From a81acab553ff2bcfa8cd7315e18204560166bb18 Mon Sep 17 00:00:00 2001 From: William Hogan Date: Fri, 19 Apr 2024 08:35:26 -0500 Subject: [PATCH] release 2024-04-19 includes new classes and ODK update --- apollo_sv-base.json | 24114 ++------------------------ apollo_sv-base.obo | 9049 +--------- apollo_sv-base.owl | 17771 +++---------------- apollo_sv-full.json | 271 +- apollo_sv-full.obo | 149 +- apollo_sv-full.owl | 187 +- apollo_sv.json | 271 +- apollo_sv.obo | 149 +- apollo_sv.owl | 187 +- src/ontology/imports/geo_import.owl | 59 +- src/ontology/imports/ido_import.owl | 31 +- src/ontology/imports/mf_import.owl | 4 +- src/ontology/imports/pno_import.owl | 69 +- src/ontology/imports/ro_import.owl | 77 +- 14 files changed, 5800 insertions(+), 46588 deletions(-) diff --git a/apollo_sv-base.json b/apollo_sv-base.json index 4e47885..e14042d 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" : "2024-02-23" + "val" : "2024-04-19" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-02-23/apollo_sv-base.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-04-19/apollo_sv-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", @@ -77,38 +77,6 @@ "val" : "William R. Hogan" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/UO_0000034", - "lbl" : "week", - "type" : "INDIVIDUAL", - "meta" : { - "comments" : [ "\"A time unit which is equal to 7 days.\" [Wikipedia:Wikipedia]" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/UO_0000003", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.org/obo/owl/UO" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "unitOfTime" - } ] - } - }, { - "id" : "http://purl.obolibrary.obo/obo/NCBITaxon_7160", - "lbl" : "Aedes albopictus", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "Stegomyia albopicta" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "forest day mosquito" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000000", "lbl" : "purely intentional entity", @@ -248,6 +216,28 @@ "val" : "simulator" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", + "lbl" : "software development", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A planned process that has specified output a software product and that involves the creation of source code." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Mathias Brochhausen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Software_development" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A planned process resulting in a software product involving the creation of source code." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000009", "lbl" : "simulator developer identifier", @@ -3576,7 +3566,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000238", - "lbl" : "host", + "lbl" : "host organism", "type" : "CLASS", "meta" : { "definition" : { @@ -9198,7 +9188,20 @@ }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000522", "lbl" : "source code repository", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc." + }, + "comments" : [ "Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "software source code version control repository" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000523", "lbl" : "human readable synopsis", @@ -11265,7 +11268,7 @@ "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." + "val" : "A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11278,7 +11281,7 @@ "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." + "val" : "An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11291,7 +11294,7 @@ "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." + "val" : "A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11304,7 +11307,7 @@ "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." + "val" : "An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11317,7 +11320,7 @@ "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." + "val" : "A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11330,7 +11333,7 @@ "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." + "val" : "An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11343,7 +11346,7 @@ "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." + "val" : "A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11356,7 +11359,7 @@ "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." + "val" : "An incident vaccination count 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 reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11409,23521 +11412,3162 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", - "lbl" : "epidemic simulator action specification", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000640", + "lbl" : "cumulative vaccination count", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "epidemic simulator action specification" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000794", - "lbl" : "infectious disease control strategy action specification", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000641", + "lbl" : "incident vaccination count", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "infectious disease control strategy action specification" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000795", - "lbl" : "individual treatment control strategy action specification", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000642", + "lbl" : "cumulative infection count", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A count of infections in a population that is the total number of infections that occur during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "individual treatment control strategy action specification" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", - "lbl" : "dataset creating", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000643", + "lbl" : "incident infection count", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A planned process that has a data set as its specified output." + "val" : "A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval." }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "creating a data set" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "data set creation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "dataset creation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000797", - "lbl" : "creating a copyright license", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000644", + "lbl" : "cumulative hospitalization count", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A planned process that has a copyright license as its specified output." + "val" : "A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval." }, - "comments" : [ "Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time." ], + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "creating a copyright license" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "copyright license creation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000798", - "lbl" : "copyright license", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000645", + "lbl" : "incident hospitalization count", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A document that is about the legal rights, claims, and obligations of a legal person (person or organization) under copyright law, and how that legal person intends for those rights, claims, and obligations to be handled/managed by users of the creative work to which this document is attached." + "val" : "A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval." }, - "comments" : [ "Can be for any creative work including fiction. But the license itself is an ICE, and refers to real claims and obligations." ], + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "copyright license for a creative work" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000799", - "lbl" : "data service software", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000646", + "lbl" : "cumulative death count", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A software application that implements a data service." + "val" : "A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval." }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data service software application" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00001008", - "lbl" : "TODO", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00002024", - "lbl" : "facultative role", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000647", + "lbl" : "incident death count", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A role borne by an organism in virtue of the fact that it is in intimate association with one or more organisms of different species, and is realized by bodily benefit to that organism as an occurrent part of a symbiosis with the other organisms. This bodily benefit takes the place of the organism or some relatively isolated part of the organism realizing some normal homeostasis disposition itself." + "val" : "A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval." }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "facultative role" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000027", - "lbl" : "object_aggregate", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000648", + "lbl" : "cumulative case count", "type" : "CLASS", "meta" : { - "comments" : [ "Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.", "Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital", "Synonyms: substance aggregate" ] + "definition" : { + "val" : "A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000038", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000649", + "lbl" : "incident case count", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "Interval" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000054", - "lbl" : "is realized by", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650", + "lbl" : "intent to have a ward vaccinated", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]" + "val" : "An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role." }, + "comments" : [ "Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "obsolete_is_realized_by" - }, { - "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" : "replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "GROUP:OBI:" + "val" : "guardian's intent to have a ward under their care vaccinated" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executed_during" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_realization" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is_realized_as" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "realized by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "realized_by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000228" + "val" : "William R. Hogan" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "The intent of a guardian to have a ward under their care vaccinated in the near future." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000055", - "lbl" : "realizes", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000652", + "lbl" : "intent to have a child vaccinated", + "type" : "CLASS", "meta" : { + "definition" : { + "val" : "An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child." + }, + "comments" : [ "The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "realizes" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Intent to have one's child vaccinated." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", + "lbl" : "epidemic simulator action specification", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "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." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" + "val" : "epidemic simulator action specification" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000794", + "lbl" : "infectious disease control strategy action specification", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" + "val" : "infectious disease control strategy action specification" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "unfolds_in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000795", + "lbl" : "individual treatment control strategy action specification", + "type" : "CLASS", "meta" : { - "comments" : [ "Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ido.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "individual treatment control strategy action specification" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "relationship" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", + "lbl" : "dataset creating", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001" + "val" : "A planned process that has a data set as its specified output." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "contains-process" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "creating a data set" }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "containsProcess" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "data set creation" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "dataset creation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000075", - "lbl" : "is aggregate of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000797", + "lbl" : "creating a copyright license", + "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A planned process that has a copyright license as its specified output." + }, + "comments" : [ "Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is aggregate of" + "val" : "creating a copyright license" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "aggregate of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "aggregate_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" + "val" : "copyright license creation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000108", - "lbl" : "exists at", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000113", - "lbl" : "has material basis at all times", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000798", + "lbl" : "copyright license", + "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A document that is about the legal rights, claims, and obligations of a legal person (person or organization) under copyright law, and how that legal person intends for those rights, claims, and obligations to be handled/managed by users of the creative work to which this document is attached." + }, + "comments" : [ "Can be for any creative work including fiction. But the license itself is an ICE, and refers to real claims and obligations." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "has-material-basis_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "hasMaterialBasisAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the material basis of John’s disposition to cough is the viral infection in John’s upper respiratory tract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the material basis of the disposition to wear unevenly of John’s tires is the worn suspension of his car." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has material basis at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has material basis@en(x,y,t)'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b has_material_basis c at t means: b is a disposition & c is a material entity & there is some d bearer_of b at t& c continuant_part_of d at t& d has_disposition b at t because c continuant_part_of d at t. (axiom label in BFO2 Reference: [071-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (hasMaterialBasisAt x y t) (and (Disposition x) (MaterialEntity y) (exists (z) (and (bearerOfAt z x t) (continuantPartOfAt y z t) (exists (w) (and (Disposition w) (if (hasDisposition z w) (continuantPartOfAt y z t))))))))) // axiom label in BFO2 CLIF: [071-002] " + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "copyright license for a creative work" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000117", - "lbl" : "has occurrent part", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000799", + "lbl" : "data service software", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" + "val" : "A software application that implements a data service." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "o-has-part" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "hasOccurrentPart" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data service software application" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "[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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000118", - "lbl" : "has proper occurrent part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "o-has-ppart" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "hasProperOccurrentPart" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000121", - "lbl" : "has temporal part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "has-t-part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000132", - "lbl" : "part of occurrent", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "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://purl.obolibrary.org/obo/BFO_0000179", - "val" : "o-part-of" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "occurrentPartOf" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mary’s 5th birthday occurrent_part_of Mary’s life" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the first set of the tennis match occurrent_part_of the tennis match." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: occurrent" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000136", - "lbl" : "proper temporal part of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "t-ppart-of" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "properTemporalPartOf" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000138", - "lbl" : "proper part of occurrent", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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])" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "o-ppart-of" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "properOccurrentPartOf" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000139", - "lbl" : "temporal part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "t-part-of" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "temporalPartOf" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the process boundary which separates the 3rd and 4th years of your life." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000155", - "lbl" : "occupies temporal region", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "spans" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "occupiesTemporalRegion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000156", - "lbl" : "has temporal occupant", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "span-of" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "spanOf" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000157", - "lbl" : "during which exists", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000169", - "lbl" : "specifically depends on at some time", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "specificallyDependsOn" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A pain s-depends_on the organism that is experiencing the pain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a gait s-depends_on the walking object. (All at some specific time.)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a shape s-depends_on the shaped object" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "reciprocal s-dependence between occurrents: a process of buying and the associated process of selling" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the one-sided dependence of an occurrent on an independent continuant: handwave on a hand" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the two-sided reciprocal s-dependence of the roles of husband and wife [20" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: specifically dependent continuant\\; process; process boundary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000179", - "lbl" : "BFO OWL specification label", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000180", - "lbl" : "BFO CLIF specification label", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000181", - "lbl" : "has proper temporal part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "has-t-ppart" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000182", - "lbl" : "history", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. " - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000184", - "lbl" : "history of", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000185", - "lbl" : "has history", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/CHEBI_36044", - "lbl" : "antiviral drug", - "type" : "CLASS", - "meta" : { - "comments" : [ "The usage or intended usage of a drug product to act against a viral infection of a host." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/DOID_0060478", - "lbl" : "Zika fever", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A viral infectious disease that has_material_basis in Zika virus, which is transmitted_by Aedes aegypti mosquitoes and targets neural progenitor cells and neuronal cells in all stages of maturity and has_symptom fever, has_symptom rash, has_symptom headaches and has_symptom joint pain." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Zika virus disease" - } ], - "xrefs" : [ { - "val" : "ICD10:U06" - }, { - "val" : "ICD10CM:A92.8" - }, { - "val" : "MESH:D000071243" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/doid.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/DOID_12205", - "lbl" : "dengue disease", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A viral infectious disease that results_in infection, has_material_basis_in Dengue virus [NCBITaxon:12637] with four serotypes (Dengue virus 1, 2, 3 and 4), which are transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom severe headache, has_symptom severe pain behind the eyes, has_symptom joint pain, has_symptom muscle and bone pain, has_symptom rash, and has_symptom mild bleeding." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/doid#zoonotic_infectious_disease" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Dengue Fever" - }, { - "pred" : "hasExactSynonym", - "val" : "breakbone fever" - }, { - "pred" : "hasExactSynonym", - "val" : "classic dengue" - }, { - "pred" : "hasRelatedSynonym", - "val" : "classical dengue" - } ], - "xrefs" : [ { - "val" : "ICD10CM:A90" - }, { - "val" : "ICD9CM:061" - }, { - "val" : "MESH:D003715" - }, { - "val" : "NCI:C34528" - }, { - "val" : "SNOMEDCT_US_2016_03_01:154345006" - }, { - "val" : "SNOMEDCT_US_2016_03_01:266194002" - }, { - "val" : "SNOMEDCT_US_2016_03_01:38362002" - }, { - "val" : "UMLS_CUI:C0011311" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/doid.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "DOID:0050142" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "disease_ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/DOID_12206", - "lbl" : "dengue hemorrhagic fever", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A dengue disease that occurs when a person experiences a second infection with a heterologous Dengue virus serotype, which is transmitted_by Aedes mosquito bite. The infection has_symptom hemorrhagic lesions of the skin, has_symptom thrombocytopenia, has_symptom reduction in the fluid part of the blood, and has_symptom high fever." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/doid#zoonotic_infectious_disease" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DHF" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Dengue haemorrhagic fever" - } ], - "xrefs" : [ { - "val" : "ICD10CM:A91" - }, { - "val" : "MESH:D019595" - }, { - "val" : "NCI:C34683" - }, { - "val" : "SNOMEDCT_US_2016_03_01:186598001" - }, { - "val" : "SNOMEDCT_US_2016_03_01:186599009" - }, { - "val" : "SNOMEDCT_US_2016_03_01:20927009" - }, { - "val" : "UMLS_CUI:C0019100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/doid.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "disease_ontology" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/DOID_3292", - "lbl" : "monkeypox", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus, which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/doid#NCIthesaurus", "http://purl.obolibrary.org/obo/doid#zoonotic_infectious_disease" ], - "xrefs" : [ { - "val" : "GARD:10722" - }, { - "val" : "ICD10CM:B04" - }, { - "val" : "ICD9CM:059.01" - }, { - "val" : "MESH:D045908" - }, { - "val" : "NCI:C128421" - }, { - "val" : "SNOMEDCT_US_2021_09_01:240466002" - }, { - "val" : "UMLS_CUI:C0276180" - }, { - "val" : "url:http://www.cdc.gov/ncidod/monkeypox/factsheet2.htm" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl" - }, { - "pred" : "http://purl.org/dc/elements/1.1/type", - "val" : "http://purl.obolibrary.org/obo/ECO_0007637" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "disease_ontology" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/DOID_8469", - "lbl" : "influenza", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A viral infectious disease that results_in infection, located_in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Influenza with non-respiratory manifestation (disorder)" - }, { - "pred" : "hasExactSynonym", - "val" : "Influenza with other manifestations" - }, { - "pred" : "hasExactSynonym", - "val" : "Influenza with other manifestations (disorder)" - }, { - "pred" : "hasExactSynonym", - "val" : "Influenza with other manifestations NOS (disorder)" - }, { - "pred" : "hasExactSynonym", - "val" : "flu" - }, { - "pred" : "hasExactSynonym", - "val" : "influenza with non-respiratory manifestation" - } ], - "xrefs" : [ { - "val" : "ICD10CM:J11.1" - }, { - "val" : "ICD9CM:487" - }, { - "val" : "MESH:D007251" - }, { - "val" : "NCI:C53482" - }, { - "val" : "SNOMEDCT_US_2016_03_01:155559006" - }, { - "val" : "SNOMEDCT_US_2016_03_01:155562009" - }, { - "val" : "SNOMEDCT_US_2016_03_01:195931008" - }, { - "val" : "SNOMEDCT_US_2016_03_01:266353003" - }, { - "val" : "SNOMEDCT_US_2016_03_01:266393000" - }, { - "val" : "SNOMEDCT_US_2016_03_01:6142004" - }, { - "val" : "UMLS_CUI:C0021400" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/doid.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "DOID:8468" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "disease_ontology" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/DRON_00000005", - "lbl" : "drug product", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/dron.owl" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "William Hogan" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_00010483", - "lbl" : "environmental material", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system." - }, - "comments" : [ "Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, \"ENVO:water\" is to be understood as \"environmental material composed primarly of some CHEBI:water\". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of environmental material" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "ENVO" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000203", - "lbl" : "environmental condition", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system." - }, - "comments" : [ "A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional." ], - "subsets" : [ "\"envoPolar\"" ], - "xrefs" : [ { - "val" : "DOI:10.1186/2041-1480-4-43" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000121" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "ORCID:0000-0002-4366-3088" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2013-04-07T14:35:18Z" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000266", - "lbl" : "water vapour", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Water vapour is a vapour which is the gas phase of water." - }, - "comments" : [ "Perhaps a better relation between water vapour and water can be found in or added to RO?" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "aqueous vapor" - }, { - "pred" : "hasExactSynonym", - "val" : "aqueous vapour" - }, { - "pred" : "hasExactSynonym", - "val" : "water vapor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "ORCID:0000-0002-4366-3088" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2013-10-10T07:58:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "ENVO" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000268", - "lbl" : "atmospheric water vapour", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Atmospheric water vapour is water vapour that is part of an atmosphere." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "atmospheric water vapor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "ORCID:0000-0002-4366-3088" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2013-10-10T08:22:07Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "ENVO" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000703", - "lbl" : "hydrological precipitation process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity." - }, - "comments" : [ "\"process\" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet)" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "precipitation" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000753", - "lbl" : "air temperature", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A temperature that inheres in some portion of air." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Draft class. In discussion in Issue #278." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000797", - "lbl" : "gaseous environmental material", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely." - }, - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "gas" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This class is to be populated by inference." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001078", - "lbl" : "weather", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Environmental variability which inheres in an astronomical body part or in outer space." - }, - "comments" : [ "This class refers to all weather, including atmospheric and space weather. Please use a subclass for more specificity." ], - "xrefs" : [ { - "val" : "https://en.wikipedia.org/wiki/Space_weather" - }, { - "val" : "https://en.wikipedia.org/wiki/Weather" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001079", - "lbl" : "atmospheric weather", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Weather which inheres in an atmosphere." - }, - "comments" : [ "This class refers to the common usage of \"weather\", referencing the state of a (part of) an astronomical body's atmosphere." ], - "xrefs" : [ { - "val" : "https://en.wikipedia.org/wiki/Weather" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001081", - "lbl" : "environmental variability", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A condition which inheres in an environmental system by virtue of that system undergoing variation in its composition, the distribution of the qualities its components bear, and/or in the processes which occur within it and which it participates in." - }, - "comments" : [ "This class is very general, but the nature of environmental variability is indeed quite variable. This class may be refined once we have more subclasses to consider." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_02500000", - "lbl" : "environmental system process", - "type" : "CLASS", - "meta" : { - "comments" : [ "Should environmental feature become something more towards a disposition, the assert would be updated to something like \"has participant (environmental system or (material entity and has disposition some environmental feature))\". There are several issues surrounding the reconcilliation of environmental feature and environmental system, both theoretical and practical." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_09200000", - "lbl" : "temperature of environmental material", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The temperature of a environmental material." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "environmental material temperature" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_09200001", - "lbl" : "temperature of air", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The temperature of a air." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "air temperature" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/envo.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0000480", - "lbl" : "hasURL", - "type" : "PROPERTY", - "meta" : { - "comments" : [ "There are several URL and hasURL annotation properties out there in the ontology world. This one had the most sensible source ontology and OBO ID URI combination out there." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "VIVO-ISF" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0000657", - "lbl" : "metagenomics analysis", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Nicole Vasilevsky" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "community genomic analysis" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ecogenomic analysis" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "environmental genomic analysis" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Metagenomics" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ero.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/FBcv_0000667", - "lbl" : "website", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A set of related web pages containing content such as text, images, video, audio, etc., prepared and maintained as a collection of information on a particular subject." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/fbcv.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "pub_type" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/FBcv_0000787", - "lbl" : "journal", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A publication issued on a regular, ongoing basis containing separate research articles and other writings such as reviews, comments and conference reports." - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Periodicals" - } ], - "xrefs" : [ { - "val" : "MeSH:D020492" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/fbcv.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "djs93" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-07-10T04:08:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "pub_type" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000005", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "administrativeLocations" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000372", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A site designated by some relative spatial orientation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Matthew Diller" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. 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Instead, select a child term or, if no appropriate child term exists, please request a new term. 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To annotate host gene products, consider the biological process term 'positive regulation of apoptosis ; GO:0043065'." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gosubset_prok" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "activation by organism of host apoptosis" - }, { - "pred" : "hasExactSynonym", - "val" : "activation by organism of host apoptotic programmed cell death" - }, { - "pred" : "hasExactSynonym", - "val" : "induction by organism of host apoptotic programmed cell death" - }, { - "pred" : "hasExactSynonym", - "val" : "induction by symbiont of host apoptosis" - }, { - "pred" : "hasExactSynonym", - "val" : "positive regulation by organism of host apoptotic programmed cell death" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation by organism of host apoptotic programmed cell death" - }, { - "pred" : "hasExactSynonym", - "val" : "up regulation by symbiont of host apoptosis" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation by organism of host apoptotic programmed cell death" - }, { - "pred" : "hasExactSynonym", - "val" : "up-regulation by symbiont of host apoptosis" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation by organism of host apoptotic programmed cell death" - }, { - "pred" : "hasExactSynonym", - "val" : "upregulation by symbiont of host apoptosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation by symbiont of host apoptosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation by symbiont of host apoptosis" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation by symbiont of host apoptosis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0033669" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0052030" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0052248", - "lbl" : "modulation of programmed cell death in other organism involved in symbiotic interaction", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism, where the two organisms are in a symbiotic interaction." