoonotic disposition", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host." + }, + "comments" : [ "An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000457", + "lbl" : "immunocompetent organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organism that has immunocompetence." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000463", + "lbl" : "infectious agent transmissibility", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process." + }, + "comments" : [ "The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000464", + "lbl" : "infectivity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "This quality is measured by the proportion of exposed who become infected." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000466", + "lbl" : "virulence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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. " + }, + "comments" : [ "This quality is measured by the proportion of clinically apparent cases that are severe or fatal." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000467", + "lbl" : "susceptibility", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality that inheres in an entity and is the degree to which it can be harmed by another entity." + }, + "comments" : [ "Low susceptibility is often referred to as resistance. In this sense, resistance is a quality." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000479", + "lbl" : "infectious disease incidence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000480", + "lbl" : "infection incidence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000481", + "lbl" : "infectious disease incidence proportion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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. " + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "cumulative incidence of infectious disease" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000482", + "lbl" : "infection incidence proportion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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. " + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "cumulative incidence of infection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000483", + "lbl" : "infectious disease incidence rate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000484", + "lbl" : "infection incidence rate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A quality that inheres in an organism population and is the infection incidence proportion per unit time." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000485", + "lbl" : "infectious disease prevalence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000486", + "lbl" : "infection prevalence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000487", + "lbl" : "infectious disease lifetime prevalence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000488", + "lbl" : "infectious agent seroprevalence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000489", + "lbl" : "infectious disease mortality rate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000490", + "lbl" : "infectious disease endemicity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000494", + "lbl" : "infectious disease sporadicity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "Sporadic quality of infectious disease is relational to previous prevalence of the disease." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000509", + "lbl" : "organism population", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An aggregate of organisms of the same Species." + }, + "comments" : [ "The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000528", + "lbl" : "pathogen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity with a pathogenic disposition." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000530", + "lbl" : "primary pathogen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious agent with a primary infectious disposition." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "principal pathogen" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000531", + "lbl" : "host", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organism bearing a host role." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000596", + "lbl" : "infectious agent", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organism that has an infectious disposition." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000610", + "lbl" : "immunosuppression", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that attenuates an immune response." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000618", + "lbl" : "immunocompetence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disposition that is the ability to mount a normal immune response." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000623", + "lbl" : "communicability", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission." + }, + "comments" : [ "The disposition is realized in a direct, horizontal transmission process between members of the same Species." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000625", + "lbl" : "establishment of localization in host", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Requested addition of this term to the GO." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000626", + "lbl" : "appearance of disorder", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process by which a disorder comes into existence." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000629", + "lbl" : "host role", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alexander Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000654", + "lbl" : "opportunistic pathogen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious agent with an opportunistic infectious disposition." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alex Diehl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "opportunist" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000656", + "lbl" : "horizontal pathogen transmission process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Lindsay Cowell" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000660", + "lbl" : "results_in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/MF_0000073", + "lbl" : "intentionality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/MF_0000074", + "lbl" : "bodily quality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A bodily quality is a quality that inheres in some extended organism." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/MF_0000075", + "lbl" : "mental quality", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning." + } + } }, { "id" : "http://purl.obolibrary.org/obo/NBO_0000034", "lbl" : "sexual activity", @@ -23959,8 +25275,14 @@ } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", - "lbl" : "Virus", - "type" : "CLASS" + "lbl" : "Viruses", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10240", "lbl" : "Poxviridae", @@ -27575,7 +28897,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2", "lbl" : "Bacteria", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_201174", "lbl" : "Actinobacteria ", @@ -27741,6 +29069,16 @@ "val" : "Mirela L Vasconcelos" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2157", + "lbl" : "Archaea", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_223472", "lbl" : "Psoroptidia", @@ -27932,7 +29270,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", "lbl" : "Eukaryota", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_27592", "lbl" : "Bovinae", @@ -34507,7 +35851,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A device is a processed material which is designed to perform some function or functions" + "val" : "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." }, "comments" : [ "would include reagents" ], "basicPropertyValues" : [ { @@ -34516,9 +35860,18 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A voltmeter is a measurement device which is intended to perform some measure function." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." + }, { + "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" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "food should not classify as a device - counter example for using manufacturer and not device. macroscopic only" @@ -34534,6 +35887,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI Vancouver workshop 2010" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI development call 2012-12-17." } ] } }, { @@ -35062,6 +36418,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000121" + }, { + "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" : "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" @@ -35074,6 +36433,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://en.wikipedia.org/wiki/Organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", "val" : "Individual" @@ -35517,6 +36879,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "creation date: 2009-06-23T11:21:20Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ogms.owl" }, { "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", "val" : "disease" @@ -35573,6 +36938,23 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ogms.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ogms.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OGMS_0000060", + "lbl" : "bodily process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process in which at least one bodily component of an organsim participates." + }, + "comments" : [ "From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.jbiomedsem.com/content/1/1/10" } ] } }, { @@ -35595,6 +36977,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "creation date: 2009-06-23T11:55:44Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ogms.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ido.owl" @@ -35611,6 +36996,7 @@ "definition" : { "val" : "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." }, + "comments" : [ "From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Albert Goldfain" @@ -35623,6 +37009,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ogms.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/ogms.owl" } ] } }, { @@ -36778,7 +38167,7 @@ "subsets" : [ "http://purl.org/obo/owl/obo#attribute_slim" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147486889" + "val" : "_:genid2147487112" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" @@ -36999,22 +38388,31 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", + "lbl" : "inheres in", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + "val" : "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" }, "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility inheres in this vase" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color inheres in this apple" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A dependent inheres in its bearer at all times for which the dependent exists." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inheres_in" @@ -37029,7 +38427,7 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -37058,6 +38456,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -37123,6 +38524,9 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } }, { @@ -37388,49 +38792,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "location_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001018", - "lbl" : "contained in", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "contained in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " + "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contained_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001019", - "lbl" : "contains", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "contains" + "val" : "location_of" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -37460,6 +38827,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "located_in" @@ -37469,6 +38839,12 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" } ] } }, { @@ -37482,6 +38858,9 @@ "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://xmlns.com/foaf/0.1/page", + "val" : "https://github.com/oborel/obo-relations/wiki/ROAndTime" } ] } }, { @@ -37564,7 +38943,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -37581,7 +38960,7 @@ "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -37598,7 +38977,7 @@ "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -37612,7 +38991,7 @@ "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -37628,7 +39007,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -37642,7 +39021,7 @@ "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -37655,11 +39034,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -37672,11 +39051,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -37689,12 +39068,12 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -37909,10 +39288,16 @@ "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + "val" : "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" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-7476-6306" }, { @@ -37921,6 +39306,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Hill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Tanya Berardini" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" @@ -38319,6 +39713,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "consumes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -38356,7 +39753,32 @@ "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "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" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" } ] } }, { @@ -38375,6 +39797,9 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -38392,6 +39817,9 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -38506,6 +39934,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -38559,7 +39990,7 @@ "val" : "enables part of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -38574,6 +40005,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -38747,6 +40181,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -38766,6 +40203,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -38938,7 +40378,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -38954,6 +40394,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes activity in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -39419,6 +40862,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -39439,6 +40885,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -39490,7 +40939,7 @@ "val" : "2018-01-26T23:49:30Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -39508,6 +40957,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:51Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -39530,7 +40982,7 @@ "val" : "2018-01-26T23:53:14Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -39553,7 +41005,7 @@ "val" : "2018-01-26T23:53:22Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -39570,6 +41022,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -39586,6 +41041,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -39614,7 +41072,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -39719,7 +41177,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -39735,7 +41193,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -40138,18 +41596,45 @@ "val" : "https://github.com/ISA-tools/stato/issues/59" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/TRANS_0000000", + "lbl" : "transmission process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Suggested label: pathogen transmission process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/trans.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0000061", "lbl" : "anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome." + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.", + "xrefs" : [ "CARO:0000003" ] }, - "subsets" : [ "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" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological structure" + }, { + "pred" : "hasExactSynonym", + "val" : "connected biological structure", + "xrefs" : [ "CARO:0000003" ] } ], "xrefs" : [ { "val" : "AAO:0010825" @@ -40165,6 +41650,8 @@ "val" : "EMAPA:0" }, { "val" : "FBbt:00007001" + }, { + "val" : "FMA:305751" }, { "val" : "FMA:67135" }, { @@ -40175,6 +41662,8 @@ "val" : "MA:0003000" }, { "val" : "MESH:A13" + }, { + "val" : "MESH:D000825" }, { "val" : "SCTID:362889002" }, { @@ -40195,6 +41684,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/uberon.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -40206,9 +41701,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that has mass." + "val" : "Anatomical entity that has mass.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "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" ], "xrefs" : [ { "val" : "AAO:0010264" }, { @@ -40235,6 +41731,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/uberon.