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gosubset_prok" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "modulation by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction" - }, { - "pred" : "hasRelatedSynonym", - "val" : "modulation of programmed cell death in other organism during symbiotic interaction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0052459" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0052501", - "lbl" : "positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism, where the two organisms are in a symbiotic interaction." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gosubset_prok" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "induction by organism of apoptosis in other organism involved in symbiotic interaction" - }, { - "pred" : "hasNarrowSynonym", - "val" : "activation by organism of apoptosis in other organism during symbiotic interaction" - }, { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation by organism of apoptosis in other organism involved in symbiotic interaction" - }, { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction" - }, { - "pred" : "hasNarrowSynonym", - "val" : "stimulation by organism of apoptosis in other organism during symbiotic interaction" - }, { - "pred" : "hasRelatedSynonym", - "val" : "activation by organism of apoptotic programmed cell death in other organism during symbiotic interaction" - }, { - "pred" : "hasRelatedSynonym", - "val" : "induction by organism of apoptosis in other organism during symbiotic interaction" - }, { - "pred" : "hasRelatedSynonym", - "val" : "induction by organism of apoptotic programmed cell death in other organism during symbiotic interaction" - }, { - "pred" : "hasRelatedSynonym", - "val" : "positive regulation by organism of apoptosis in other organism during symbiotic interaction" - }, { - "pred" : "hasRelatedSynonym", - "val" : "positive regulation by organism of apoptotic programmed cell death in other organism during symbiotic interaction" - }, { - "pred" : "hasRelatedSynonym", - "val" : "up regulation by organism of apoptosis in other organism during symbiotic interaction" - }, { - "pred" : "hasRelatedSynonym", - "val" : "up-regulation by organism of apoptosis in other organism during symbiotic interaction" - }, { - "pred" : "hasRelatedSynonym", - "val" : "upregulation by organism of apoptosis in other organism during symbiotic interaction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0052388" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0060139", - "lbl" : "positive regulation of apoptotic process by virus", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process." - }, - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "positive regulation of apoptosis by virus" - } ], - "basicPropertyValues" : [ { - "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" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0060153", - "lbl" : "modulation by virus of host cell cycle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any viral process that modulates the rate or extent of progression through the cell cycle." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_virus" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "modulation of host cell cycle by virus" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation by virus of host cell cycle" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of host cell cycle by virus" - }, { - "pred" : "hasExactSynonym", - "val" : "viral process regulating host cell cycle" - } ], - "xrefs" : [ { - "val" : "VZ:1636" - } ], - "basicPropertyValues" : [ { - "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" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0060403", - "lbl" : "post-mating oviposition", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.org/obo/owl/gene_ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0065007", - "lbl" : "biological regulation", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates a measurable attribute of any biological process, quality or function." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#gosubset_prok" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "regulation" - } ], - "basicPropertyValues" : [ { - "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" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0065008", - "lbl" : "regulation of biological quality", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gosubset_prok" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulation of biological attribute" - }, { - "pred" : "hasExactSynonym", - "val" : "regulation of biological characteristic" - } ], - "basicPropertyValues" : [ { - "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" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0071684", - "lbl" : "organism emergence from protective structure", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.org/obo/owl/gene_ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000001", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000003", - "lbl" : "measurement unit label", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "measurement unit label" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Examples of measurement unit labels are liters, inches, weight per volume." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "unitId" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000004", - "lbl" : "has measurement value", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000005", - "lbl" : "objective specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "objective specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "purpose of a study; support of hypothesis, discovery of new information" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: original definition when imported from OBI read: \"objective is an\nnon realizable information entity which can serve as that proper part\nof a plan towards which the realization of the plan is directed.\"" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Answers the question, why did you do this experiment?" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Barry Smith" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Jennifer Fostel" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI Plan and Planned Process/Roles Branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000217" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000007", - "lbl" : "action specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a directive information entity that describes an action the bearer will take" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Pour the contents of flask 1 into flask 2" - }, { - "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_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI Plan and Planned Process branch" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000009", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "label" - }, { - "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" : "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "GROUP: IAO" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "label" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000010", - "lbl" : "software", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "software" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP: OBI" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000027", - "lbl" : "data item", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Data items include counts of things, analyte concentrations, and statistical summaries." - }, { - "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" : "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Jonathan Rees" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "data" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000028", - "lbl" : "symbol", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a smallish, word-like datum..." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "symbol" - }, { - "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" : "20091104, MC: this needs work and will most probably change" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Jonathan Rees" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000029", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000030", - "lbl" : "information content entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "information content entity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Examples of information content entites include journal articles, data, graphical layouts, and graphs." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000142" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000032", - "lbl" : "scalar measurement datum", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "10 feet. 3 ml." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Melanie Courtot" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000033", - "lbl" : "directive information entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An information content entity whose concretizations indicate to their bearer how to realize them in a process." - }, - "basicPropertyValues" : [ { - "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" : "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be\nconcretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Bjoern Peters" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000038", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000039", - "lbl" : "has measurement unit label", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000055", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000124" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000064", - "lbl" : "algorithm", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "algorithm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PlanAndPlannedProcess Branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000270" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000100", - "lbl" : "data set", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data set" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "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" : "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "person:Allyson Lister" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "person:Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000042" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "dataSets" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000104", - "lbl" : "plan specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications." - }, - "comments" : [ "2/3/2009 Comment from OBI review.\n \n Action specification not well enough specified.\n Conditional specification not well enough specified.\n Question whether all plan specifications have objective specifications.\n \n Request that IAO either clarify these or change definitions not to use them" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "plan specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "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" : "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI Plan and Planned Process branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000344" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000109", - "lbl" : "measurement datum", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "measurement datum" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "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" : "2/2/2009 is_specified_output of some assay?" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "person:Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000305" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000111", - "lbl" : "editor preferred term~editor preferred label", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000112", - "lbl" : "example of usage", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000114", - "lbl" : "has curation status", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "textual definition", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000117", - "lbl" : "term editor", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000118", - "lbl" : "alternative term", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000119", - "lbl" : "definition source", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000129", - "lbl" : "version number", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "version number" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000124" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. 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The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. 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The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." - }, { - "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" : "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:\n\n1) there are organization_member_roles (president, treasurer, branch\neditor), with individual persons as bearers\n\n2) there are organization_roles (employer, owner, vendor, patent holder)\n\n3) an organization has a charter / rules / bylaws, which specify what roles\nthere are, how they should be realized, and how to modify the\ncharter/rules/bylaws themselves.\n\nIt is debatable what the organization itself is (some kind of dependent\ncontinuant or an aggregate of people). This also determines who/what the\nbearer of organization_roles' are. 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We leave further clarifications to BFO, and close this issue\nfor now." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Susanna Sansone" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP: OBI" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000417", - "lbl" : "achieves_planned_objective", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "achieves_planned_objective" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A cell sorting process achieves the objective specification 'material separation objective'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "BP, AR, PPPB branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "PPPB branch derived" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000425", - "lbl" : "averaging objective", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "averaging objective" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. 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The DOI system is particularly used for electronic documents such as journal articles." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "digital object identifier" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The doi symbol: \"10.1109/5.771073\" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Discussed on Aug 22, 2016 OBI dev call. Details see tracker:\nhttps://sourceforge.net/p/obi/obi-terms/818/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "OBI developers" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "DOI" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Digital_object_identifier\nhttps://www.doi.org/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0100026", - "lbl" : "organism", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000121" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "Individual" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0200000", - "lbl" : "data transformation", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A data transformation is a process which produces output data from input data" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data transformation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." - 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}, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "PERSON: James Malone" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0200170", - "lbl" : "averaging data transformation", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An averaging data transformation is a data transformation that has objective averaging." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "averaging data transformation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "James Malone" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "PERSON: James Malone" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0300311", - "lbl" : "observation design", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "observation design" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study." - }, { - "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" : "Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI branch derived" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - 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It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra; Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0302914", - "lbl" : "digital curation", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "digital curation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "wikipedia" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0400107", - "lbl" : "computer", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "computer" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Apple PowerBook, Dell OptiPlex" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Trish Whetzel" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Computer" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0500000", - "lbl" : "study design", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "study design" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design." - }, { - "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" : "Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "experimental design" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0500020", - "lbl" : "time series design", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Groups of assays that are related as part of a time series." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "time series design" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. 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The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources." - }, { - "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" : "Philippe Rocca-Serra on behalf of MO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "MO_887" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBIws_0000050", - "lbl" : "software execution", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A planned process that realizes the concretization of a software." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "ITPPR" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - 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}, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2009-06-23T10:21:58Z" - }, { - "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" : "result" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000023", - "lbl" : "phenotype", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - 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}, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Barry Smith" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Richard H. 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Disorders are the physical basis of disease." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2009-06-23T11:39:44Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ogms.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000063", - "lbl" : "disease course", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The totality of all processes through which a given disease instance is realized." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "disease course" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf" - }, { - "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/ido.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ogms.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000087", - "lbl" : "extended organism", - "type" : "CLASS", - "meta" : { - "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://code.google.com/p/ogms/issues/detail?id=3" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2010-01-25T04:51:11Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ogms.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000090", - "lbl" : "treatment", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder" - }, - "comments" : [ "Apollo-SV currently defines two subclasses of treatment.\nSee vaccination and antiviral treatment. \n" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://code.google.com/p/ogms/issues/detail?id=35" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2010-03-31T04:51:11Z" - 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"val" : "A processual entity which has as parts all the processes in which a given organism is participant." - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "LifeCycle" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000096", - "lbl" : "health care process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2011-02-21T09:57:44Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ogms.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000097", - "lbl" : "health care encounter", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2011-02-21T09:57:44Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ogms.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000098", - "lbl" : "hospitalization", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2011-02-21T09:57:44Z" - }, { - "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" : "hospitalization" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000099", - "lbl" : "outpatient encounter", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2011-02-21T09:57:44Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ogms.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000100", - "lbl" : "inpatient encounter", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2011-02-21T09:57:44Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ogms.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000101", - "lbl" : "ED encounter", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "creation date: 2011-02-21T09:57:44Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ogms.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000105", - "lbl" : "relapse", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Albert Goldfain" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://code.google.com/p/ogms/issues/detail?id=73" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ogms.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", - "lbl" : "owns", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Reinach, A. 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" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000019", - "lbl" : "unique resource locator", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A CRID that constitutes a reference to an Internet resource." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "uri" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Uniform_resource_locator" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omiabis.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "url" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000048", - "lbl" : "is owned by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000001", - "lbl" : "human social role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A social role inhering in a human being." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000007", - "lbl" : "gender role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Gender_role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "sex" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000008", - "lbl" : "male gender role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "male gender" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000009", - "lbl" : "female gender role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "female gender" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000010", - "lbl" : "human health care role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. " - }, - "comments" : [ "Mathias Brochhausen" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "health care role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000011", - "lbl" : "patient role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role borne by an organism being as the recipient of a health care service." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "patient" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Patient" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000015", - "lbl" : "health care provider organization role", - "type" : "CLASS", - "meta" : { - "comments" : [ "Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division)." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "lbl" : "collection of organisms", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An object aggregate of organisms." - }, - "comments" : [ "Any arbitrary collection of organisms. They need not be of the same taxonomic class. " ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000023", - "lbl" : "collection of humans", - "type" : "CLASS", - "meta" : { - "comments" : [ "An object aggregate all of whose components are human beings." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000025", - "lbl" : "organization social role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role in human social processes that inheres in an organization." - }, - "comments" : [ "Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000026", - "lbl" : "organism social role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role in human social processes that inheres in an organism." - }, - "comments" : [ "Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants.", "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.", "Previous definition: A role in human social processes played by an organism." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan\nMathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000027", - "lbl" : "organization health care role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An organization social role that is realized by a health care process." - }, - "comments" : [ "Previous definition: An organization social role played by an organization in health care processes." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000033", - "lbl" : "aggregate of organizations", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of organizations that have some feature in common, but is not itself an organization." - }, - "comments" : [ "It is often convenient to group organizations together that otherwise might not even interact with one another. " ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000052", - "lbl" : "hospital function", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000053", - "lbl" : "school function", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A function inhering in a facility that manifests by the facility participating in providing formal education to a student population." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000054", - "lbl" : "hospital role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000055", - "lbl" : "school role", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "An organization social role that inheres in an organization and is realized by providing formal education to students." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000056", - "lbl" : "hospital organization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An organization that is the bearer of a hospital role." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000057", - "lbl" : "school organization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An organization that is the bearer of a school role." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000058", - "lbl" : "student role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A human social role that is realized by the process of formal education that the bearer undergoes." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000059", - "lbl" : "nursery school role", - "type" : "CLASS", - "meta" : { - "comments" : [ "Key motivating use case was Synthia synthetic population data.\n" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "preschool" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000060", - "lbl" : "primary school role", - "type" : "CLASS", - "meta" : { - "comments" : [ "Key motivating use case was Synthia synthetic population data." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "primarySchool" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000061", - "lbl" : "architectural structure", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A material entity that is a human made strcuture with firm connection between its foundation and the ground." - }, - "comments" : [ "\"Building\" is a subclass of this. ", "This type of entity is referred to as \"Bauwerk\" or \"Bauliche Anlage\"." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://de.wikipedia.org/wiki/Bauwerk" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000062", - "lbl" : "facility", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An architectural structure that bears some function." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000063", - "lbl" : "hospital facility", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A facility that is run by a hospital organization and is the bearer of a hospital function." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "HealthcareFacility" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000064", - "lbl" : "school facility", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A facility that is run by a school organization and is the bearer of a school function." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "SchoolFacility" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000065", - "lbl" : "secondary school role", - "type" : "CLASS", - "meta" : { - "comments" : [ "Key motivating use case was Synthia synthetic population data." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "secondarySchool" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000070", - "lbl" : "is enrolled in school", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000071", - "lbl" : "is admitted to hospital", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000074", - "lbl" : "housing unit", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function." - }, - "comments" : [ "Housing units are individuated by their residence functions." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "houses" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000076", - "lbl" : "household", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "Household" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000078", - "lbl" : "workplace facility", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "workplace" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000079", - "lbl" : "workplace function", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000098", - "lbl" : "racial identity datum", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "race" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000102", - "lbl" : "health care facility", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000132", - "lbl" : "identity datum", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00002072", - "lbl" : "role in human social processes", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role inhering in an entity realized by social interactions in human society." - }, - "comments" : [ "Previous definition: A role played by an entity in human social processes." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Matthew Diller" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000040", - "lbl" : "distance", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A quality that is the extent of space between two entities." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim", "http://purl.obolibrary.org/obo/pato#relational_slim", "http://purl.obolibrary.org/obo/pato#scalar_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "Distance" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000047", - "lbl" : "biological sex", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "biological sex" - }, { - "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" : "biologicalSex" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000051", - "lbl" : "morphology", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000122", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.org/obo/owl/PATO" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000125", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.org/obo/owl/PATO" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000141", - "lbl" : "structure", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "conformation" - }, { - "pred" : "hasExactSynonym", - "val" : "relational structural quality" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001452" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000146", - "lbl" : "temperature", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A physical quality of the thermal energy of a system." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim", "http://purl.obolibrary.org/obo/pato#scalar_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000383", - "lbl" : "female", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "female" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000384", - "lbl" : "male", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "male" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001018", - "lbl" : "physical quality", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "relational physical quality" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Physical_property" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001241", - "lbl" : "physical object quality", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A quality which inheres in a continuant." - }, - "comments" : [ "Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "monadic quality of a continuant" - }, { - "pred" : "hasExactSynonym", - "val" : "multiply inhering quality of a physical entity " - }, { - "pred" : "hasExactSynonym", - "val" : "quality of a continuant" - }, { - "pred" : "hasExactSynonym", - "val" : "quality of a single physical entity" - }, { - "pred" : "hasExactSynonym", - "val" : "quality of an object" - }, { - "pred" : "hasExactSynonym", - "val" : "quality of continuant" - }, { - "pred" : "hasNarrowSynonym", - "val" : "monadic quality of an object" - }, { - "pred" : "hasNarrowSynonym", - "val" : "monadic quality of continuant" - } ], - "xrefs" : [ { - "val" : "snap:Quality" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001708", - "lbl" : "1-D extent", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A size quality inhering in an bearer by virtue of the bearer's extension in one dimension." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "1-D size" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001961", - "lbl" : "in contact with", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A structural quality inhering in a bearer by virtue of the bearer's touching another entity." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#relational_slim", "http://purl.obolibrary.org/obo/pato#value_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "contiguous" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0002390", - "lbl" : "radius", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim", "http://purl.obolibrary.org/obo/pato#scalar_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "radius" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "gkoutos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-15T05:17:15Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000000", - "lbl" : "PCO:collection of organisms", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A material entity that consists of two or more organisms, viruses, or viroids." - }, - "comments" : [ "May be of the same or different species." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "group of organisms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "organism collection" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000001", - "lbl" : "population", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A collection of organisms, all of the same species, that live in the same place." - }, - "comments" : [ "It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ISBN:0878932739" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "Population" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000018", - "lbl" : "collection of organisms of the same species", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "is bearer of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "bearer of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "bearer_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has_participant", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has_participant" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000059", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is_concretization_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001900", - "lbl" : "temporal interpretation", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002087", - "lbl" : "immediately_preceded_by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "directly preceded by" - }, { - "pred" : "hasExactSynonym", - "val" : "is directly preceded by" - }, { - "pred" : "hasExactSynonym", - "val" : "is immediately preceded by" - }, { - "pred" : "hasExactSynonym", - "val" : "starts_at_end_of" - } ], - "xrefs" : [ { - "val" : "RO:0002087" - }, { - "val" : "http://semanticscience.org/resource/SIO_000251" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/uberon.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002090", - "lbl" : "immediately_precedes", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002093", - "lbl" : "ends during", - "type" : "PROPERTY", - "meta" : { - "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "o" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "overlaps" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", - "lbl" : "spatially disjoint from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "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" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://xmlns.com/foaf/0.1/page", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" - }, - "basicPropertyValues" : [ { - "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" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002218", - "lbl" : "has active participant", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x has participant y if and only if x realizes some active role that inheres in y" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'heart development' has active participant some Shh protein" - }, { - "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" : "This may be obsoleted and replaced by the original 'has agent' relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has agent" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002220", - "lbl" : "adjacent to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x adjacent to y if and only if x and y share a boundary." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "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." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "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." - }, { - "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" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl" - }, { - "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/jhpoelen/eol-globi-data/issues/225#issuecomment-218584934" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002222", - "lbl" : "temporally related to", - "type" : "PROPERTY", - "meta" : { - "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "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" : "move to BFO?" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002224", - "lbl" : "starts with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002229", - "lbl" : "ends", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of ends with" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002230", - "lbl" : "ends with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished with" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002325", - "lbl" : "colocalizes with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Gene Ontology Consortium" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002404", - "lbl" : "causally downstream of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of upstream of" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002411", - "lbl" : "causally upstream of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002501", - "lbl" : "causal relation between processes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/STATO_0000032", - "lbl" : "STATO alternative term", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "an alternative term used for STATO statistical ontology and ISA team" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alejandra Gonzalez-Beltran" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Orlaith Burke" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/STATO_0000085", - "lbl" : "effect size estimate", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alejandra Gonzalez-Beltran" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Orlaith Burke" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "AGB,PRS" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/stato.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/STATO_0000032", - "val" : "effect size" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/STATO_0000088", - "lbl" : "study group population size", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "statistical sample size is a count evaluating the number of individual experimental units" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alejandra Gonzalez-Beltran" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Orlaith Burke" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "AGB-PRS" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/stato.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/STATO_0000032" - }, { - "pred" : "http://purl.obolibrary.org/obo/STATO_0000032", - "val" : "statistical sample size" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "sampleSize" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/STATO_0000134", - "lbl" : "true negative rate", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alejandra Gonzalez-Beltran" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Orlaith Burke" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "specificity" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/STATO_0000233", - "lbl" : "true positive rate", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alejandra Gonzalez-Beltran" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Orlaith Burke" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "recall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "sensitivity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "adapted from:\nhttp://en.wikipedia.org/wiki/Sensitivity_and_specificity\nand\nhttp://mathworld.wolfram.com/Sensitivity.html" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/STATO_0000245", - "lbl" : "relative risk", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alejandra Gonzalez-Beltran" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Orlaith Burke" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "risk ratio" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/stato.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/STATO_0000032" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/STATO_0000252", - "lbl" : "categorical variable", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alejandra Gonzalez-Beltran" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Orlaith Burke" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Philippe Rocca-Serra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "discrete variable" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "nominal variable" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "qualitative factor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - 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"obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://www.obofoundry.org/ro/ro.owl#has_proper_part", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://www.obofoundry.org/ro/ro.owl#inheres_in", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://www.obofoundry.org/ro/ro.owl#location_of", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://www.obofoundry.org/ro/ro.owl#proper_part_of", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000055" - } ], - "equivalentNodesSets" : [ { - "representativeNodeId" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "nodeIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000022", "http://purl.obolibrary.org/obo/PCO_0000000" ] } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000006", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000009", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] @@ -35205,6 +14620,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000312", "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", + "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000041", "restrictions" : [ { @@ -35649,86 +15071,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000798" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0000178", - "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0000679", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000027" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000312", - "fillerId" : "http://purl.obolibrary.org/obo/OBI_0200170" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0001530", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0001173" ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000056", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000245" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/OMRSE_00000054" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000057", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000245" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/OMRSE_00000055" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/VO_0000001", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000047" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000312", - "fillerId" : "http://purl.obolibrary.org/obo/VO_0000590" - } ] - } ], - "domainRangeAxioms" : [ { - "predicateId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000067", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/APOLLO_SV_00000070" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000543", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000019" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000155", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000008" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000156", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000008" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000184", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000185", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000581", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000582" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000416" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000583", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000582" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002222", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000039", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000003" ] } ] } ] } \ No newline at end of file diff --git a/apollo_sv-base.obo b/apollo_sv-base.obo index 8a28910..81d1fef 100644 --- a/apollo_sv-base.obo +++ b/apollo_sv-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: apollo_sv/releases/2024-02-23/apollo_sv-base.owl +data-version: apollo_sv/releases/2024-04-19/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 "2024-02-23" xsd:string +property_value: owl:versionInfo "2024-04-19" xsd:string property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -45,7 +45,6 @@ id: APOLLO_SV:00000002 name: basic reproduction number def: "The average number of transmissions of an infectious agent from an infectious organism to a susceptible organism within a completely susceptible population." [] comment: MB: Here we run into the well know DL problem that we cannot specify that the infectious agent that is transmitted is of the same type that the infectious agent the population is susceptible to. -is_a: APOLLO_SV:00000043 ! reproduction number property_value: APOLLO_SV:0000040 "basicReproductionNumbers" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "The number of organisms that each infected organism infects in a completely susceptible population during its infectious period." xsd:string @@ -64,7 +63,7 @@ id: APOLLO_SV:00000005 name: simulating of process of type X def: "a planned process that (1) has at least one process part that has as participants representations of participants (in place of those participants) of processes of type X, and where all such process parts substitute for parts of processes of type X, and (2) is carried out for the purpose of planning for processes of type X, learning more about processes of type X, or teaching about processes of type X." [] comment: For example, in a simulated volcano eruption, representations of lava, lava tubes, vents, etc. take the place of actual lava, lava tubes, vents, etc.\n\nEven in the case of a simulated disaster scenario where actual ambulances, fire trucks, and people participate, representations of catastrophic events and injuries, etc. take the place of real ones. -is_a: OBI:0000011 ! planned process +is_a: OBI:0000011 property_value: APOLLO_SV:0000040 "simulating of process of type X" xsd:string property_value: IAO:0000600 "A process that replaces the essential participants of another type of process with representations of those participants." xsd:string @@ -85,6 +84,16 @@ property_value: APOLLO_SV:0000040 "simulator" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Simulation_software" xsd:string property_value: IAO:0000600 "A software application that provides a model of a real phenomenon based on a set of mathematical formulas." xsd:string +[Term] +id: APOLLO_SV:00000008 +name: software development +def: "A planned process that has specified output a software product and that involves the creation of source code." [] +is_a: OBI:0000011 +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Software_development" xsd:string +property_value: IAO:0000600 "A planned process resulting in a software product involving the creation of source code." xsd:string + [Term] id: APOLLO_SV:00000009 name: simulator developer identifier @@ -96,10 +105,11 @@ property_value: IAO:0000600 "An identifier that refers to the person or organiza id: APOLLO_SV:00000010 name: simulator identifier def: "An identifier that refers to all version of a specific simulator." [] -is_a: IAO:0020000 +is_a: APOLLO_SV:00000109 ! software identifier intersection_of: IAO:0020000 intersection_of: IAO:0000219 APOLLO_SV:00000007 ! simulation software application relationship: BFO:0000050 APOLLO_SV:00000054 ! complete simulator identifier +relationship: IAO:0000219 APOLLO_SV:00000007 ! simulation software application property_value: IAO:0000600 "An identifier that refers to all versions of a specific simulator, such as “FRED”. We intend that it uniquely identify a simulator when combined with simulator developer. For example, the combination www.psc.edu/FRED would differentiate the FRED simulator created by a Pittsburgh organization from another “FRED” simulator maintained elsewhere. The implementation of namespace control for simulator name (i.e., making sure that they don’t use “FRED” twice) is the responsibility of simulator developer." xsd:string [Term] @@ -193,7 +203,6 @@ id: APOLLO_SV:00000022 name: count of simulated population def: "The count of (simulated organisms) in a simulated population." [] comment: MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. \n\nAny ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’\n -is_a: APOLLO_SV:00000617 ! population count property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "The number of simulated organisms in a simulated population. The number does not have to be an integer. " xsd:string @@ -210,7 +219,7 @@ name: vaccination compliance def: "The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination." [] comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly. comment: MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy” and “control measure efficacy delay.” We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level. We have not represented those control measures yet.