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -40449,6 +41951,59 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "lbl" : "anatomical entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.", + "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "AAO:0010841" + }, { + "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" + }, { + "val" : "BILA:0000000" + }, { + "val" : "BIRNLEX:6" + }, { + "val" : "CARO:0000000" + }, { + "val" : "EHDAA2:0002229" + }, { + "val" : "FMA:62955" + }, { + "val" : "HAO:0000000" + }, { + "val" : "MA:0000001" + }, { + "val" : "NCIT:C12219" + }, { + "val" : "TAO:0100000" + }, { + "val" : "TGMA:0001822" + }, { + "val" : "UMLS:C1515976" + }, { + "val" : "WBbt:0000100" + }, { + "val" : "XAO:0000000" + }, { + "val" : "ZFA:0100000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0002405", "lbl" : "immune system", @@ -40507,12 +42062,14 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure that has more than one cell as a part." + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] }, - "subsets" : [ "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" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "multicellular structure" + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] } ], "xrefs" : [ { "val" : "CARO:0010000" @@ -40522,6 +42079,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/uberon.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -40571,6 +42134,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/uberon.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/uberon.owl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -41056,7 +42622,7 @@ "val" : "http://www.geneontology.org/formats/oboInOwl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147486870" + "val" : "_:genid2147487093" } ] } }, { @@ -41200,6 +42766,7 @@ "type" : "PROPERTY" }, { "id" : "http://www.w3.org/2002/07/owl#topObjectProperty", + "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a." @@ -43883,6 +45450,78 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000621", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000229" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000622", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000498" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000623", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000498" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000629", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000630", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000631", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000632", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000633", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000634", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000635", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000636", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000637", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/MF_0000073" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000638", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/MF_0000073" + }, { + "sub" : 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"http://purl.obolibrary.org/obo/NCBITaxon_2157", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_223472", "pred" : "is_a", @@ -48131,6 +50074,14 @@ "sub" : "http://purl.obolibrary.org/obo/OGMS_0000045", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OGMS_0000060", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/OGMS_0000060", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000167", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000087" }, { "sub" : "http://purl.obolibrary.org/obo/OGMS_0000063", "pred" : "is_a", @@ -48475,6 +50426,10 @@ "sub" : "http://purl.obolibrary.org/obo/STATO_0000398", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000679" + }, { + "sub" : "http://purl.obolibrary.org/obo/TRANS_0000000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000061", "pred" : "is_a", @@ -48483,6 +50438,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000467", "pred" : "is_a", @@ -48495,6 +50454,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000480", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002405", "pred" : "is_a", @@ -48587,6 +50550,10 @@ "sub" : "http://www.ebi.ac.uk/efo/EFO_0004600", "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://www.geneontology.org/formats/oboInOwl#Subset", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", "pred" : "type", @@ -48715,6 +50682,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000051", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000051", + "pred" : "subPropertyOf", + "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", "pred" : "subPropertyOf", @@ -49179,6 +51150,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002264", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002297", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/IDO_0000660" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002304", "pred" : "subPropertyOf", @@ -49607,6 +51582,10 @@ "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", @@ -49663,10 +51642,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0001015", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001025" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0001018", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001019" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002000", "pred" : "inverseOf", @@ -50288,6 +52263,55 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020000" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000457", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000618" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000528", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000450" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000530", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000407" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000531", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000629" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000596", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000452" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000610", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0006955" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IDO_0000654", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0100026" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000091", + "fillerId" : "http://purl.obolibrary.org/obo/IDO_0000406" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0000679", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000027" ], @@ -50334,6 +52358,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50351,6 +52379,13 @@ "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000312", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], @@ -50388,7 +52423,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000083", @@ -50468,7 +52503,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", @@ -50493,10 +52528,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -50662,9 +52693,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/apollo_sv.obo b/apollo_sv.obo index 078fd8d..44c1268 100644 --- a/apollo_sv.obo +++ b/apollo_sv.obo @@ -1,6 +1,7 @@ format-version: 1.2 -data-version: releases/2023-06-02 +data-version: releases/2024-02-23 subsetdef: attribute_slim "" +subsetdef: common_anatomy "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -10,6 +11,7 @@ subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" subsetdef: unit_group_slim "" +subsetdef: upper_level "" remark: 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). ontology: apollo_sv property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string @@ -24,7 +26,7 @@ property_value: http://purl.org/dc/elements/1.1/title "Apollo Structured Vocabul property_value: http://purl.org/dc/terms/description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string property_value: owl:versionInfo "2023-01-10" xsd:string -property_value: owl:versionInfo "2023-06-02" xsd:string +property_value: owl:versionInfo "2024-02-23" xsd:string property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -1164,7 +1166,7 @@ name: disposition to become contaminated with a pathogen is_a: BFO:0000016 ! disposition intersection_of: BFO:0000016 ! disposition intersection_of: BFO:0000054 APOLLO_SV:00000167 {all_some="true", all_only="true"} ! is realized by contamination acquisition -relationship: RO:0000052 BFO:0000040 ! characteristic of material entity +relationship: RO:0000052 BFO:0000040 ! inheres in material entity property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -3471,8 +3473,8 @@ comment: The disposition of Influenza A virus H3N2 subtype to infect human being is_a: BFO:0000016 ! disposition intersection_of: BFO:0000016 ! disposition intersection_of: BFO:0000054 APOLLO_SV:00000114 {all_only="true"} ! is realized by infection -intersection_of: RO:0000052 OBI:0100026 ! characteristic of organism -relationship: RO:0000052 OBI:0100026 ! characteristic of organism +intersection_of: RO:0000052 OBI:0100026 ! inheres in organism +relationship: RO:0000052 OBI:0100026 ! inheres in organism property_value: IAO:0000111 "infectious disposition" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "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." xsd:string @@ -4231,7 +4233,7 @@ property_value: IAO:0000600 "A predicted data item that is the maximum value of [Term] id: APOLLO_SV:00000480 -name: geographical migration of organism +name: geographical movement of organism def: "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." [] is_a: GO:0007610 ! behavior property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -4711,7 +4713,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string 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 migration of organism +is_a: APOLLO_SV:00000480 ! geographical movement of organism property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5520,8 +5522,8 @@ def: "A monkeypox disease inhering in a human being." [] comment: requested by MIDAS CC is_a: DOID:3292 ! monkeypox intersection_of: DOID:3292 ! monkeypox -intersection_of: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens -relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens +intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens +relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens property_value: http://purl.org/dc/elements/1.1/date "2022-09-18T18:51:00" xsd:dateTime property_value: IAO:0000111 "monkeypox disease inhering in a human being" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5577,6 +5579,148 @@ is_a: APOLLO_SV:00000229 ! place closure control strategy property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string +[Term] +id: APOLLO_SV:00000622 +name: cumulative epidemic case count +def: "A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic." [] +comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. +is_a: APOLLO_SV:00000498 ! count of cases in an epidemic +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "A count of cases from the beginning of the epidemic until recently." xsd:string + +[Term] +id: APOLLO_SV:00000623 +name: incident epidemic case count +def: "A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic." [] +comment: Incident case counts are measured according to regular intervals, typically day or week. +comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. +is_a: APOLLO_SV:00000498 ! count of cases in an epidemic +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week." xsd:string + +[Term] +id: APOLLO_SV:00000624 +name: count of events occurring in a population +def: "A count of processes in which a population and/or its members participate during a given temporal region." [] +comment: As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time. +is_a: APOLLO_SV:00000032 ! count +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000625 +name: count of deaths in a population +def: "A count of death events that occurred in a population in a given temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population death count" xsd:string + +[Term] +id: APOLLO_SV:00000626 +name: count of vaccinations in a population +def: "A count of vaccination events that occurred in a population during a temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population vaccination count" xsd:string +property_value: IAO:0000600 "A count of vaccinations in a population during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000627 +name: count of hospital stays in a population +def: "A count of hospital stays in a population during a temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population hospitalization count" xsd:string +property_value: IAO:0000600 "A count of hospitalizations in a population during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000628 +name: count of infections in a population +def: "A count of infections (process) that occurred in a population in a given temporal region." [] +is_a: APOLLO_SV:00000624 ! count of events occurring in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000118 "population infection count" xsd:string +property_value: IAO:0000600 "A count of infections in a population during a particular time." xsd:string + +[Term] +id: APOLLO_SV:00000629 +name: cumulative epidemic infection count +def: "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000630 +name: incident epidemic infection count +def: "A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000631 +name: cumulative epidemic death count +def: "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000632 +name: incident epidemic death count +def: "A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000633 +name: cumulative epidemic hospitalization count +def: "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000627 ! count of hospital stays in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000634 +name: incident epidemic hospitalization count +def: "A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000627 ! count of hospital stays in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000635 +name: cumulative epidemic vaccination count +def: "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000636 +name: incident epidemic vaccination count +def: "A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000637 +name: intent to be vaccinated +def: "An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization." [] +is_a: MF:0000073 ! intentionality +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "An intent to be vaccinated in the future." xsd:string + +[Term] +id: APOLLO_SV:00000638 +name: intent to vaccinate +def: "An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system." [] +is_a: MF:0000073 ! intentionality +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "An intention to give a vaccine to someone or an animal." xsd:string + +[Term] +id: APOLLO_SV:00000639 +name: vaccination with nirsevimab +def: "A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab." [] +is_a: APOLLO_SV:00000142 ! vaccination +property_value: IAO:0000117 "William R. Hogan" xsd:string + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification @@ -5693,8 +5837,8 @@ property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string property_value: IAO:0000116 "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" xsd:string -property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} -property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: IAO:0000116 "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" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5707,15 +5851,15 @@ relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part_of continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: IAO:0000116 "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" xsd:string -property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} -property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} -property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000116 "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" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5728,22 +5872,24 @@ property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} -property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} -property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} -property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} -property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000020 ! characteristic +disjoint_from: BFO:0000020 ! characteristic disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part_of independent continuant property_value: BFO:0000179 "ic" xsd:string @@ -5758,11 +5904,11 @@ property_value: IAO:0000112 "an orchestra." xsd:string property_value: IAO:0000112 "an organism" xsd:string property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string property_value: IAO:0000112 "the interior of your mouth" xsd:string -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} -property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} -property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5770,15 +5916,16 @@ id: BFO:0000006 name: spatial region is_a: BFO:0000141 ! immaterial entity disjoint_from: BFO:0000029 ! site +disjoint_from: BFO:0000029 ! site disjoint_from: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "s-region" xsd:string property_value: BFO:0000180 "SpatialRegion" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Spatial regions do not participate in processes." xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} -property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} -property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} +property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} +property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5786,17 +5933,18 @@ id: BFO:0000008 name: temporal region is_a: BFO:0000003 ! occurrent disjoint_from: BFO:0000011 ! spatiotemporal region +disjoint_from: BFO:0000011 ! spatiotemporal region disjoint_from: BFO:0000015 ! process disjoint_from: BFO:0000035 ! process boundary property_value: BFO:0000179 "t-region" xsd:string property_value: BFO:0000180 "TemporalRegion" xsd:string -property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} -property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} -property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} -property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} -property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} +property_value: IAO:0000116 "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" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} +property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} +property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} +property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} +property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5808,8 +5956,8 @@ property_value: BFO:0000179 "2d-s-region" xsd:string property_value: BFO:0000180 "TwoDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an infinitely thin plane in space." xsd:string property_value: IAO:0000112 "the surface of a sphere-shaped part of space" xsd:string -property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} -property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} +property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} +property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5821,25 +5969,27 @@ property_value: BFO:0000180 "SpatiotemporalRegion" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a human life" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a process of cellular meiosis." xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by the development of a cancer tumor" xsd:string -property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} -property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} -property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} -property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} +property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} +property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} +property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} +property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} property_value: IAO:0000601 "Every spatiotemporal region occupies_spatiotemporal_region itself." xsd:string -property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} -property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} -property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} -property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} +property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} +property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} +property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} +property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000015 {all_only="true"} ! part_of process property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string @@ -5850,7 +6000,7 @@ property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string property_value: IAO:0000116 "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)" xsd:string -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5865,17 +6015,18 @@ property_value: IAO:0000112 "certain people have a predisposition to colon cance property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 +name: realizable name: realizable entity def: "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." [] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic disjoint_from: BFO:0000019 ! quality relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part_of realizable entity property_value: BFO:0000179 "realizable" xsd:string @@ -5885,10 +6036,10 @@ property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:str property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5898,14 +6049,14 @@ is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "0d-s-region" xsd:string property_value: BFO:0000180 "ZeroDimensionalSpatialRegion" xsd:string -property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} -property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} +property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} +property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part_of quality property_value: BFO:0000179 "quality" xsd:string property_value: BFO:0000180 "Quality" xsd:string @@ -5915,20 +6066,24 @@ property_value: IAO:0000112 "the length of the circumference of your waist" xsd: property_value: IAO:0000112 "the mass of this piece of gold." xsd:string property_value: IAO:0000112 "the shape of your nose" xsd:string property_value: IAO:0000112 "the shape of your nostril" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000601 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 +name: characteristic name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part_of specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part_of characteristic +relationship: BFO:0000051 BFO:0000020 {all_only="true"} ! has part characteristic property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string @@ -5942,9 +6097,12 @@ property_value: IAO:0000112 "the pink color of a medium rare piece of grilled fi property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string [Term] id: BFO:0000023 @@ -5961,14 +6119,16 @@ property_value: IAO:0000112 "the role of a stone in marking a property boundary" property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000024 +name: fiat object name: fiat object part is_a: BFO:0000040 ! material entity +property_value: BFO:0000179 "fiat-object" xsd:string property_value: BFO:0000179 "fiat-object-part" xsd:string property_value: BFO:0000180 "FiatObjectPart" xsd:string property_value: IAO:0000112 "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" xsd:string @@ -5979,8 +6139,8 @@ property_value: IAO:0000112 "the FMA:regional parts of an intact human body." xs property_value: IAO:0000112 "the upper and lower lobes of the left lung" xsd:string property_value: IAO:0000112 "the Western hemisphere of the Earth" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -5991,8 +6151,8 @@ disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "1d-s-region" xsd:string property_value: BFO:0000180 "OneDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an edge of a cube-shaped portion of space." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} -property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} +property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6018,12 +6178,12 @@ 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 {http://purl.obolibrary.org/obo/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 {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +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"} 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 {http://purl.obolibrary.org/obo/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 {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +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"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6034,8 +6194,8 @@ property_value: BFO:0000179 "3d-s-region" xsd:string property_value: BFO:0000180 "ThreeDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "a cube-shaped region of space" xsd:string property_value: IAO:0000112 "a sphere-shaped region of space," xsd:string -property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} -property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} +property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} +property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6059,8 +6219,8 @@ property_value: IAO:0000112 "the interior of your refrigerator" xsd:string property_value: IAO:0000112 "the lumen of your gut" xsd:string property_value: IAO:0000112 "the Piazza San Marco" xsd:string property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} -property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6085,14 +6245,15 @@ property_value: IAO:0000116 "BFO 2 Reference: BFO rests on the presupposition th property_value: IAO:0000116 "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)." xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant def: "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." [] -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +comment: 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. is_a: BFO:0000002 ! continuant relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part_of generically dependent continuant property_value: BFO:0000179 "gdc" xsd:string @@ -6100,7 +6261,7 @@ property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string -property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6113,21 +6274,21 @@ property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:str property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000035 name: process boundary -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "p-boundary" xsd:string property_value: BFO:0000180 "ProcessBoundary" xsd:string property_value: IAO:0000112 "the boundary between the 2nd and 3rd year of your life." xsd:string -property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} -property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} -property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} +property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} +property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} +property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6140,8 +6301,8 @@ property_value: BFO:0000179 "1d-t-region" xsd:string property_value: BFO:0000180 "OneDimensionalTemporalRegion" xsd:string property_value: IAO:0000112 "the temporal region during which a process occurs." xsd:string property_value: IAO:0000116 "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)." xsd:string -property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} -property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} +property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} +property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6167,26 +6328,26 @@ property_value: IAO:0000112 "the undetached arm of a human being" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000140 name: continuant fiat boundary -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} is_a: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "cf-boundary" xsd:string property_value: BFO:0000180 "ContinuantFiatBoundary" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"} property_value: IAO:0000601 "Every continuant fiat boundary is located at some spatial region at every time at which it exists" xsd:string -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6211,14 +6372,14 @@ property_value: IAO:0000112 "all lines of latitude and longitude" xsd:string property_value: IAO:0000112 "The Equator" xsd:string property_value: IAO:0000112 "the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin." xsd:string property_value: IAO:0000112 "the median sulcus of your tongue" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} -property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} +property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000144 name: process profile -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} is_a: BFO:0000015 ! process disjoint_from: BFO:0000182 ! history property_value: BFO:0000179 "process-profile" xsd:string @@ -6226,21 +6387,21 @@ property_value: BFO:0000180 "ProcessProfile" xsd:string property_value: IAO:0000112 "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" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000112 "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." xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} -property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} +property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000145 name: relational quality -def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} +def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} is_a: BFO:0000019 ! quality property_value: BFO:0000179 "r-quality" xsd:string property_value: BFO:0000180 "RelationalQuality" xsd:string property_value: IAO:0000112 "a marriage bond, an instance of requited love, an obligation between one person and another." xsd:string property_value: IAO:0000112 "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." xsd:string -property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} +property_value: IAO:0000602 "(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] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6249,8 +6410,8 @@ name: two-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "2d-cf-boundary" xsd:string property_value: BFO:0000180 "TwoDimensionalContinuantFiatBoundary" xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} -property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} +property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6262,9 +6423,9 @@ property_value: BFO:0000180 "ZeroDimensionalContinuantFiatBoundary" xsd:string property_value: IAO:0000112 "the geographic North Pole" xsd:string property_value: IAO:0000112 "the point of origin of some spatial coordinate system." xsd:string property_value: IAO:0000112 "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet" xsd:string -property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", http://www.w3.org/2000/01/rdf-schema#seeAlso="ZDRnpiIi:TUJ"} -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} -property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} +property_value: IAO:0000116 "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." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", seeAlso="ZDRnpiIi:TUJ"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} +property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6279,8 +6440,8 @@ property_value: IAO:0000112 "the moment at which a child is born" xsd:string property_value: IAO:0000112 "the moment at which a finger is detached in an industrial accident" xsd:string property_value: IAO:0000112 "the moment of death." xsd:string property_value: IAO:0000118 "temporal instant." xsd:string -property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} -property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} +property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} +property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6290,7 +6451,7 @@ is_a: BFO:0000015 ! process property_value: BFO:0000179 "history" xsd:string property_value: BFO:0000180 "History" xsd:string property_value: IAO:0000600 "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. " xsd:string -property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} +property_value: IAO:0000600 "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])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -6941,21 +7102,27 @@ namespace: biological_process alt_id: GO:0019952 alt_id: GO:0050876 def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [] +def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok is_a: GO:0008150 ! biological_process property_value: APOLLO_SV:0000040 "Reproduction" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string property_value: IAO:0000600 "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." xsd:string [Term] id: GO:0003674 +name: gene product or complex activity name: molecular_function -def: "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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt] +def: "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." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +comment: This is the same as GO molecular function synonym: "molecular function" EXACT [] +is_a: BFO:0000015 ! process +disjoint_from: GO:0008150 ! biological_process [Term] id: GO:0006950 @@ -7002,14 +7169,21 @@ xref: Wikipedia:Inflammation is_a: GO:0006952 ! defense response property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string +[Term] +id: GO:0006955 +name: immune response +def: "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." [] +is_a: GO:0008150 ! biological_process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0007562 name: eclose name: eclosion namespace: biological_process def: "The emergence of an adult insect from a pupa case." [] -xref: _:genid2147486879 -xref: _:genid2147486880 +xref: _:genid2147487102 +xref: _:genid2147487103 is_a: GO:0071684 ! organism emergence from protective structure property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -7041,10 +7215,10 @@ name: aging namespace: biological_process alt_id: GO:0016280 subset: goslim_generic -synonym: "_:genid2147486881" EXACT [] -synonym: "_:genid2147486882" EXACT [] -xref: _:genid2147486883 -xref: _:genid2147486884 +synonym: "_:genid2147487104" EXACT [] +synonym: "_:genid2147487105" EXACT [] +xref: _:genid2147487106 +xref: _:genid2147487107 is_a: GO:0032502 ! developmental process property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -7052,6 +7226,7 @@ property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string id: GO:0007610 name: behavior namespace: biological_process +def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [] def: "The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate @@ -7062,7 +7237,9 @@ synonym: "behaviour" EXACT [] synonym: "behavioural response to stimulus" EXACT [] xref: Wikipedia:Behavior is_a: GO:0008150 ! biological_process +is_a: OGMS:0000060 ! bodily process property_value: APOLLO_SV:0000040 "Behavior" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string [Term] @@ -7074,13 +7251,16 @@ synonym: "mating behaviour" EXACT [] xref: Wikipedia:Mating_behaviour is_a: GO:0044705 ! multi-organism reproductive behavior property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008150 name: biological process name: biological_process -def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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." [GOC:pdt] +def: "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." [GOC:pdt] +def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." [] def: "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." [] +comment: A biological process is an evolved process comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] @@ -7088,7 +7268,9 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process +relationship: BFO:0000051 GO:0003674 ! has part molecular_function property_value: IAO:0000111 "biological_process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -7123,13 +7305,15 @@ is_a: GO:0003674 ! molecular_function id: GO:0018991 name: oviposition namespace: biological_process -synonym: "_:genid2147486871" BROAD [] -synonym: "_:genid2147486872" BROAD [] -synonym: "_:genid2147486873" BROAD [] -synonym: "_:genid2147486874" BROAD [] -xref: _:genid2147486875 -xref: _:genid2147486876 +def: "The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water." [] +synonym: "_:genid2147487094" BROAD [] +synonym: "_:genid2147487095" BROAD [] +synonym: "_:genid2147487096" BROAD [] +synonym: "_:genid2147487097" BROAD [] +xref: _:genid2147487098 +xref: _:genid2147487099 is_a: GO:0019098 ! reproductive behavior +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string [Term] @@ -7186,10 +7370,12 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0019098 name: reproductive behavior namespace: biological_process -synonym: "_:genid2147486887" EXACT [] -synonym: "_:genid2147486888" EXACT [] +def: "The specific behavior of an organism that is associated with reproduction." [] +synonym: "_:genid2147487110" EXACT [] +synonym: "_:genid2147487111" EXACT [] is_a: GO:0007610 ! behavior is_a: GO:0048609 ! multicellular organismal reproductive process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string [Term] @@ -7205,12 +7391,14 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0032502 name: developmental process namespace: biological_process +def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [] subset: goslim_aspergillus subset: goslim_pir subset: gosubset_prok -synonym: "_:genid2147486885" NARROW [] -synonym: "_:genid2147486886" NARROW [] +synonym: "_:genid2147487108" NARROW [] +synonym: "_:genid2147487109" NARROW [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string [Term] @@ -7225,8 +7413,8 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0033057 name: multicellular organismal reproductive behavior namespace: biological_process -synonym: "_:genid2147486877" EXACT [] -synonym: "_:genid2147486878" EXACT [] +synonym: "_:genid2147487100" EXACT [] +synonym: "_:genid2147487101" EXACT [] is_a: GO:0019098 ! reproductive behavior property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string @@ -7240,7 +7428,9 @@ synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior is_a: GO:0044419 ! interspecies interaction between organisms +is_a: GO:0051705 ! multi-organism behavior property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035821 @@ -7291,7 +7481,8 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0044409 name: entry into host def: "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." [] -is_a: GO:0008150 ! biological_process +is_a: GO:0051704 ! multi-organism process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044419 @@ -7325,10 +7516,19 @@ name: multi-organism reproductive behavior namespace: biological_process def: "The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species." [] is_a: GO:0019098 ! reproductive behavior +is_a: GO:0051705 ! multi-organism behavior property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl created_by: janelomax creation_date: 2012-09-19T16:02:12Z +[Term] +id: GO:0045297 +name: post-mating behavior +def: "The specific behavior of an organism following mating." [] +is_a: GO:0019098 ! reproductive behavior +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0048609 name: multicellular organismal reproductive process @@ -7380,9 +7580,12 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string [Term] id: GO:0051234 name: establishment of localization +def: "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [] def: "The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location." [] is_a: GO:0008150 ! biological_process property_value: IAO:0000111 "establishment of localization" xsd:string +property_value: IAO:0000412 "Gene Ontology: http://purl.obolibrary.org/obo/go.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string [Term] @@ -7399,6 +7602,7 @@ id: GO:0051704 name: multi-organism process def: "A biological process which involves another organism of the same or different species." [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051705 @@ -7417,6 +7621,7 @@ synonym: "behavioural interaction with other organism" EXACT [] xref: GOC:ai xref: GOC:mah is_a: GO:0007610 ! behavior +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go/releases/2019-07-01/go.owl" xsd:string [Term] @@ -7563,7 +7768,10 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string id: GO:0060403 name: post-mating oviposition namespace: biological_process +def: "The deposition of eggs, either fertilized or not, upon a surface or into a medium, following mating." [] is_a: GO:0018991 ! oviposition +is_a: GO:0045297 ! post-mating behavior +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string [Term] @@ -7575,6 +7783,7 @@ subset: goslim_pir subset: gosubset_prok synonym: "regulation" BROAD [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string [Term] @@ -8215,9 +8424,11 @@ 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" [] +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 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 [Term] id: IAO:0000104 @@ -8899,8 +9110,11 @@ def: "A denotator type indicates how a term should be interpreted from an ontolo is_a: IAO:0000102 ! data about an ontology part property_value: IAO:0000111 "denotator type" xsd:string property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string [Term] id: IAO:0000414 @@ -10259,6 +10473,440 @@ name: EL++ ontology module is_a: IAO:8000019 ! ontology module subsetted by OWL profile property_value: IAO:0000111 "EL++ ontology module" xsd:string +[Term] +id: IDO:0000406 +name: opportunistic infectious disposition +def: "An infectious disposition to become part of a disorder only in organisms whose defenses are compromised." [] +comment: The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host. +comment: This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin). +is_a: IDO:0000452 ! infectious disposition +disjoint_from: IDO:0000407 ! primary infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "opportunitistic pathogenic disposition" xsd:string + +[Term] +id: IDO:0000407 +name: primary infectious disposition +def: "An infectious disposition to become part of a disorder in organisms that have intact defenses." [] +comment: A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. +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." +is_a: IDO:0000452 ! infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000450 +name: pathogenic disposition +def: "A disposition to initiate processes that result in a disorder." [] +comment: A pathogenic disposition is realized in processes that create a disorder. +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. +is_a: BFO:0000016 ! disposition +disjoint_from: IDO:0000618 ! immunocompetence +disjoint_from: OGMS:0000031 ! disease +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "pathogenicity" xsd:string + +[Term] +id: IDO:0000452 +name: infectious disposition +def: "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." [] +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. +is_a: IDO:0000450 ! pathogenic disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000453 +name: zoonotic disposition +def: "An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host." [] +comment: An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis. +is_a: IDO:0000452 ! infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000454 +name: reverse zoonotic disposition +def: "An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host." [] +comment: An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. +is_a: IDO:0000452 ! infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000457 +name: immunocompetent organism +def: "An organism that has immunocompetence." [] +is_a: OBI:0100026 ! organism +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000091 IDO:0000618 ! has disposition immunocompetence +relationship: RO:0000091 IDO:0000618 ! has disposition immunocompetence +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000463 +name: infectious agent transmissibility +def: "A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process." [] +comment: The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. +is_a: BFO:0000019 ! quality +disjoint_from: IDO:0000464 ! infectivity +relationship: RO:0000052 IDO:0000596 ! inheres in infectious agent +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000464 +name: infectivity +def: "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." [] +comment: This quality is measured by the proportion of exposed who become infected. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000466 +name: virulence +def: "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. " [] +comment: This quality is measured by the proportion of clinically apparent cases that are severe or fatal. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000596 ! inheres in infectious agent +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000467 +name: susceptibility +def: "A quality that inheres in an entity and is the degree to which it can be harmed by another entity." [] +comment: Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 BFO:0000040 ! inheres in material entity +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000479 +name: infectious disease incidence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000480 +name: infection incidence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000481 +name: infectious disease incidence proportion +def: "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. " [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "cumulative incidence of infectious disease" xsd:string + +[Term] +id: IDO:0000482 +name: infection incidence proportion +def: "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. " [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "cumulative incidence of infection" xsd:string + +[Term] +id: IDO:0000483 +name: infectious disease incidence rate +def: "A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000484 +name: infection incidence rate +def: "A quality that inheres in an organism population and is the infection incidence proportion per unit time." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000485 +name: infectious disease prevalence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000486 +name: infection prevalence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000487 +name: infectious disease lifetime prevalence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000488 +name: infectious agent seroprevalence +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000489 +name: infectious disease mortality rate +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000490 +name: infectious disease endemicity +def: "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." [] +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. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000494 +name: infectious disease sporadicity +def: "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." [] +comment: Sporadic quality of infectious disease is relational to previous prevalence of the disease. +is_a: BFO:0000019 ! quality +relationship: RO:0000052 IDO:0000509 ! inheres in organism population +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000509 +name: organism population +def: "An aggregate of organisms of the same Species." [] +comment: The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. +is_a: BFO:0000027 ! object aggregate +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000528 +name: pathogen +def: "A material entity with a pathogenic disposition." [] +is_a: BFO:0000040 ! material entity +intersection_of: BFO:0000040 ! material entity +intersection_of: RO:0000091 IDO:0000450 ! has disposition pathogenic disposition +relationship: RO:0000091 IDO:0000450 ! has disposition pathogenic disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000530 +name: primary pathogen +def: "An infectious agent with a primary infectious disposition." [] +is_a: IDO:0000596 ! infectious agent +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000091 IDO:0000407 ! has disposition primary infectious disposition +relationship: RO:0000091 IDO:0000407 ! has disposition primary infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "principal pathogen" xsd:string + +[Term] +id: IDO:0000531 +name: host +def: "An organism bearing a host role." [] +is_a: OBI:0100026 ! organism +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000087 IDO:0000629 ! has role host role +relationship: RO:0000087 IDO:0000629 ! has role host role +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000596 +name: infectious agent +def: "An organism that has an infectious disposition." [] +is_a: IDO:0000528 ! pathogen +is_a: OBI:0100026 ! organism +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000091 IDO:0000452 ! has disposition infectious disposition +relationship: RO:0000091 IDO:0000452 ! has disposition infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000610 +name: immunosuppression +def: "A process that attenuates an immune response." [] +is_a: BFO:0000015 ! process +intersection_of: BFO:0000015 ! process +intersection_of: RO:0002212 GO:0006955 ! negatively regulates immune response +relationship: RO:0002212 GO:0006955 ! negatively regulates immune response +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000618 +name: immunocompetence +def: "A disposition that is the ability to mount a normal immune response." [] +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. +is_a: BFO:0000016 ! disposition +disjoint_from: OGMS:0000031 ! disease +relationship: BFO:0000054 GO:0006955 ! is realized by immune response +relationship: RO:0000052 OBI:0100026 ! inheres in organism +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000623 +name: communicability +def: "An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission." [] +comment: The disposition is realized in a direct, horizontal transmission process between members of the same Species. +is_a: IDO:0000452 ! infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000625 +name: establishment of localization in host +def: "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." [] +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. +is_a: GO:0051234 ! establishment of localization +relationship: BFO:0000066 IDO:0000531 ! occurs in host +property_value: IAO:0000116 "Requested addition of this term to the GO." xsd:string +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000626 +name: appearance of disorder +def: "A process by which a disorder comes into existence." [] +is_a: BFO:0000015 ! process +relationship: results_in_formation_of OGMS:0000045 ! disorder +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000629 +name: host role +def: "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism." [] +is_a: BFO:0000023 ! role +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alexander Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: IDO:0000654 +name: opportunistic pathogen +def: "An infectious agent with an opportunistic infectious disposition." [] +is_a: IDO:0000596 ! infectious agent +intersection_of: OBI:0100026 ! organism +intersection_of: RO:0000091 IDO:0000406 ! has disposition opportunistic infectious disposition +relationship: RO:0000091 IDO:0000406 ! has disposition opportunistic infectious disposition +property_value: IAO:0000117 "Albert Goldfain" xsd:string +property_value: IAO:0000117 "Alex Diehl" xsd:string +property_value: IAO:0000117 "Lindsay Cowell" xsd:string +property_value: IAO:0000118 "opportunist" xsd:string + +[Term] +id: IDO:0000656 +name: horizontal pathogen transmission process +def: "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." [] +is_a: TRANS:0000000 ! transmission process +property_value: IAO:0000117 "Lindsay Cowell" xsd:string + +[Term] +id: MF:0000073 +name: intentionality +def: "Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something." [] +is_a: MF:0000075 ! mental quality + +[Term] +id: MF:0000074 +name: bodily quality +def: "A bodily quality is a quality that inheres in some extended organism." [] +is_a: BFO:0000019 ! quality + +[Term] +id: MF:0000075 +name: mental quality +def: "A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning." [] +is_a: MF:0000074 ! bodily quality + [Term] id: NBO:0000034 name: sexual activity @@ -10280,7 +10928,9 @@ property_value: IAO:0000118 "House mouse" xsd:string [Term] id: NCBITaxon:10239 name: Virus +name: Viruses is_a: OBI:0100026 ! organism +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:10240 @@ -12030,6 +12680,7 @@ property_value: has_rank NCBITaxon:species id: NCBITaxon:2 name: Bacteria is_a: OBI:0100026 ! organism +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:201174 @@ -12112,6 +12763,12 @@ name: Campylobacterales is_a: NCBITaxon:29547 ! Epsilonproteobacteria property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string +[Term] +id: NCBITaxon:2157 +name: Archaea +is_a: OBI:0100026 ! organism +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl + [Term] id: NCBITaxon:223472 name: Psoroptidia @@ -12203,6 +12860,7 @@ property_value: has_rank NCBITaxon:family id: NCBITaxon:2759 name: Eukaryota is_a: OBI:0100026 ! organism +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:27592 @@ -15153,15 +15811,20 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: OBI:0000968 name: device def: "A device is a processed material which is designed to perform some function or functions" [] +def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [] comment: would include reagents is_a: OBI:0000047 ! processed material property_value: IAO:0000111 "device" xsd:string property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string +property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string +property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." xsd:string property_value: IAO:0000116 "food should not classify as a device - counter example for using manufacturer and not device. macroscopic only" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string property_value: IAO:0000118 "instrument" xsd:string +property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string property_value: IAO:0000119 "OBI Vancouver workshop 2010" xsd:string [Term] @@ -15368,6 +16031,11 @@ id: OBI:0100026 name: organism def: "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." [] is_a: BFO:0000040 ! material entity +union_of: NCBITaxon:10239 ! Virus +union_of: NCBITaxon:2 ! Bacteria +union_of: NCBITaxon:2157 ! Archaea +union_of: NCBITaxon:2759 ! Eukaryota +disjoint_from: OGMS:0000045 ! disorder property_value: APOLLO_SV:0000040 "Individual" xsd:string property_value: IAO:0000111 "organism" xsd:string property_value: IAO:0000112 "animal" xsd:string @@ -15375,10 +16043,12 @@ property_value: IAO:0000112 "fungus" xsd:string property_value: IAO:0000112 "plant" xsd:string property_value: IAO:0000112 "virus" xsd:string property_value: IAO:0000114 IAO:0000121 +property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" xsd:string property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0200000 @@ -15573,6 +16243,7 @@ property_value: APOLLO_SV:0000040 "disease" xsd:string property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:21:20Z" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl [Term] id: OGMS:0000032 @@ -15595,8 +16266,18 @@ is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:39:44Z" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string +[Term] +id: OGMS:0000060 +name: bodily process +def: "A process in which at least one bodily component of an organsim participates." [] +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:0000119 "http://www.jbiomedsem.com/content/1/1/10" xsd:string + [Term] id: OGMS:0000063 name: disease course @@ -15607,17 +16288,20 @@ property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:55:44Z" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string [Term] id: OGMS:0000087 name: extended organism def: "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." [] +comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087 is_a: BFO:0000027 ! object aggregate property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=3" xsd:string property_value: IAO:0000232 "creation date: 2010-01-25T04:51:11Z" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl [Term] id: OGMS:0000090 @@ -15725,7 +16409,7 @@ id: OMRSE:00000001 name: human social role def: "A social role inhering in a human being." [] is_a: OMRSE:00000026 ! organism social role -relationship: RO:0000052 NCBITaxon:9606 ! characteristic of Homo sapiens +relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens property_value: IAO:0000117 "Mathias Brochhausen\n" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string @@ -15827,7 +16511,7 @@ comment: Defined class that we will ultimately move to an application ontology. comment: Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. comment: Previous definition: A role in human social processes played by an organism. is_a: BFO:0000023 ! role -relationship: RO:0000052 OBI:0100026 ! characteristic of organism +relationship: RO:0000052 OBI:0100026 ! inheres in organism property_value: IAO:0000117 "William R. Hogan\nMathias Brochhausen" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string @@ -16056,7 +16740,7 @@ property_value: IAO:0000412 "http://www.geneontology.org/formats/oboInOwl" xsd:s id: PATO:0000001 name: quality def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic [Term] id: PATO:0000040 @@ -16167,8 +16851,8 @@ synonym: "relational physical quality" EXACT [] xref: Wikipedia:Physical_property is_a: PATO:0001241 ! physical object quality property_value: IAO:0000111 "physical quality" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" 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:0001025 @@ -16412,13 +17096,30 @@ property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Weighted_arithmetic_m property_value: STATO:0000041 "" xsd:string property_value: STATO:0000391 "https://docs.scipy.org/doc/numpy/reference/generated/numpy.average.html\n\nnp.average(range(1,11), weights=range(10,0,-1))" xsd:string +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: TRANS:0000000 +name: transmission process +def: "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." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000116 "Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species." xsd:string +property_value: IAO:0000116 "Suggested label: pathogen transmission process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/trans.owl +property_value: IAO:0000412 "Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl" xsd:string + [Term] id: UBERON:0000061 name: anatomical structure namespace: uberon def: "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome." [] +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003] +subset: common_anatomy subset: upper_level synonym: "biological structure" EXACT [] +synonym: "connected biological structure" EXACT [CARO:0000003] xref: AAO:0010825 xref: AEO:0000003 xref: BILA:0000003 @@ -16426,12 +17127,14 @@ xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 xref: FBbt:00007001 +xref: FMA:305751 xref: FMA:67135 xref: GAID:781 xref: HAO:0000003 xref: http://dbpedia.org/ontology/AnatomicalStructure xref: MA:0003000 xref: MESH:A13 +xref: MESH:D000825 xref: SCTID:362889002 xref: TAO:0000037 xref: TGMA:0001823 @@ -16441,12 +17144,15 @@ xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 name: material anatomical entity namespace: uberon -def: "Anatomical entity that has mass." [] +def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy subset: upper_level xref: AAO:0010264 xref: AEO:0000006 @@ -16460,7 +17166,10 @@ xref: TAO:0001836 xref: TGMA:0001826 xref: VHOG:0001721 is_a: BFO:0000040 ! material entity +is_a: UBERON:0001062 ! anatomical entity property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -16562,6 +17271,33 @@ xref: ZFA:0001512 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +[Term] +id: UBERON:0001062 +name: anatomical entity +def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737] +subset: common_anatomy +subset: upper_level +xref: AAO:0010841 +xref: AEO:0000000 +xref: BFO:0000004 +xref: BILA:0000000 +xref: BIRNLEX:6 +xref: CARO:0000000 +xref: EHDAA2:0002229 +xref: FMA:62955 +xref: HAO:0000000 +xref: MA:0000001 +xref: NCIT:C12219 +xref: TAO:0100000 +xref: TGMA:0001822 +xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} +xref: WBbt:0000100 +xref: XAO:0000000 +xref: ZFA:0100000 +is_a: BFO:0000004 ! independent continuant +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 + [Term] id: UBERON:0002405 name: immune system @@ -16593,13 +17329,16 @@ property_value: UBPROP:0000003 "The antibody-based immune system defined by the id: UBERON:0010000 name: multicellular anatomical structure namespace: uberon -def: "An anatomical structure that has more than one cell as a part." [] +def: "An anatomical structure that has more than one cell as a part." [CARO:0010000] +subset: common_anatomy subset: upper_level -synonym: "multicellular structure" EXACT [] +synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 xref: FBbt:00100313 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0035943 @@ -16622,6 +17361,7 @@ synonym: "moment of death" EXACT [] synonym: "time of death" EXACT [] is_a: UBERON:0035943 ! life cycle temporal boundary property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UO:0000000 @@ -16830,6 +17570,7 @@ property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 @@ -16843,6 +17584,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_reflexive: true is_transitive: true is_a: RO:0002131 ! overlaps @@ -16861,6 +17603,7 @@ property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant p property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 @@ -16894,6 +17637,9 @@ property_value: IAO:0000231 IAO:0000228 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: TV_pl "BFO_0000054" xsd:string +property_value: TV_sg "BFO_0000054s" xsd:string +property_value: TV_vbg "BFO_0000054ed" xsd:string domain: BFO:0000017 ! realizable entity range: BFO:0000015 ! process inverse_of: BFO:0000055 ! realizes @@ -16908,6 +17654,9 @@ property_value: IAO:0000112 "this investigation realizes this investigator role" property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +property_value: TV_pl "BFO_0000055" xsd:string +property_value: TV_sg "BFO_0000055s" xsd:string +property_value: TV_vbg "BFO_0000055ed" xsd:string domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity @@ -16917,6 +17666,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -16960,7 +17710,9 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process @@ -17023,6 +17775,10 @@ property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a tern 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 +property_value: TV_pl "BFO_0000110" xsd:string +property_value: TV_sg "BFO_0000110s" xsd:string +property_value: TV_vbg "BFO_0000110ed" xsd:string +is_transitive: true [Typedef] id: BFO:0000111 @@ -17033,6 +17789,10 @@ 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 +property_value: TV_pl "BFO_0000111" xsd:string +property_value: TV_sg "BFO_0000111s" xsd:string +property_value: TV_vbg "BFO_0000111ed" xsd:string +is_transitive: true is_a: BFO:0000110 ! has continuant part at all times [Typedef] @@ -17063,6 +17823,11 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string property_value: IAO:0000600 "[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])" xsd:string property_value: IAO:0000602 "(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] " xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: TV_pl "BFO_0000117" xsd:string +property_value: TV_sg "BFO_0000117s" xsd:string +property_value: TV_vbg "BFO_0000117ed" xsd:string +is_transitive: true +inverse_of: BFO:0000132 ! part of occurrent [Typedef] id: BFO:0000118 @@ -17073,6 +17838,10 @@ property_value: BFO:0000179 "o-has-ppart" xsd:string property_value: BFO:0000180 "hasProperOccurrentPart" 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 +property_value: TV_pl "BFO_0000118" xsd:string +property_value: TV_sg "BFO_0000118s" xsd:string +property_value: TV_vbg "BFO_0000118ed" xsd:string +is_transitive: true is_a: BFO:0000117 ! has occurrent part [Typedef] @@ -17124,6 +17893,10 @@ property_value: IAO:0000602 "(forall (x y t) (if (exists (v) (and (occurrentPart property_value: IAO:0000602 "(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] " xsd:string property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] " xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: TV_pl "BFO_0000132" xsd:string +property_value: TV_sg "BFO_0000132s" xsd:string +property_value: TV_vbg "BFO_0000132ed" xsd:string +is_transitive: true [Typedef] id: BFO:0000136 @@ -17207,6 +17980,13 @@ is_a: BFO:0000157 ! during which exists id: BFO:0000157 name: during which exists +[Typedef] +id: BFO:0000167 +name: has participant at all times +property_value: TV_pl "BFO_0000167" xsd:string +property_value: TV_sg "BFO_0000167s" xsd:string +property_value: TV_vbg "BFO_0000167ed" xsd:string + [Typedef] id: BFO:0000169 name: specifically depends on at some time @@ -17295,7 +18075,7 @@ id: BFO:0000184 name: history of domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: BFO:0000066 ! unfolds_in +is_a: BFO:0000066 ! occurs in [Typedef] id: BFO:0000185 @@ -17559,6 +18339,10 @@ is_a: ObsoleteProperty ! ObsoleteProperty is_obsolete: true is_asymmetric: true +[Typedef] +id: IDO:0000660 +name: results_in + [Typedef] id: OBI:0000293 name: has_specified_input @@ -17675,11 +18459,16 @@ name: ObsoleteProperty [Typedef] id: RO:0000052 name: characteristic of +name: inheres in def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 is_functional: true @@ -17688,9 +18477,11 @@ inverse_of: RO:0000053 ! is bearer of [Typedef] id: RO:0000053 +name: bearer of name: bearer_of name: has characteristic name: is bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] def: "Inverse of characteristic_of" [] property_value: IAO:0000111 "bearer of" xsd:string property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string @@ -17701,7 +18492,8 @@ property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string +range: BFO:0000020 ! characteristic is_inverse_functional: true [Typedef] @@ -17724,6 +18516,7 @@ name: has participant name: has_participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000111 "has_participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string @@ -17733,6 +18526,7 @@ property_value: IAO:0000116 "Has_participant is a primitive instance-level relat property_value: IAO:0000118 "has_participant" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -17745,7 +18539,7 @@ property_value: IAO:0000112 "A journal article is an information artifact that i property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string domain: BFO:0000031 ! generically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic inverse_of: RO:0000059 ! concretizes [Typedef] @@ -17757,7 +18551,7 @@ property_value: IAO:0000111 "is_concretization_of" xsd:string property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -domain: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic range: BFO:0000031 ! generically dependent continuant [Typedef] @@ -17770,7 +18564,7 @@ property_value: IAO:0000116 "A function inheres in its bearer at all times for w property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function -is_a: RO:0000052 ! characteristic of +is_a: RO:0000052 ! inheres in inverse_of: RO:0000085 ! has function [Typedef] @@ -17782,7 +18576,7 @@ property_value: IAO:0000112 "this red color is a quality of this apple" xsd:stri property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string -is_a: RO:0000052 ! characteristic of +is_a: RO:0000052 ! inheres in inverse_of: RO:0000086 ! has quality [Typedef] @@ -17794,7 +18588,7 @@ property_value: IAO:0000112 "this investigator role is a role of this person" xs property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string -is_a: RO:0000052 ! characteristic of +is_a: RO:0000052 ! inheres in inverse_of: RO:0000087 ! has role [Typedef] @@ -17844,7 +18638,7 @@ name: disposition of def: "inverse of has disposition" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. subset: RO:0002259 -is_a: RO:0000052 ! characteristic of +is_a: RO:0000052 ! inheres in [Typedef] id: RO:0001000 @@ -17875,48 +18669,30 @@ property_value: IAO:0000111 "is location of" xsd:string property_value: IAO:0000112 "my head is the location of my brain" xsd:string property_value: IAO:0000112 "this cage is the location of this rat" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000118 "location_of" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true inverse_of: RO:0001025 ! located in -[Typedef] -id: RO:0001018 -name: contained in -subset: ro-eco -property_value: IAO:0000111 "contained in" xsd:string -property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string -property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string -property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string -property_value: IAO:0000118 "contained_in" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000004 ! independent continuant -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains - -[Typedef] -id: RO:0001019 -name: contains -subset: ro-eco -property_value: IAO:0000111 "contains" xsd:string -property_value: RO:0001900 RO:0001901 - [Typedef] id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {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."} ! independent continuant +range: BFO:0000004 {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."} ! independent continuant is_transitive: true transitive_over: BFO:0000050 ! part_of @@ -17953,7 +18729,7 @@ name: has regulatory component activity def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] is_a: RO:0002017 ! has component activity is_a: RO:0002334 ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -17963,7 +18739,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002335 ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -17973,7 +18749,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -17981,7 +18757,7 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -17991,44 +18767,44 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002180 ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -18084,7 +18860,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -18125,12 +18901,18 @@ is_a: BFO:0000051 ! has part id: RO:0002211 name: regulates def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] +def: "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" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string @@ -18206,7 +18988,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -18235,7 +19017,7 @@ def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -18360,6 +19142,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: RO:0002224 RO:0002233 is_a: RO:0000057 ! has_participant @@ -18382,7 +19165,7 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -18395,6 +19178,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -18406,6 +19190,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -18419,7 +19204,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part_of @@ -18460,6 +19245,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -18478,7 +19264,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -18488,7 +19274,7 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -18500,6 +19286,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: RO:0000057 ! has_participant is_a: RO:0002328 ! functionally related to @@ -18599,6 +19386,7 @@ def: "p indirectly positively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 @@ -18614,6 +19402,7 @@ def: "p indirectly negatively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true @@ -18720,12 +19509,13 @@ is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -18815,7 +19605,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002481 @@ -18975,6 +19765,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates @@ -18988,6 +19779,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -19016,7 +19808,7 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -19027,6 +19819,7 @@ id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -19038,7 +19831,7 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect @@ -19051,7 +19844,7 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect @@ -19062,6 +19855,7 @@ creation_date: 2018-01-26T23:53:22Z id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -19070,6 +19864,7 @@ creation_date: 2018-03-13T23:55:05Z id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -19089,7 +19884,7 @@ is_obsolete: true id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 @@ -19145,7 +19940,7 @@ id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: RO:0002411 ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -19154,7 +19949,7 @@ name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] @@ -19279,3 +20074,13 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string is_a: ObsoleteProperty ! ObsoleteProperty is_obsolete: true +[Typedef] +id: results_in_formation_of +name: results in formation of +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string +is_a: IDO:0000660 ! results_in + diff --git a/apollo_sv.owl b/apollo_sv.owl index a0ce076..da97fef 100644 --- a/apollo_sv.owl +++ b/apollo_sv.owl @@ -9,6 +9,7 @@ xmlns:www="http://www.referent-tracking.com/" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" @@ -22,9 +23,10 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:apollo_sv="http://purl.obolibrary.org/obo/apollo_sv.owl/" - xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> + xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" + xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -40,7 +42,7 @@ 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). 2023-01-10 - 2023-06-02 + 2024-02-23 @@ -56,6 +58,24 @@ + + + + + + + + + + + + + + + + + + @@ -322,6 +342,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. + example example of usage 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. @@ -353,6 +374,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot + OBI_0000281 has curation status has curation status @@ -364,6 +386,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. definition + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -402,6 +425,7 @@ We also have the outstanding issue of how to aim different definitions to differ 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. PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note @@ -432,12 +456,15 @@ We also have the outstanding issue of how to aim different definitions to differ alternative label + alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee 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 alternative term @@ -451,7 +478,9 @@ We also have the outstanding issue of how to aim different definitions to differ definition source 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 + 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 PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -552,6 +581,7 @@ 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)" 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 + Chris Mungall Chris Mungall expand expression to @@ -602,6 +632,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. + 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 . 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 . PERSON:Alan Ruttenberg PERSON:Bjoern Peters @@ -810,6 +841,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] term replaced by + Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg @@ -883,10 +915,17 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] temporal interpretation temporal interpretation + https://github.com/oborel/obo-relations/wiki/ROAndTime + + + + + + @@ -1095,6 +1134,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1245,6 +1312,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -1393,6 +1466,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -1604,6 +1683,7 @@ For example, the disposition of a piece of glass to bend light and the lattice s a core relation that holds between a part and its whole 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. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 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'. @@ -1620,11 +1700,13 @@ A continuant cannot be part of an occurrent: use 'participates in'. An + part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -1633,6 +1715,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An + has part @@ -1642,6 +1725,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An a core relation that holds between a whole and its part 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. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + 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 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'. @@ -1650,6 +1734,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has part has part @@ -1662,6 +1747,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. + BFO_0000054 + BFO_0000054s + BFO_0000054ed obsolete_is_realized_by realized in this disease is realized in this disease course @@ -1695,6 +1783,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. + BFO_0000055 + BFO_0000055s + BFO_0000055ed realizes this disease course realizes this disease this investigation realizes this investigator role @@ -1727,6 +1818,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. preceded_by http://purl.obolibrary.org/obo/ro.owl http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1759,6 +1851,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -1782,8 +1875,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + occurs in occurs in unfolds_in + https://wiki.geneontology.org/Occurs_in @@ -1855,6 +1950,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + BFO_0000110 + BFO_0000110s + BFO_0000110ed 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) @@ -1873,6 +1972,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + BFO_0000111 + BFO_0000111s + BFO_0000111ed c-has-ppart_at hasProperContinuantPartAt b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001 @@ -1906,6 +2009,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + BFO_0000117 + BFO_0000117s + BFO_0000117ed o-has-part hasOccurrentPart [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life @@ -1927,6 +2035,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + BFO_0000118 + BFO_0000118s + BFO_0000118ed o-has-ppart hasProperOccurrentPart [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) @@ -1975,6 +2087,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + BFO_0000132 + BFO_0000132s + BFO_0000132ed o-part-of occurrentPartOf Mary’s 5th birthday occurrent_part_of Mary’s life @@ -2112,6 +2228,17 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + BFO_0000167 + BFO_0000167s + BFO_0000167ed + has participant at all times + + + + @@ -2705,6 +2832,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + + + + results_in + + + + @@ -2883,13 +3018,18 @@ Werner suggests a solution based on "Magnitudes" a proposal for which inheres in + this fragility inheres in this vase this fragility is a characteristic of this vase + this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + 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 + A dependent inheres in its bearer at all times for which the dependent exists. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of + inheres in @@ -2904,15 +3044,19 @@ Werner suggests a solution based on "Magnitudes" a proposal for which this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of + 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 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. bearer of bearer_of is bearer of http://purl.obolibrary.org/obo/omrse.owl + bearer of bearer_of + has characteristic has characteristic is bearer of + https://github.com/oborel/obo-relations/pull/284 @@ -2941,6 +3085,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + @@ -2961,6 +3106,8 @@ Werner suggests a solution based on "Magnitudes" a proposal for which 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 has participant has_participant has_participant @@ -3159,6 +3306,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location 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/ + 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 location_of location of @@ -3166,42 +3314,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - - - - - contained in - Containment is location not involving parthood, and arises only where some immaterial continuant is involved. - Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - - contained_in - - - contained in - - - - - - - - contains - - - contains - - - - @@ -3238,11 +3350,14 @@ range: spatial region or site (immaterial continuant) a relation between two independent continuants, the target and the location, in which the target is entirely within the location 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 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/ + 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 located_in http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in + https://wiki.geneontology.org/Located_in @@ -3300,7 +3415,7 @@ range: spatial region or site (immaterial continuant) A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z has regulatory component activity @@ -3313,7 +3428,7 @@ range: spatial region or site (immaterial continuant) A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -3327,7 +3442,7 @@ range: spatial region or site (immaterial continuant) A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -3339,7 +3454,7 @@ range: spatial region or site (immaterial continuant) - dos + 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -3354,7 +3469,7 @@ range: spatial region or site (immaterial continuant) w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z has component process @@ -3366,7 +3481,7 @@ range: spatial region or site (immaterial continuant) - dos + 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -3375,7 +3490,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -3386,7 +3501,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z directly negatively regulated by @@ -3394,7 +3509,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -3405,7 +3520,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z directly positively regulated by @@ -3413,7 +3528,7 @@ range: spatial region or site (immaterial continuant) Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -3424,7 +3539,7 @@ range: spatial region or site (immaterial continuant) A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -3433,7 +3548,7 @@ range: spatial region or site (immaterial continuant) A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -3634,10 +3749,16 @@ range: spatial region or site (immaterial continuant) + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. + 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 + 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 + Chris Mungall + David Hill + Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -3963,6 +4084,7 @@ range: spatial region or site (immaterial continuant) has input + https://wiki.geneontology.org/Has_input @@ -3997,7 +4119,22 @@ range: spatial region or site (immaterial continuant) affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within + + + + + + + + + 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. + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + Chris Mungall + GOC:mtg_berkeley_2013 + results_in_formation_of + results in formation of @@ -4014,6 +4151,7 @@ range: spatial region or site (immaterial continuant) 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 causally upstream of, positive effect + @@ -4029,6 +4167,7 @@ range: spatial region or site (immaterial continuant) causally upstream of, negative effect + @@ -4123,6 +4262,7 @@ range: spatial region or site (immaterial continuant) This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables + https://wiki.geneontology.org/Enables @@ -4181,7 +4321,7 @@ range: spatial region or site (immaterial continuant) actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -4194,7 +4334,9 @@ range: spatial region or site (immaterial continuant) inverse of enables + enabled by enabled by + https://wiki.geneontology.org/Enabled_by @@ -4358,6 +4500,7 @@ range: spatial region or site (immaterial continuant) indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -4385,6 +4528,7 @@ range: spatial region or site (immaterial continuant) indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -4575,6 +4719,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different enables activity in is active in + https://wiki.geneontology.org/Is_active_in @@ -4589,8 +4734,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -4994,6 +5139,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -5011,6 +5157,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -5062,7 +5209,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -5080,6 +5227,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -5099,7 +5247,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -5119,7 +5267,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -5132,6 +5280,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -5144,6 +5293,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -5193,7 +5343,7 @@ For example, A and B may be gene products and binding of B by A positively regul triggered by process - RO:cjm + @@ -5258,7 +5408,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -5271,7 +5421,7 @@ For example, A and B may be gene products and binding of B by A positively regul p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -5291,7 +5441,7 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -5456,10 +5606,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a. A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl - + @@ -16002,7 +16152,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s Matthew Diller William R. Hogan 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. - geographical migration of organism + geographical movement of organism @@ -18409,6 +18559,304 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic. + William R. Hogan + A count of cases from the beginning of the epidemic until recently. + The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. + cumulative epidemic case count + + + + + + + + + A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic. + William R. Hogan + A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week. + Incident case counts are measured according to regular intervals, typically day or week. + The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. + incident epidemic case count + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of processes in which a population and/or its members participate during a given temporal region. + William R. Hogan + A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time. + As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time. + count of events occurring in a population + + + + + + + + + A count of death events that occurred in a population in a given temporal region. + William R. Hogan + population death count + count of deaths in a population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of vaccination events that occurred in a population during a temporal region. + William R. Hogan + population vaccination count + A count of vaccinations in a population during a particular time. + count of vaccinations in a population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of hospital stays in a population during a temporal region. + William R. Hogan + population hospitalization count + A count of hospitalizations in a population during a particular time. + count of hospital stays in a population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A count of infections (process) that occurred in a population in a given temporal region. + William R. Hogan + population infection count + A count of infections in a population during a particular time. + count of infections in a population + + + + + + + + + A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic infection count + + + + + + + + + A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic infection count + + + + + + + + + A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic death count + + + + + + + + + A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic death count + + + + + + + + + A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic hospitalization count + + + + + + + + + A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic hospitalization count + + + + + + + + + A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic vaccination count + + + + + + + + + A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic vaccination count + + + + + + + + + An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization. + William R. Hogan + An intent to be vaccinated in the future. + intent to be vaccinated + + + + + + + + + An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system. + William R. Hogan + An intention to give a vaccine to someone or an animal. + intent to vaccinate + + + + + + + + + A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. + William R. Hogan + vaccination with nirsevimab + + + + @@ -18780,6 +19228,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (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] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -19057,6 +19506,12 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + process Process a process of cell-division, \ a beating of the heart @@ -19070,6 +19525,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si 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]) 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) (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] + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -19158,6 +19614,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si (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] (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] + realizable realizable entity @@ -19276,6 +19733,12 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + sdc SpecificallyDependentContinuant @@ -19291,12 +19754,24 @@ By "similar vaccines" we typically mean same pathogen, but could be si the shape of this hole. the smell of this portion of mozzarella 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. + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) 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]) 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. + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (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] + 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. + characteristic specifically dependent continuant + https://github.com/OBOFoundry/COB/issues/65 + https://github.com/oborel/obo-relations/pull/284 + + + + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + + @@ -19310,6 +19785,12 @@ By "similar vaccines" we typically mean same pathogen, but could be si per discussion with Barry Smith + + + + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + + @@ -19358,6 +19839,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si + fiat-object fiat-object-part FiatObjectPart 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 @@ -19371,6 +19853,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si 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]) (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] + fiat object fiat object part @@ -19602,6 +20085,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si 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. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + 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. generically dependent continuant @@ -21260,6 +21744,8 @@ Date accessed: 2015-04-13 The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. + The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. + http://purl.org/obo/owl/gene_ontology The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. Reproduction @@ -21270,6 +21756,7 @@ Date accessed: 2015-04-13 + reproduction reproduction @@ -21278,16 +21765,20 @@ Date accessed: 2015-04-13 - 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + + + 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. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + This is the same as GO molecular function + gene product or complex activity molecular_function - 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + 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. GOC:pdt @@ -21353,6 +21844,17 @@ Date accessed: 2015-04-13 + + + + + Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. + + immune response + + + + @@ -21433,7 +21935,10 @@ Date accessed: 2015-04-13 + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. + http://purl.obolibrary.org/obo/go.owl Behavior Wikipedia:Behavior @@ -21456,6 +21961,7 @@ Date accessed: 2015-04-13 The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. + http://purl.obolibrary.org/obo/go.owl Wikipedia:Mating_behaviour mating behaviour @@ -21470,9 +21976,18 @@ Date accessed: 2015-04-13 + + + + + + biological_process - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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. + 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. + A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. + 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. 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. + http://purl.obolibrary.org/obo/ido.owl jl 2012-09-19T15:05:24Z @@ -21482,6 +21997,7 @@ Date accessed: 2015-04-13 single organism process single-organism process GO:0008150 + A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological process biological_process @@ -21489,7 +22005,7 @@ Date accessed: 2015-04-13 - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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. + 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. GOC:pdt @@ -21564,6 +22080,8 @@ Date accessed: 2015-04-13 + The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water. + http://purl.org/obo/owl/gene_ontology @@ -21584,6 +22102,7 @@ Date accessed: 2015-04-13 biological_process + oviposition oviposition @@ -21659,6 +22178,8 @@ Date accessed: 2015-04-13 + The specific behavior of an organism that is associated with reproduction. + http://purl.org/obo/owl/gene_ontology @@ -21667,6 +22188,7 @@ Date accessed: 2015-04-13 biological_process + reproductive behavior reproductive behavior @@ -21690,6 +22212,8 @@ Date accessed: 2015-04-13 + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. + http://purl.org/obo/owl/gene_ontology @@ -21701,6 +22225,7 @@ Date accessed: 2015-04-13 + developmental process developmental process @@ -21740,7 +22265,9 @@ Date accessed: 2015-04-13 + Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + http://purl.obolibrary.org/obo/go.owl Wikipedia:Social_behavior social behaviour @@ -21821,8 +22348,10 @@ Date accessed: 2015-04-13 - + 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. + + entry into host entry into host @@ -21872,7 +22401,9 @@ Date accessed: 2015-04-13 + The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species. + http://purl.obolibrary.org/obo/go.owl janelomax 2012-09-19T16:02:12Z @@ -21883,6 +22414,17 @@ Date accessed: 2015-04-13 + + + + + The specific behavior of an organism following mating. + + post-mating behavior + + + + @@ -21956,7 +22498,10 @@ Date accessed: 2015-04-13 establishment of localization + Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. + + Gene Ontology: http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/ido.owl establishment of localization establishment of localization @@ -21983,6 +22528,8 @@ Date accessed: 2015-04-13 A biological process which involves another organism of the same or different species. + + multi-organism process multi-organism process @@ -21993,6 +22540,7 @@ Date accessed: 2015-04-13 Any process in which an organism has a behavioral effect on another organism of the same or different species. + http://purl.obolibrary.org/obo/go/releases/2019-07-01/go.owl GO:0023032 GO:0044709 @@ -22196,8 +22744,12 @@ Date accessed: 2015-04-13 + + The deposition of eggs, either fertilized or not, upon a surface or into a medium, following mating. + http://purl.org/obo/owl/gene_ontology biological_process + post-mating oviposition post-mating oviposition @@ -22208,6 +22760,7 @@ Date accessed: 2015-04-13 Any process that modulates a measurable attribute of any biological process, quality or function. + http://purl.obolibrary.org/obo/go.owl regulation biological_process @@ -23132,6 +23685,8 @@ XML document; The instructions in a XSD file" data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg Person:Alan Ruttenberg data about an ontology part @@ -23541,6 +24096,17 @@ clustering algorithm. + + + + + + + + + + + @@ -24331,10 +24897,15 @@ GO gene ontology denotator type + 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. 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. + A denotator type indicates how a term should be interpreted from an ontological perspective. A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg Alan Ruttenberg + Barry Smith, Werner Ceusters Barry Smith, Werner Ceusters + denotator type denotator type @@ -26672,6 +27243,1011 @@ No imports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious disposition to become part of a disorder only in organisms whose defenses are compromised. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + opportunitistic pathogenic disposition + The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host. + This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin). + opportunistic infectious disposition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious disposition to become part of a disorder in organisms that have intact defenses. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. + 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." + primary infectious disposition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A disposition to initiate processes that result in a disorder. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + pathogenicity + A pathogenic disposition is realized in processes that create a disorder. + 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. + pathogenic disposition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disposition + + + + + + + + + An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis. + zoonotic disposition + + + + + + + + + An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. + reverse zoonotic disposition + + + + + + + + + + + + + + + + + + + + + + + + + + An organism that has immunocompetence. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + immunocompetent organism + + + + + + + + + + + + + + + A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. + infectious agent transmissibility + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + This quality is measured by the proportion of exposed who become infected. + infectivity + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + This quality is measured by the proportion of clinically apparent cases that are severe or fatal. + virulence + + + + + + + + + + + + + + + A quality that inheres in an entity and is the degree to which it can be harmed by another entity. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. + susceptibility + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease incidence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infection incidence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + cumulative incidence of infectious disease + 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. + infectious disease incidence proportion + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + cumulative incidence of infection + 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. + infection incidence proportion + + + + + + + + + + + + + + + A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease incidence rate + + + + + + + + + + + + + + + A quality that inheres in an organism population and is the infection incidence proportion per unit time. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infection incidence rate + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease prevalence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infection prevalence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease lifetime prevalence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious agent seroprevalence + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease mortality rate + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + infectious disease endemicity + + + + + + + + + + + + + + + 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. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + Sporadic quality of infectious disease is relational to previous prevalence of the disease. + infectious disease sporadicity + + + + + + + + + An aggregate of organisms of the same Species. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. + organism population + + + + + + + + + + + + + + + + + + + + + + + + + + A material entity with a pathogenic disposition. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + pathogen + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious agent with a primary infectious disposition. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + principal pathogen + primary pathogen + + + + + + + + + + + + + + + + + + + + + + + + + + An organism bearing a host role. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + host + + + + + + + + + + + + + + + + + + + + + + + + + + + An organism that has an infectious disposition. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + infectious agent + + + + + + + + + + + + + + + + + + + + + + + + + + A process that attenuates an immune response. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + immunosuppression + + + + + + + + + + + + + + + + + + + + + + + + A disposition that is the ability to mount a normal immune response. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + immunocompetence + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + The disposition is realized in a direct, horizontal transmission process between members of the same Species. + communicability + + + + + + + + + + + + + + + + + + + + + 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. + Requested addition of this term to the GO. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + 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. + establishment of localization in host + + + + + + + + + + + + + + + + + + + + + A process by which a disorder comes into existence. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + appearance of disorder + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + host role + + + + + + + + + + + + + + + + + + + + + + + + + + An infectious agent with an opportunistic infectious disposition. + Albert Goldfain + Alex Diehl + Lindsay Cowell + opportunist + opportunistic pathogen + + + + + + + + + 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. + Lindsay Cowell + horizontal pathogen transmission process + + + + + + + + + Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something. + intentionality + + + + + + + + + A bodily quality is a quality that inheres in some extended organism. + bodily quality + + + + + + + + + A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning. + mental quality + + + + @@ -26702,7 +28278,9 @@ No imports + Virus + Viruses @@ -30271,6 +31849,8 @@ No imports + + Bacteria Bacteria @@ -30421,6 +32001,16 @@ No imports + + + + + + Archaea + + + + @@ -30606,6 +32196,8 @@ No imports + + Eukaryota Eukaryota @@ -35926,6 +37518,7 @@ No imports Homo sapiens human being + Homo sapiens Homo sapiens @@ -36826,13 +38419,28 @@ for now. device A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + A device is a processed material which is designed to perform some function or functions + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + +2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: + +(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. + +(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. + +(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. + +In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. food should not classify as a device - counter example for using manufacturer and not device. macroscopic only 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. PERSON: Helen Parkinson instrument OBI Vancouver workshop 2010 + OBI development call 2012-12-17. would include reagents device @@ -37168,13 +38776,25 @@ https://www.doi.org/ + + + + + + + + + + + organism animal fungus plant virus + 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. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: @@ -37182,6 +38802,7 @@ OBI doesn't take position as to when an organism starts or ends being an o This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism + Individual organism @@ -37459,6 +39080,7 @@ This issue is outside the scope of OBI. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:21:20Z + disease disease @@ -37492,12 +39114,31 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:39:44Z + http://purl.obolibrary.org/obo/ogms.owl disorder + + + + + + + + + + + A process in which at least one bodily component of an organsim participates. + http://www.jbiomedsem.com/content/1/1/10 + From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060 + bodily process + + + + @@ -37507,6 +39148,7 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z + http://purl.obolibrary.org/obo/ido.owl http://purl.obolibrary.org/obo/ogms.owl disease course @@ -37522,7 +39164,9 @@ Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z + http://purl.obolibrary.org/obo/ogms.owl + From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087 extended organism @@ -38751,12 +40395,29 @@ np.average(range(1,11), weights=range(10,0,-1)) + + + + + 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. + Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species. + Suggested label: pathogen transmission process + + Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl + transmission process + + + + Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. http://purl.obolibrary.org/obo/uberon.owl + + AAO:0010825 AEO:0000003 BILA:0000003 @@ -38764,11 +40425,13 @@ np.average(range(1,11), weights=range(10,0,-1)) EHDAA2:0003003 EMAPA:0 FBbt:00007001 + FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:A13 + MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 @@ -38778,11 +40441,25 @@ np.average(range(1,11), weights=range(10,0,-1)) ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure + connected biological structure uberon UBERON:0000061 + anatomical structure + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + + + + + connected biological structure + CARO:0000003 + @@ -38790,8 +40467,11 @@ np.average(range(1,11), weights=range(10,0,-1)) + Anatomical entity that has mass. http://purl.obolibrary.org/obo/uberon.owl + + AAO:0010264 AEO:0000006 BILA:0000006 @@ -38805,9 +40485,16 @@ np.average(range(1,11), weights=range(10,0,-1)) VHOG:0001721 uberon UBERON:0000465 + material anatomical entity + + + + Anatomical entity that has mass. + http://orcid.org/0000-0001-9114-8737 + @@ -38926,6 +40613,51 @@ np.average(range(1,11), weights=range(10,0,-1)) + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + AAO:0010841 + AEO:0000000 + BFO:0000004 + BILA:0000000 + BIRNLEX:6 + CARO:0000000 + EHDAA2:0002229 + FMA:62955 + HAO:0000000 + MA:0000001 + NCIT:C12219 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + WBbt:0000100 + XAO:0000000 + ZFA:0100000 + UBERON:0001062 + + + anatomical entity + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + FMA:62955 + http://orcid.org/0000-0001-9114-8737 + + + + + UMLS:C1515976 + ncithesaurus:Anatomic_Structure_System_or_Substance + + + + @@ -38964,14 +40696,29 @@ np.average(range(1,11), weights=range(10,0,-1)) An anatomical structure that has more than one cell as a part. http://purl.obolibrary.org/obo/uberon.owl + + CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 + multicellular anatomical structure + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + + + + + multicellular structure + FBbt:00100313 + @@ -38994,6 +40741,7 @@ np.average(range(1,11), weights=range(10,0,-1)) A life cycle temporal boundary that marks the end of the life cycle of the organism. + http://purl.obolibrary.org/obo/uberon.owl end of life cycle moment of death @@ -39332,12 +41080,28 @@ np.average(range(1,11), weights=range(10,0,-1)) + Obsolete Class Obsolete Class obsolete_class + + + + + + + + + + + + + + + + + +## Elucidation + +This is used when the statement/axiom is assumed to hold true 'eternally' + +## How to interpret (informal) + +First the "atemporal" FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + + ## Elucidation This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; @@ -39741,6 +41554,63 @@ This interpretation is *not* the same as an at-all-times relation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -39774,10 +41644,10 @@ This interpretation is *not* the same as an at-all-times relation - + - + @@ -39795,66 +41665,54 @@ This interpretation is *not* the same as an at-all-times relation - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -39867,8 +41725,8 @@ This interpretation is *not* the same as an at-all-times relation - - + + @@ -39878,7 +41736,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -39888,7 +41746,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -39905,8 +41763,8 @@ This interpretation is *not* the same as an at-all-times relation - - + + @@ -40168,7 +42026,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40178,8 +42036,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40189,8 +42047,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40207,8 +42065,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40227,7 +42085,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40237,8 +42095,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40248,8 +42106,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40266,8 +42124,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40283,8 +42141,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40294,7 +42152,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40304,8 +42162,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40315,8 +42173,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40335,8 +42193,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40354,8 +42212,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40365,8 +42223,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40376,8 +42234,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40394,8 +42252,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40412,8 +42270,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40423,8 +42281,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40434,8 +42292,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40452,8 +42310,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40470,8 +42328,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40481,8 +42339,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40492,8 +42350,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40510,8 +42368,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40527,9 +42385,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40538,9 +42396,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40555,8 +42413,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40572,9 +42430,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40583,9 +42441,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40600,8 +42458,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40617,9 +42475,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40628,9 +42486,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40645,8 +42503,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40662,9 +42520,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40673,9 +42531,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40690,8 +42548,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40707,9 +42565,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40718,9 +42576,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40735,8 +42593,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40752,9 +42610,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40763,9 +42621,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40780,7 +42638,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40790,7 +42648,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40808,9 +42666,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40819,9 +42677,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40836,7 +42694,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40846,7 +42704,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40863,7 +42721,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40874,7 +42732,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -40907,9 +42765,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40918,9 +42776,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40935,8 +42793,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -40951,9 +42809,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40962,9 +42820,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40978,9 +42836,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -40995,7 +42853,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -41006,7 +42864,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -41022,7 +42880,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -41039,9 +42897,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -41050,9 +42908,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -41084,8 +42942,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -41095,8 +42953,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -41123,5 +42981,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/src/ontology/apollo_sv-edit.owl b/src/ontology/apollo_sv-edit.owl index 659a939..8411988 100644 --- a/src/ontology/apollo_sv-edit.owl +++ b/src/ontology/apollo_sv-edit.owl @@ -13071,7 +13071,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si A count of processes in which a population and/or its members participate during a given temporal region. William R. Hogan - A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on. during a particular time. + A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time. As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time. count of events occurring in a population diff --git a/src/ontology/imports/geo_import.owl b/src/ontology/imports/geo_import.owl index e53e73c..138634e 100644 --- a/src/ontology/imports/geo_import.owl +++ b/src/ontology/imports/geo_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-02-22") + +Annotation(owl:versionInfo "2024-02-23") Declaration(Class()) Declaration(Class()) @@ -2690,7 +2690,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "geopolitical dependency"@en) SubClassOf( ) -# Class: (group of major administrative subdivisions) +# Class: (aggregate of major administrative subdivisions) AnnotationAssertion( "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( "Amanda Hicks"@en) @@ -2700,7 +2700,7 @@ AnnotationAssertion(rdfs:label "g EquivalentClasses( ObjectIntersectionOf(ObjectComplementOf() ObjectAllValuesFrom( ) ObjectMinCardinality(2 ))) SubClassOf( ) -# Class: (group of dependencies) +# Class: (aggregate of dependencies) AnnotationAssertion( "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( "Amanda Hicks"@en) diff --git a/src/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl index 7415e77..af40396 100644 --- a/src/ontology/imports/ido_import.owl +++ b/src/ontology/imports/ido_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-02-22") +Annotation(owl:versionInfo "2024-02-23") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/mf_import.owl b/src/ontology/imports/mf_import.owl index 0e3e30c..4bcee0d 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 "2024-02-22") +Annotation(owl:versionInfo "2024-02-23") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pno_import.owl b/src/ontology/imports/pno_import.owl index 7341ffc..f2f8229 100644 --- a/src/ontology/imports/pno_import.owl +++ b/src/ontology/imports/pno_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-02-22") +Annotation(owl:versionInfo "2024-02-23") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 15a04af..f512b09 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 "2024-02-22") +Annotation(owl:versionInfo "2024-02-23") Declaration(Class()) Declaration(Class())