\n -is_a: OBI:0302867 ! predicted data item +is_a: OBI:0302867 property_value: IAO:0000600 "The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint." xsd:string [Term] @@ -227,7 +236,7 @@ property_value: IAO:0000600 "The degree to which a particular vaccination reduce id: APOLLO_SV:00000026 name: facility survey def: "A planned process involving counting numbers of facilities in a specific region." [] -is_a: OBI:0000011 ! planned process +is_a: OBI:0000011 property_value: IAO:0000600 "A planned process involving counting numbers of facilities in a specific region." xsd:string [Term] @@ -236,23 +245,25 @@ name: school facility census comment: Motivating use case is Synthia synthetic population data. is_a: APOLLO_SV:00000173 ! census intersection_of: APOLLO_SV:00000173 ! census -intersection_of: IAO:0000136 OMRSE:00000064 ! is about school facility +intersection_of: IAO:0000136 OMRSE:00000064 intersection_of: OBI:0000312 APOLLO_SV:00000026 ! facility survey intersection_of: OBI:0000312 APOLLO_SV:00000026 {all_only="true"} ! facility survey +relationship: IAO:0000136 OMRSE:00000064 +relationship: OBI:0000312 APOLLO_SV:00000026 ! facility survey property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] id: APOLLO_SV:00000029 name: infectious disease control strategy execution def: "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. " [] -is_a: OBI:0000011 ! planned process +is_a: OBI:0000011 property_value: IAO:0000600 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. " xsd:string [Term] id: APOLLO_SV:00000030 name: hospital patient population comment: Key motivating use case was Synthia synthetic population data. -is_a: OMRSE:00000023 ! collection of humans +is_a: OMRSE:00000023 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -260,8 +271,10 @@ id: APOLLO_SV:00000031 name: simulated population def: "A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval." [] is_a: APOLLO_SV:00000070 ! simulation -intersection_of: APOLLO_SV:00000067 PCO:0000000 ! simulates PCO:collection of organisms +intersection_of: APOLLO_SV:00000067 PCO:0000000 ! simulates intersection_of: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X +relationship: APOLLO_SV:00000067 PCO:0000000 ! simulates +relationship: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X property_value: APOLLO_SV:0000040 "simulatorReferencablePopulation" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A simulated population is a set of simulated organisms. The set can be null (e.g., the set of 200 year-old H. sapiens). A simulated population can include more than one species, in which case it may be convenient to define each species as a simulated population and form the overall simulated population by set union. Similarly, it may be convenient to define sociodemographic or geographic strata within a simulated population as simulated populations and obtain the overall simulated population by set union. See examples in “Programmer’s Guide, page x)" xsd:string @@ -270,9 +283,10 @@ property_value: IAO:0000600 "A simulated population is a set of simulated organi id: APOLLO_SV:00000032 name: count def: "A measurement datum that is the output of counting." [] -is_a: IAO:0000109 ! measurement datum -intersection_of: IAO:0000027 ! data item +is_a: IAO:0000109 +intersection_of: IAO:0000027 intersection_of: OBI:0000312 APOLLO_SV:00000033 ! counting +relationship: OBI:0000312 APOLLO_SV:00000033 ! counting property_value: APOLLO_SV:0000040 "count" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A measurement datum that is the output of counting." xsd:string @@ -281,6 +295,10 @@ property_value: IAO:0000600 "A measurement datum that is the output of counting. id: APOLLO_SV:00000033 name: counting def: "The planned process of finding the number of elements in a finite set of objects." [] +is_a: OBI:0000011 +intersection_of: OBI:0000011 +intersection_of: OBI:0000299 APOLLO_SV:00000032 ! count +relationship: OBI:0000299 APOLLO_SV:00000032 ! count property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Counting" xsd:string property_value: IAO:0000600 "The planned process of finding the number of elements in a finite set of objects." xsd:string @@ -289,8 +307,11 @@ property_value: IAO:0000600 "The planned process of finding the number of elemen id: APOLLO_SV:00000034 name: simulation of organism comment: a simulation that is about an organism -intersection_of: APOLLO_SV:00000067 OBI:0100026 {all_some="true"} ! simulates organism +is_a: APOLLO_SV:00000070 ! simulation +intersection_of: APOLLO_SV:00000067 OBI:0100026 {all_some="true"} ! simulates intersection_of: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X +relationship: APOLLO_SV:00000067 OBI:0100026 ! simulates +relationship: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X [Term] id: APOLLO_SV:00000036 @@ -342,7 +363,6 @@ property_value: IAO:0000600 "The disease being simulated." xsd:string id: APOLLO_SV:00000043 name: reproduction number def: "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. " [] -is_a: OBI:0000679 ! average value property_value: APOLLO_SV:0000040 "ReproductionNumber" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "The number of susceptible organisms that each infected organism infects. ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation." xsd:string @@ -358,7 +378,7 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string id: APOLLO_SV:00000045 name: obsolete asymptomatic infection fraction def: "The fraction given to express the probability that an organism will become infected, but stay asymptomatic." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: APOLLO_SV:0000040 "asymptomatic infection fraction" xsd:string property_value: IAO:0000600 "The fraction of infectious individuals who do not develop symptoms during the course of their infections." xsd:string is_obsolete: true @@ -399,7 +419,7 @@ name: antiviral compliance def: "The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible." [] comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly. comment: MW: Since the estimates that modelers use are from real populations, I have two questions:\n1. Should we distinguish between real and simulated population?\n2. If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population?\n\nMB: This issue will need to be taken care of in the axiomatization of simulated population -is_a: OBI:0302867 ! predicted data item +is_a: OBI:0302867 property_value: APOLLO_SV:0000040 "antiviral cm compliance" xsd:string property_value: IAO:0000600 "The fraction of individuals in a simulated population that will accept antiviral treatment if offered. " xsd:string @@ -435,6 +455,7 @@ comment: MB: I am not 100% happy with the elucidation. Can't we just say that th is_a: IAO:0020000 intersection_of: IAO:0020000 intersection_of: IAO:0000219 APOLLO_SV:00000001 ! epidemic model +relationship: IAO:0000219 APOLLO_SV:00000001 ! epidemic model property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "The combination of simulator developer, simulator name, and simulator version, for example “www.psc.edu/FRED/2.0” The combination is intended to uniquely identify the simulation algorithm that produced output X, given input Y to support scientific audit, error analysis, and reproducibility of results." xsd:string @@ -442,7 +463,6 @@ property_value: IAO:0000600 "The combination of simulator developer, simulator n id: APOLLO_SV:00000055 name: epidemic simulating def: "A simulating of a disease epidemic or pandemic." [] -is_a: APOLLO_SV:00000005 ! simulating of process of type X property_value: APOLLO_SV:0000040 "epidemic simulation" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "the process of simulating a disease epidemic or pandemic. This term is not currently used in Apollo-WS." xsd:string @@ -453,7 +473,8 @@ name: hospital patient population census comment: Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast). is_a: APOLLO_SV:00000153 ! population census intersection_of: APOLLO_SV:00000153 ! population census -intersection_of: IAO:0000136 APOLLO_SV:00000030 ! is about hospital patient population +intersection_of: IAO:0000136 APOLLO_SV:00000030 ! hospital patient population +relationship: IAO:0000136 APOLLO_SV:00000030 ! hospital patient population property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -506,7 +527,7 @@ id: APOLLO_SV:00000064 name: simulation time series def: "A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation." [] comment: MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.\n -is_a: IAO:0000584 ! time sampled measurement data set +is_a: IAO:0000584 property_value: IAO:0000600 "A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation." xsd:string [Term] @@ -518,6 +539,7 @@ is_a: IAO:0000029 intersection_of: IAO:0000029 intersection_of: IAO:0000219 APOLLO_SV:00000005 ! simulating of process of type X intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} +relationship: IAO:0000219 APOLLO_SV:00000005 ! simulating of process of type X property_value: IAO:0000600 "The run id indexes a run of a specific simulator version on a specific simulated population, disease(s), and optionally control measures. The simulator is responsible for generating a run id and ensuring its uniqueness." xsd:string [Term] @@ -535,7 +557,7 @@ def: "An action specification that specifies the length of the time steps interv comment: simulation time step value\nsimulation time step unit\nsimulation run length\n\nThe time step value and unit are specified using a scalar value specification. is_a: APOLLO_SV:00000793 ! epidemic simulator action specification relationship: BFO:0000050 APOLLO_SV:00000007 ! simulation software application -relationship: IAO:0000136 APOLLO_SV:00000066 ! is about simulation of time step +relationship: IAO:0000136 APOLLO_SV:00000066 ! simulation of time step relationship: OBI:0001938 OBI:0001931 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "An action specification that specifies the length of the time steps interval assumed in a simulation." xsd:string @@ -548,6 +570,7 @@ is_a: IAO:0000029 intersection_of: IAO:0000029 intersection_of: IAO:0000219 APOLLO_SV:00000066 ! simulation of time step intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} +relationship: IAO:0000219 APOLLO_SV:00000066 ! simulation of time step property_value: APOLLO_SV:0000040 "simulatorTime" xsd:string property_value: IAO:0000600 "The time step number of a simulation." xsd:string @@ -558,6 +581,7 @@ def: "A purely intentional entity that simulates an entity and its properties.\n is_a: APOLLO_SV:00000000 ! purely intentional entity intersection_of: APOLLO_SV:00000000 ! purely intentional entity intersection_of: APOLLO_SV:00000067 BFO:0000001 ! simulates +relationship: APOLLO_SV:00000067 BFO:0000001 ! simulates property_value: APOLLO_SV:0000040 "simulation" xsd:string property_value: IAO:0000600 "A purely intentional entity that simulates an entity and its properties.\n\n" xsd:string @@ -565,7 +589,7 @@ property_value: IAO:0000600 "A purely intentional entity that simulates an entit id: APOLLO_SV:00000071 name: obsolete simulation of population location def: "The simulation of geographical location in which a population is assumed to be located." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: APOLLO_SV:0000040 "simulated population location" xsd:string property_value: IAO:0000600 "An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes." xsd:string is_obsolete: true @@ -591,6 +615,7 @@ def: "A simulation of an asymptomatic infectious agent host." [] is_a: APOLLO_SV:00000034 ! simulation of organism intersection_of: APOLLO_SV:00000067 APOLLO_SV:00000236 ! simulates asymptomatic host intersection_of: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X +relationship: APOLLO_SV:00000067 APOLLO_SV:00000236 ! simulates asymptomatic host property_value: IAO:0000600 "A simulated organism in a simulated population that has no symptoms caused by a particular simulated disease." xsd:string [Term] @@ -598,13 +623,13 @@ id: APOLLO_SV:00000075 name: infectious disease control objective specification def: "An objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population." [] comment: typically, the process endpoint is achievement of R0 < 1 -is_a: IAO:0000005 ! objective specification +is_a: IAO:0000005 property_value: IAO:0000600 "an objective of achieving satisfactory control of epidemic spread through a population" xsd:string [Term] id: APOLLO_SV:00000076 name: μ -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: APOLLO_SV:0000040 "μ" xsd:string property_value: IAO:0000600 "the mean or expectation of a distribution" xsd:string is_obsolete: true @@ -612,7 +637,7 @@ is_obsolete: true [Term] id: APOLLO_SV:00000077 name: σ -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: APOLLO_SV:0000040 "sigma" xsd:string property_value: IAO:0000600 "standard deviation" xsd:string is_obsolete: true @@ -627,7 +652,7 @@ property_value: IAO:0000600 "A continuous probability distribution whose charact [Term] id: APOLLO_SV:00000079 name: deprecated log normal distribution -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000600 "a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm" xsd:string is_obsolete: true @@ -671,7 +696,7 @@ property_value: IAO:0000600 "A control strategy dose schedule specifies the inte id: APOLLO_SV:00000085 name: age data in age brackets data set def: "A data set consisting of measurements of age organized in age brackets." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 property_value: IAO:0000111 "age structure data set" xsd:string property_value: IAO:0000600 "A data set consisting of measurements of age organized in age brackets." xsd:string @@ -680,9 +705,10 @@ id: APOLLO_SV:00000086 name: infectious disease control strategy def: "A plan specification whose objective specification is an infectious disease control objective specification." [] comment: The essential goal of an infectious disease control strategy is to protect the susceptible organisms in a population. -is_a: IAO:0000104 ! plan specification -intersection_of: IAO:0000104 ! plan specification +is_a: IAO:0000104 +intersection_of: IAO:0000104 intersection_of: BFO:0000051 APOLLO_SV:00000075 ! infectious disease control objective specification +relationship: BFO:0000051 APOLLO_SV:00000075 ! infectious disease control objective specification property_value: APOLLO_SV:0000040 "InfectiousDiseaseControlMeasure" xsd:string property_value: IAO:0000600 "A plan with the goal of preventing or mitigating the effects of infections in a population due to one or more pathogens." xsd:string @@ -705,7 +731,7 @@ id: APOLLO_SV:00000089 name: measured vaccination efficacy def: "A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study." [] comment: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.\n -is_a: IAO:0000109 ! measurement datum +is_a: IAO:0000109 property_value: APOLLO_SV:0000040 "VaccinationEfficacyMeasured" xsd:string property_value: IAO:0000600 "A vaccination efficacy that results from a vaccination efficacy study." xsd:string @@ -717,13 +743,15 @@ is_a: OBI:0000471 intersection_of: OBI:0000471 intersection_of: BFO:0000051 APOLLO_SV:00000142 ! vaccination intersection_of: OBI:0000299 APOLLO_SV:00000089 ! measured vaccination efficacy +relationship: BFO:0000051 APOLLO_SV:00000142 ! vaccination +relationship: OBI:0000299 APOLLO_SV:00000089 ! measured vaccination efficacy property_value: APOLLO_SV:0000040 "VaccinationEfficacyStudy" xsd:string property_value: IAO:0000600 "an experiment that measures vaccination efficacy from a sample of vaccinated and possibly unvaccinated individuals" xsd:string [Term] id: APOLLO_SV:00000091 name: obsolete immune -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: APOLLO_SV:0000040 "immune" xsd:string property_value: IAO:0000600 "an organism that has the property of being immune to a specific disease agent" xsd:string is_obsolete: true @@ -746,7 +774,7 @@ property_value: IAO:0000600 "a type of interval estimate of a population paramet id: APOLLO_SV:00000094 name: community def: "Two or more distinct populations that are part of the same biotic ecosystem." [] -is_a: BFO:0000027 ! object_aggregate +is_a: BFO:0000027 property_value: APOLLO_SV:0000040 "community" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "William R. Hogan" xsd:string property_value: IAO:0000600 "Two or more distinct populations that are part of the same biotic ecosystem." xsd:string @@ -754,7 +782,7 @@ property_value: IAO:0000600 "Two or more distinct populations that are part of t [Term] id: APOLLO_SV:00000095 name: deprecated discrete probability distribution -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: APOLLO_SV:0000040 "discrete probability distribution" xsd:string property_value: IAO:0000600 "a probability distribution over a discrete random variable" xsd:string is_obsolete: true @@ -838,6 +866,7 @@ def: "An identifier that refers to a specific piece of software." [] is_a: IAO:0020000 intersection_of: IAO:0020000 intersection_of: IAO:0000219 IAO:0000594 {cardinality="1"} +relationship: IAO:0000219 IAO:0000594 property_value: APOLLO_SV:0000040 "SoftwareIdentification" xsd:string property_value: IAO:0000600 "An identifier that refers to a specific piece of software." xsd:string @@ -866,8 +895,9 @@ name: software identifier def: "An identifier that refers to all version of a specific software." [] is_a: IAO:0020000 intersection_of: IAO:0020000 -intersection_of: IAO:0000219 IAO:0000010 ! software +intersection_of: IAO:0000219 IAO:0000010 relationship: BFO:0000050 APOLLO_SV:00000106 ! complete software identifier +relationship: IAO:0000219 IAO:0000010 property_value: APOLLO_SV:0000040 "softwareName" xsd:string property_value: IAO:0000600 "An identifier that refers to all version of a specific software." xsd:string @@ -880,7 +910,7 @@ is_a: GEO:000000371 id: APOLLO_SV:00000111 name: obsolete educational institution def: "An educational institution is an place organization which provides the necessary system for people of different ages gain an education. It includes (among others) preschools, childcare, elementary schools, and universities." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Types_of_educational_institutions (amended)" xsd:string property_value: IAO:0000600 "An educational institution is an place organization which provides the necessary system for people of different ages gain an education. It includes (among others) preschools, childcare, elementary schools, and universities." xsd:string is_obsolete: true @@ -889,7 +919,7 @@ is_obsolete: true id: APOLLO_SV:00000112 name: school closure target facilities def: "An information content entity about educational institutions that is part of the action sepcification of a school closure control measure." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: IAO:0000600 "The specification of which facilities to target in a school closure control measure." xsd:string [Term] @@ -897,8 +927,8 @@ id: APOLLO_SV:00000114 name: infection def: "A reproduction of a pathogen organism of a particular biological taxon in a tissue of a host organism from another taxon." [] comment: infection is reproduction of a pathogen inside some tissue of a host. By associating infection with the classes latent period and infectious period, which are associated with specific pathogen species and host species, Apollo-SV defines infection further as reproduction of a particular pathogen taxon inside some tissue of a particular host taxon. -is_a: GO:0000003 ! reproduction -relationship: immediately_preceded_by APOLLO_SV:00000115 ! infection acquisition +is_a: GO:0000003 +relationship: RO:0002087 APOLLO_SV:00000115 ! infection acquisition property_value: http://purl.org/dc/elements/1.1/creator "M. Brochhausen" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "infection process" xsd:string @@ -911,7 +941,8 @@ name: infection acquisition def: "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources" [] comment: Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use. The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient. \nAn infection is acquired from an infectious organism or a contaminated thing. \n comment: Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing -is_a: GO:0044409 ! entry into host +is_a: GO:0044409 +relationship: RO:0002411 APOLLO_SV:00000114 ! infection property_value: APOLLO_SV:0000040 "InfectionAcquisition" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A process where a susceptible organism from a particular species becomes infected by a particular pathogen. The infection is acquired from an infected organism of a particular species or from a contaminated thing. \n\nNote that the susceptible and infectious organisms can be of different species.\n\n" xsd:string @@ -929,6 +960,7 @@ property_value: IAO:0000600 "A unique identifier for a vaccine." xsd:string id: APOLLO_SV:00000118 name: latent period is_a: BFO:0000015 +relationship: BFO:0000139 APOLLO_SV:00000114 ! infection property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -936,7 +968,7 @@ id: APOLLO_SV:00000119 name: vaccination identifier def: "a unique identifier that refers to a protocol for vaccinating one person" [] is_a: IAO:0020000 -relationship: IAO:0000219 IAO:0000033 ! directive information entity +relationship: IAO:0000219 IAO:0000033 property_value: IAO:0000600 "A unique identifier for a vaccination protocol (the process of vaccinating one person)" xsd:string [Term] @@ -985,7 +1017,7 @@ is_obsolete: true [Term] id: APOLLO_SV:00000126 name: control strategy target facilities -is_a: OMRSE:00000062 ! facility +is_a: OMRSE:00000062 property_value: APOLLO_SV:0000040 "control strategy target facilities" xsd:string property_value: IAO:0000600 "Faciilities that are the target of a control strategy" xsd:string @@ -1007,7 +1039,7 @@ property_value: IAO:0000600 "Fraction of organisms in a target population that a id: APOLLO_SV:00000129 name: obsolete Reactive control measure def: "an epidemic control measure plan specification that has a conditional specification as part" [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: APOLLO_SV:0000040 "Reactive control measure" xsd:string property_value: IAO:0000600 "a control measure (program) that is initiated or modified by an epidemic-related event (or if you prefer, an event occurring within/during the simulation)" xsd:string is_obsolete: true @@ -1023,7 +1055,7 @@ property_value: IAO:0000600 "An event in the ecosystem that triggers the startin id: APOLLO_SV:00000131 name: reactive control strategy threshold def: "A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "reactiveControlMeasureThreshold" xsd:string property_value: IAO:0000600 "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc.\n" xsd:string @@ -1037,7 +1069,7 @@ is_a: APOLLO_SV:00000178 ! school student population id: APOLLO_SV:00000133 name: control strategy response delay def: "A measurement datum of the time interval from the decision to implement an infectious disease control strategy to the start of the control strategy expressed in number of time intervals." [] -is_a: IAO:0000109 ! measurement datum +is_a: IAO:0000109 property_value: APOLLO_SV:0000040 "controlMeasureResponseDelay" xsd:string property_value: IAO:0000600 "A period from the initiation of a control strategy until its disease-controlling actions actually begin.\n\nFor example, once a vaccination control strategy starts, individual vaccinations may not occur right away: it might take some time until workers and vaccines are deployed and ready to begin." xsd:string @@ -1045,14 +1077,14 @@ property_value: IAO:0000600 "A period from the initiation of a control strategy id: APOLLO_SV:00000134 name: ascertainment delay comment: per Mike Wagner, this is input -is_a: IAO:0000033 ! directive information entity +is_a: IAO:0000033 property_value: IAO:0000600 "Number of time steps it takes medical personnel to ascertain a symptomatic individual from onset of symptoms" xsd:string [Term] id: APOLLO_SV:00000135 name: ascertainment fraction comment: fraction of organisms (usually infected) that a surveillance system detects out of the total population -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "fractionInState" xsd:string property_value: IAO:0000600 "Fraction of all symptomatic individuals who will be ascertained" xsd:string @@ -1090,19 +1122,21 @@ property_value: IAO:0000600 "A fraction of eligible individuals in a population id: APOLLO_SV:00000140 name: infectious period is_a: BFO:0000015 +relationship: BFO:0000139 APOLLO_SV:00000114 ! infection +relationship: RO:0002087 APOLLO_SV:00000118 ! latent period property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] id: APOLLO_SV:00000141 name: protect against effect of pathogen -is_a: IAO:0000005 ! objective specification +is_a: IAO:0000005 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] id: APOLLO_SV:00000142 name: vaccination def: "A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen." [] -is_a: OGMS:0000090 ! treatment +is_a: OGMS:0000090 property_value: APOLLO_SV:0000040 "Vaccination" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Vaccination" xsd:string @@ -1120,7 +1154,8 @@ id: APOLLO_SV:00000144 name: disposition to become contaminated with a pathogen is_a: BFO:0000016 intersection_of: BFO:0000016 -intersection_of: BFO:0000054 APOLLO_SV:00000167 {all_some="true", all_only="true"} ! is realized by contamination acquisition +intersection_of: BFO:0000054 APOLLO_SV:00000167 {all_some="true", all_only="true"} ! contamination acquisition +relationship: RO:0000052 BFO:0000040 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -1156,8 +1191,8 @@ is_obsolete: true [Term] id: APOLLO_SV:00000149 name: susceptibility measurement datum -is_a: IAO:0000109 ! measurement datum -relationship: IAO:0000136 APOLLO_SV:00000172 ! is about susceptibility +is_a: IAO:0000109 +relationship: IAO:0000136 APOLLO_SV:00000172 ! susceptibility property_value: IAO:0000600 "A number between 0 and 1 indicating the degree of susceptibility of an organism" xsd:string [Term] @@ -1178,7 +1213,7 @@ property_value: IAO:0000600 "Resistance to infection that is conferred by immune id: APOLLO_SV:00000152 name: population survey def: "A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria, and that realizes some concretization of a census objective specification." [] -is_a: OBI:0000011 ! planned process +is_a: OBI:0000011 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria." xsd:string @@ -1188,9 +1223,11 @@ name: population census def: "A census that is the outcome of a population survey." [] is_a: APOLLO_SV:00000173 ! census intersection_of: APOLLO_SV:00000173 ! census -intersection_of: IAO:0000136 PCO:0000001 ! is about population +intersection_of: IAO:0000136 PCO:0000001 intersection_of: OBI:0000312 APOLLO_SV:00000152 ! population survey intersection_of: OBI:0000312 APOLLO_SV:00000152 {all_only="true"} ! population survey +relationship: IAO:0000136 PCO:0000001 +relationship: OBI:0000312 APOLLO_SV:00000152 ! population survey property_value: IAO:0000600 "A census that is the outcome of a population survey." xsd:string [Term] @@ -1227,6 +1264,8 @@ is_a: APOLLO_SV:00000173 ! census intersection_of: APOLLO_SV:00000173 ! census intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true"} ! population infection survey intersection_of: OBI:0000312 APOLLO_SV:00000155 {all_some="true", all_only="true"} ! population infection survey +relationship: OBI:0000312 APOLLO_SV:00000003 ! population immunity survey +relationship: OBI:0000312 APOLLO_SV:00000155 ! population infection survey property_value: APOLLO_SV:0000040 "PopulationInfectionAndImmunityCensus" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "PII Census" xsd:string @@ -1245,13 +1284,14 @@ is_a: APOLLO_SV:00000173 ! census intersection_of: APOLLO_SV:00000173 ! census intersection_of: OBI:0000312 APOLLO_SV:00000158 ! population demographic survey intersection_of: OBI:0000312 APOLLO_SV:00000158 {all_only="true"} ! population demographic survey +relationship: OBI:0000312 APOLLO_SV:00000158 ! population demographic survey property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A census that is the specific outcome of a population demographic survey." xsd:string [Term] id: APOLLO_SV:00000160 name: obsolete contamination -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000117 "Mathias Brochhausen" xsd:string is_obsolete: true @@ -1268,7 +1308,7 @@ id: APOLLO_SV:00000162 name: MIDAS scenario representation def: "An information content entity that is about a MIDAS scenario and contains population disease census data." [] comment: need to change the text definition. need to change label to be more consistent with current Apollo terminology (possibly 'infectious disease scenario'. -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "An information content entity that is about a MIDAS scenario and contains population disease census data." xsd:string @@ -1314,7 +1354,11 @@ property_value: IAO:0000600 "An independent continuant that is the localization id: APOLLO_SV:00000167 name: contamination acquisition def: "A biological process whereby an entity that is not in contact with a pathogen of a particular biological taxon begins to undergo contamination with that pathogen." [] -is_a: GO:0044409 ! entry into host +is_a: APOLLO_SV:00000186 ! contamination +is_a: GO:0044409 +is_a: OBI:0000011 +relationship: OBI:0000293 APOLLO_SV:00000237 ! pathogen +relationship: OBI:0000299 APOLLO_SV:00000166 ! contaminated thing property_value: APOLLO_SV:0000040 "ContaminationAcquisition" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -1326,7 +1370,8 @@ name: nursery school student population census comment: Motivating use case is Synthia synthetic population data. is_a: APOLLO_SV:00000176 ! school student population census intersection_of: APOLLO_SV:00000176 ! school student population census -intersection_of: IAO:0000136 APOLLO_SV:00000044 ! is about nursery school student population +intersection_of: IAO:0000136 APOLLO_SV:00000044 ! nursery school student population +relationship: IAO:0000136 APOLLO_SV:00000044 ! nursery school student population [Term] id: APOLLO_SV:00000169 @@ -1334,7 +1379,8 @@ name: primary school student population census comment: Motivating use case is Synthia synthetic population data. is_a: APOLLO_SV:00000176 ! school student population census intersection_of: APOLLO_SV:00000176 ! school student population census -intersection_of: IAO:0000136 APOLLO_SV:00000062 ! is about primary school student population +intersection_of: IAO:0000136 APOLLO_SV:00000062 ! primary school student population +relationship: IAO:0000136 APOLLO_SV:00000062 ! primary school student population [Term] id: APOLLO_SV:00000170 @@ -1342,7 +1388,8 @@ name: secondary school student population census comment: Motivating use case is Synthia synthetic population data. is_a: APOLLO_SV:00000176 ! school student population census intersection_of: APOLLO_SV:00000176 ! school student population census -intersection_of: IAO:0000136 APOLLO_SV:00000132 ! is about secondary school student population +intersection_of: IAO:0000136 APOLLO_SV:00000132 ! secondary school student population +relationship: IAO:0000136 APOLLO_SV:00000132 ! secondary school student population [Term] id: APOLLO_SV:00000171 @@ -1350,7 +1397,8 @@ name: antiviral treatment def: "A treatment with an antiviral drug." [] is_a: APOLLO_SV:00000318 ! drug treatment intersection_of: APOLLO_SV:00000318 ! drug treatment -intersection_of: OBI:0000293 CHEBI:36044 ! antiviral drug +intersection_of: OBI:0000293 CHEBI:36044 +relationship: OBI:0000293 CHEBI:36044 property_value: APOLLO_SV:0000040 "AntiviralTreatment" xsd:string property_value: IAO:0000600 "A treatment of a particular host with a particular antiviral drug with activity against a particular viral pathogen." xsd:string @@ -1366,7 +1414,6 @@ property_value: IAO:0000600 "The ability to participate in infection acquisition id: APOLLO_SV:00000173 name: census def: "A data set of a specific entity in a specified region at a specified time." [] -is_a: IAO:0000100 ! data set property_value: APOLLO_SV:0000040 "CensusData" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A data set of a specific entity in a specified region at a specified time." xsd:string @@ -1375,7 +1422,7 @@ property_value: IAO:0000600 "A data set of a specific entity in a specified regi id: APOLLO_SV:00000174 name: disease transmission model def: "An algorithm that models the progress of a transmissible disease in a population." [] -is_a: IAO:0000064 ! algorithm +is_a: IAO:0000064 property_value: APOLLO_SV:0000040 "disease transmission model" xsd:string property_value: IAO:0000600 "An algorithm that models the progress of a transmissible disease in a population." xsd:string @@ -1383,7 +1430,7 @@ property_value: IAO:0000600 "An algorithm that models the progress of a transmis id: APOLLO_SV:00000175 name: obsolete school organization def: "An organization created with the purpose of providing education to those of its members that are bearer of student role." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "An organization created with the purpose of providing education to those of its members that are bearer of student role." xsd:string is_obsolete: true @@ -1394,7 +1441,8 @@ name: school student population census comment: Motivating use case is Synthia synthetic population data. is_a: APOLLO_SV:00000153 ! population census intersection_of: APOLLO_SV:00000153 ! population census -intersection_of: IAO:0000136 APOLLO_SV:00000178 ! is about school student population +intersection_of: IAO:0000136 APOLLO_SV:00000178 ! school student population +relationship: IAO:0000136 APOLLO_SV:00000178 ! school student population property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -1402,7 +1450,7 @@ id: APOLLO_SV:00000178 name: school student population def: "The collection of students administrated by exaclty one school organization." [] comment: Key motivating use case was Synthia synthetic population data. -is_a: OMRSE:00000023 ! collection of humans +is_a: OMRSE:00000023 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "The collection of students administrated by exaclty one school organization." xsd:string @@ -1418,7 +1466,7 @@ property_value: IAO:0000600 "An information content entity that contains everyth id: APOLLO_SV:00000180 name: obsolete student role def: "A human social role that is realized by attending a school to receive formal education." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A human social role that is realized by attending a school to receive formal education." xsd:string is_obsolete: true @@ -1451,8 +1499,8 @@ id: APOLLO_SV:00000184 name: infectious disease scenario def: "A dataset that represents at least one pathogen population (of a particular biological taxon) in one host population (of a particular biological taxon) in an ecosystem in a particular location at a particular point in time." [] comment: An infectious disease scenario contains counts of infections of a particular pathogen in a particular host in a particular ecosystem at a particular point in time, minimally. Agent-based ecosystems represent each host individually. \n\nThe infectious disease scenario typically also includes a lot of additional data about the ecosystem, including data about things like transmission probabililites, control measures, the immunity or other resistance status of host individuals, and so on. -is_a: IAO:0000100 ! data set -relationship: IAO:0000136 APOLLO_SV:00000097 ! is about ecosystem +is_a: IAO:0000100 +relationship: IAO:0000136 APOLLO_SV:00000097 ! ecosystem property_value: APOLLO_SV:0000040 "InfectiousDiseaseScenario" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Data about an infection in an ecosystem at a specific location and point in time." xsd:string @@ -1470,7 +1518,7 @@ id: APOLLO_SV:00000186 name: contamination def: "The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity or the process of reproduction of a pathogen in or on a material entity that is not an organism." [] comment: the preferred term is biological contamination to distinguish from things like radiological contamination, contamination of the Gulf of Mexico with oil, the contamination of air with pollution, etc. -is_a: GO:0008150 ! biological process +is_a: GO:0008150 property_value: APOLLO_SV:0000040 "Contamination" xsd:string property_value: IAO:0000111 "biological contamination" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -1504,9 +1552,10 @@ property_value: IAO:0000600 "A census that is the outcome of assessing control-s id: APOLLO_SV:00000190 name: contagious organism def: "A host who is able to transmit some infection to another organism." [] -is_a: APOLLO_SV:00000238 ! host -intersection_of: APOLLO_SV:00000238 ! host -intersection_of: RO:0000053 APOLLO_SV:00000182 ! is bearer of contagiousness +is_a: APOLLO_SV:00000238 ! host organism +intersection_of: APOLLO_SV:00000238 ! host organism +intersection_of: RO:0000053 APOLLO_SV:00000182 ! contagiousness +relationship: RO:0000053 APOLLO_SV:00000182 ! contagiousness property_value: APOLLO_SV:0000040 "infectious" xsd:string property_value: IAO:0000600 "An infected organism of a particular species who is able to transmit the infection to a susceptible organism of a particular species.\n\nNote that the infected and susceptible organisms may be of different species." xsd:string @@ -1514,7 +1563,7 @@ property_value: IAO:0000600 "An infected organism of a particular species who is id: APOLLO_SV:00000191 name: transmission coefficient def: "An information content entity that represents the rate that an infection moves from infected individuals to susceptible individuals in a population." [] -is_a: OBI:0001554 ! rate measurement datum +is_a: OBI:0001554 property_value: APOLLO_SV:0000040 "beta" xsd:string property_value: IAO:0000600 "An information content entity that represents the rate that an infection moves from infected individuals to susceptible individuals in a population." xsd:string @@ -1529,7 +1578,7 @@ is_obsolete: true id: APOLLO_SV:00000193 name: vaccination efficacy inferred def: "A data item inferring a vaccination efficacy based on epidemiological data." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "VaccinationEfficacyInferred" xsd:string property_value: IAO:0000600 "A data item inferring a vaccination efficacy based on epidemiological data." xsd:string @@ -1546,7 +1595,7 @@ property_value: IAO:0000600 "An infectious disease control strategy that immedia id: APOLLO_SV:00000195 name: target population def: "An organism population that is the target for a disease control strategy." [] -is_a: PCO:0000001 ! population +is_a: PCO:0000001 property_value: APOLLO_SV:0000040 "TargetPopulation" xsd:string property_value: IAO:0000600 "An organism population that is the target for a disease control strategy." xsd:string @@ -1576,7 +1625,7 @@ is_obsolete: true [Term] id: APOLLO_SV:00000200 name: population strata definition -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "PopulationStrataDefinition" xsd:string [Term] @@ -1591,7 +1640,7 @@ property_value: IAO:0000600 "A census about contaminated things of a given type id: APOLLO_SV:00000202 name: indexable Apollo item comment: A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved. -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "ApolloIndexableItem" xsd:string [Term] @@ -1616,9 +1665,10 @@ property_value: IAO:0000600 "An event that happens during the course of a diseas id: APOLLO_SV:00000205 name: susceptible organism def: "An organism that is the bearer of a susceptibility disposition." [] -is_a: OBI:0100026 ! organism -intersection_of: OBI:0100026 ! organism -intersection_of: RO:0000053 APOLLO_SV:00000172 ! is bearer of susceptibility +is_a: OBI:0100026 +intersection_of: OBI:0100026 +intersection_of: RO:0000053 APOLLO_SV:00000172 ! susceptibility +relationship: RO:0000053 APOLLO_SV:00000172 ! susceptibility property_value: APOLLO_SV:0000040 "susceptible" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An organism of a particular species that can undergo infection with a particular pathogen." xsd:string @@ -1627,9 +1677,10 @@ property_value: IAO:0000600 "An organism of a particular species that can underg id: APOLLO_SV:00000206 name: immune organism def: "An organism that is the bearer of an immune resistance disposition." [] -is_a: OBI:0100026 ! organism -intersection_of: OBI:0100026 ! organism -intersection_of: RO:0000053 APOLLO_SV:00000151 ! is bearer of immune resistance to infection +is_a: APOLLO_SV:00000207 ! resistant organism +intersection_of: OBI:0100026 +intersection_of: RO:0000053 APOLLO_SV:00000151 ! immune resistance to infection +relationship: RO:0000053 APOLLO_SV:00000151 ! immune resistance to infection property_value: APOLLO_SV:0000040 "immune" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An organism of a particular species that has developed immune resistance to infection with a pathogen of a particular species." xsd:string @@ -1638,9 +1689,10 @@ property_value: IAO:0000600 "An organism of a particular species that has develo id: APOLLO_SV:00000207 name: resistant organism def: "an organism that is the bearer of resistance to infection" [] -is_a: OBI:0100026 ! organism -intersection_of: OBI:0100026 ! organism -intersection_of: RO:0000053 APOLLO_SV:00000145 ! is bearer of resistance to infection +is_a: OBI:0100026 +intersection_of: OBI:0100026 +intersection_of: RO:0000053 APOLLO_SV:00000145 ! resistance to infection +relationship: RO:0000053 APOLLO_SV:00000145 ! resistance to infection property_value: APOLLO_SV:0000040 "resistant" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An organism of a particular species that is unable to undergo infection with a particular pathogen." xsd:string @@ -1649,7 +1701,7 @@ property_value: IAO:0000600 "An organism of a particular species that is unable id: APOLLO_SV:00000208 name: control strategy start time information def: "An information content entity that specifies the start time of the implementation of a infectious disease control strategy." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "controlMeasureStartTime" xsd:string property_value: IAO:0000600 "A specification of when an infectious disease control strategy starts." xsd:string @@ -1657,7 +1709,7 @@ property_value: IAO:0000600 "A specification of when an infectious disease contr id: APOLLO_SV:00000209 name: infected organism def: "An infectious agent host who is NOT able to transmit the infection to another organism of the same species." [] -is_a: APOLLO_SV:00000238 ! host +is_a: APOLLO_SV:00000238 ! host organism property_value: APOLLO_SV:0000040 "infected" xsd:string property_value: IAO:0000111 "organism in latent period of infection" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -1684,7 +1736,7 @@ property_value: IAO:0000600 "The probability of the occurence of an infection ac id: APOLLO_SV:00000212 name: treatment administration capacity schedule def: "A plan specification that specifies the capacity to administer a particular treatment over a specific temporal interval in a specified geographical region." [] -is_a: IAO:0000104 ! plan specification +is_a: IAO:0000104 property_value: APOLLO_SV:0000040 "capacitySchedule" xsd:string property_value: IAO:0000600 "A specification of how many doses (of material) of an individual treatment can be administered per unit time in a particular geographical location." xsd:string @@ -1701,7 +1753,7 @@ property_value: IAO:0000600 "A specification of how many doses (of material such id: APOLLO_SV:00000214 name: vaccination efficacy for simulator configuration def: "An information content entity that specifies the vaccination efficacy that is part of a simulator configuration." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "VaccinationEfficacyForSimulatorConfiguration" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "An information content entity that specifies the vaccination efficacy that is part of a simulator configuration." xsd:string @@ -1710,7 +1762,7 @@ property_value: IAO:0000600 "An information content entity that specifies the va id: APOLLO_SV:00000215 name: probability distribution def: "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. " [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "ProbabilityDistribution" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Probability_distribution" xsd:string property_value: IAO:0000600 "An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference. " xsd:string @@ -1726,7 +1778,7 @@ property_value: IAO:0000600 "a probability distribution over a discrete random v id: APOLLO_SV:00000217 name: infection state data item def: "A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "infectionState" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen." xsd:string @@ -1735,7 +1787,7 @@ property_value: IAO:0000600 "A data item that specifies the epidemiologically-re id: APOLLO_SV:00000218 name: vaccination preventable outcome def: "An objective specification that specifies the disease outcome a vaccination seeks to prevent." [] -is_a: IAO:0000005 ! objective specification +is_a: IAO:0000005 property_value: APOLLO_SV:0000040 "vaccinationPreventableOutcome" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "An objective specification that specifies the disease outcome a vaccination seeks to prevent." xsd:string @@ -1755,6 +1807,7 @@ name: abiotic ecosystem element def: "A material entity that is part of an abiotic ecosystem." [] comment: Class was originally created to correspond with an element from Apollo XSD v3.1.0. is_a: BFO:0000040 +relationship: BFO:0000050 APOLLO_SV:00000100 ! abiotic ecosystem property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A material entity that is part of an abiotic ecosystem." xsd:string @@ -1891,25 +1944,27 @@ property_value: IAO:0000600 "A population of organisms that are all immune." xsd [Term] id: APOLLO_SV:00000236 name: asymptomatic host -is_a: APOLLO_SV:00000238 ! host +is_a: APOLLO_SV:00000238 ! host organism [Term] id: APOLLO_SV:00000237 name: pathogen def: "An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon." [] -is_a: OBI:0100026 ! organism -intersection_of: OBI:0100026 ! organism -intersection_of: RO:0000053 APOLLO_SV:00000404 ! is bearer of infectiousness +is_a: OBI:0100026 +intersection_of: OBI:0100026 +intersection_of: RO:0000053 APOLLO_SV:00000404 ! infectiousness +relationship: RO:0000053 APOLLO_SV:00000404 ! infectiousness property_value: APOLLO_SV:0000040 "pathogen" xsd:string property_value: IAO:0000600 "An organism, virus, or prion that can infect another organism." xsd:string [Term] id: APOLLO_SV:00000238 -name: host +name: host organism def: "An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon." [] -is_a: OBI:0100026 ! organism -intersection_of: OBI:0100026 ! organism -intersection_of: BFO:0000067 GO:0000003 ! contains process reproduction +is_a: OBI:0100026 +intersection_of: OBI:0100026 +intersection_of: BFO:0000067 GO:0000003 +relationship: BFO:0000067 GO:0000003 property_value: APOLLO_SV:0000040 "host" xsd:string property_value: IAO:0000600 "An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon." xsd:string @@ -1918,7 +1973,7 @@ id: APOLLO_SV:00000239 name: infectious disease def: "A disease that inheres in a host and, when realized, is realized as a disease course that is causally preceded by an infection." [] comment: Infection is the etiological process, as defined by OGMS, for infectious disease. However, OGMS does not relate its etiological process class to its disorder class as of this writing. So it is not clear how to connect infectious disease to its infection etiological process. -is_a: OGMS:0000031 ! disease +is_a: OGMS:0000031 property_value: APOLLO_SV:0000040 "InfectiousDisease" xsd:string property_value: IAO:0000600 "A disease that is caused by an infection." xsd:string @@ -1926,7 +1981,7 @@ property_value: IAO:0000600 "A disease that is caused by an infection." xsd:stri id: APOLLO_SV:00000240 name: census reference date def: "A information content entity that specifies the date of a census." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "referenceDate" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A information content entity that specifies the date of a census." xsd:string @@ -1954,7 +2009,7 @@ property_value: IAO:0000600 "An information content entity that specifies a time id: APOLLO_SV:00000243 name: duration def: "A measurement datum that quantifies a temporal region that is occupied by a processual entity." [] -is_a: IAO:0000416 ! time measurement datum +is_a: IAO:0000416 property_value: APOLLO_SV:0000040 "Duration" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A measurement datum that quantifies a temporal region that is occupied by a processual entity." xsd:string @@ -2029,14 +2084,14 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] id: APOLLO_SV:00000252 name: discrete nonparametric probability distribution -is_a: STATO:0000321 ! non-parametric distribution +is_a: STATO:0000321 property_value: APOLLO_SV:0000040 "DiscreteNonparametricProbabilityDistribution" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] id: APOLLO_SV:00000253 name: continuous nonparametric probability distribution -is_a: STATO:0000321 ! non-parametric distribution +is_a: STATO:0000321 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -2100,7 +2155,7 @@ property_value: IAO:0000600 "A hierarchical identifier beginning with an ISO 2-l id: APOLLO_SV:00000260 name: control strategy stop time information def: "An information content entity that specifies the time at which an infectious disease control strategy ends." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "controlMeasureStopTime" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "William R. Hogan" xsd:string property_value: IAO:0000600 "An information content entity that specifies the time at which an infectious disease control strategy ends." xsd:string @@ -2126,7 +2181,7 @@ property_value: IAO:0000600 "The probability of the occurence of a contamination id: APOLLO_SV:00000263 name: control strategy stand-down delay def: "A measurement datum of the time interval from the decision to cease an infectious disease control strategy to the time the control strategy ends expressed in number of time intervals." [] -is_a: IAO:0000109 ! measurement datum +is_a: IAO:0000109 property_value: APOLLO_SV:0000040 "controlMeasureStandDownDelay" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "William R. Hogan" xsd:string property_value: IAO:0000600 "A period from the conclusion of a control strategy until its disease-controlling activities actually end.\n\nFor example, it may take time to communicate to workers to stop vaccinating and thus they keep vaccinating for some time after the control strategy is concluded." xsd:string @@ -2135,7 +2190,8 @@ property_value: IAO:0000600 "A period from the conclusion of a control strategy id: APOLLO_SV:00000264 name: infection acquisition from contaminated thing def: "An infection acquisition whereby a susceptible host acquires an infection from a contaminated thing." [] -is_a: GO:0044409 ! entry into host +is_a: APOLLO_SV:00000115 ! infection acquisition +relationship: RO:0000057 APOLLO_SV:00000166 ! contaminated thing property_value: APOLLO_SV:0000040 "InfectionAcquisitionFromContaminatedAbioticThing" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An infection acquisition from a contaminated thing." xsd:string @@ -2144,7 +2200,7 @@ property_value: IAO:0000600 "An infection acquisition from a contaminated thing. id: APOLLO_SV:00000265 name: infection acquisition from infectious host def: "An infection acquisition whereby a susceptible host acquires an infection from an infectious host." [] -is_a: GO:0044409 ! entry into host +is_a: APOLLO_SV:00000115 ! infection acquisition property_value: APOLLO_SV:0000040 "InfectionAcquisitionFromInfectedHost" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An infection acquisition from an individual who is infectious.\n\nThe individual acquiring the infection can be of a different species than the one who is infectious.\n" xsd:string @@ -2215,7 +2271,7 @@ property_value: IAO:0000600 "A duration of time that has elapsed since the zero [Term] id: APOLLO_SV:00000273 name: seasonal function parameter -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "SeasonalityFunctionParameters" xsd:string [Term] @@ -2240,7 +2296,7 @@ property_value: APOLLO_SV:0000040 "seasonalTemporalOffset" xsd:string id: APOLLO_SV:00000277 name: sensitivity of case detection def: "The sensitivity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X." [] -is_a: STATO:0000233 ! true positive rate +is_a: STATO:0000233 property_value: APOLLO_SV:0000040 "sensitivityOfCaseDetection" xsd:string property_value: IAO:0000600 "The sensitivity of a process or system that detects organisms who satisfy a case definition." xsd:string @@ -2276,7 +2332,7 @@ id: APOLLO_SV:00000281 name: number of doses in a treatment course def: "The count of the number of doses that are part of a treatment course." [] is_a: APOLLO_SV:00000032 ! count -relationship: IAO:0000136 OGMS:0000090 ! is about treatment +relationship: IAO:0000136 OGMS:0000090 property_value: APOLLO_SV:0000040 "numDosesInTreatmentCourse" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "The number of doses (of material such as antiviral drug or vaccine) that constitutes a particular course of treatment" xsd:string @@ -2284,7 +2340,7 @@ property_value: IAO:0000600 "The number of doses (of material such as antiviral [Term] id: APOLLO_SV:00000282 name: target populations and prioritizations information -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "targetPopulationsAndPrioritizations" xsd:string property_value: IAO:0000600 "A specification of the target populations of a control strategy and the priority of each population in the strategy." xsd:string @@ -2343,14 +2399,14 @@ property_value: APOLLO_SV:0000040 "communityTransmissionMultiplier" xsd:string [Term] id: APOLLO_SV:00000289 name: maximum travel distance in km information -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "maximumTravelDistanceInKm" xsd:string [Term] id: APOLLO_SV:00000290 name: treatment preventable outcome def: "An objective specification that specifies the disease outcome that a treatment seeks to prevent." [] -is_a: IAO:0000005 ! objective specification +is_a: IAO:0000005 property_value: APOLLO_SV:0000040 "TreatmentPreventableOutcome" xsd:string property_value: IAO:0000117 "William Hogan" xsd:string property_value: IAO:0000600 "An objective specification that specifies the disease outcome that a treatment seeks to prevent." xsd:string @@ -2368,7 +2424,7 @@ property_value: IAO:0000600 "The duration from treatment until a treatment surve id: APOLLO_SV:00000292 name: individual treatment strategy supply schedule unit of measure def: "The unit of measure for the supply schedule of an individual treatment." [] -is_a: UO:0000000 ! unit +is_a: UO:0000000 property_value: APOLLO_SV:0000040 "supplyScheduleUnits" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "The unit of measure for the supply schedule of an individual treatment.\n\nFor example, 'daily dose'.\n" xsd:string @@ -2376,7 +2432,7 @@ property_value: IAO:0000600 "The unit of measure for the supply schedule of an i [Term] id: APOLLO_SV:00000293 name: individual treatment strategy administration capacity unit of measure -is_a: UO:0000000 ! unit +is_a: UO:0000000 property_value: APOLLO_SV:0000040 "administrationCapacityUnits" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "The unit of measure for the administration capacity of an individual treatment.\n\nFor example, 'daily dose'." xsd:string @@ -2392,7 +2448,7 @@ property_value: IAO:0000600 "A disease transmission model that explicitly repres id: APOLLO_SV:00000295 name: reactive control strategy threshold unit of measure def: "A unit of measure for a threshold in a reactive infectious disease control strategy." [] -is_a: UO:0000000 ! unit +is_a: UO:0000000 property_value: APOLLO_SV:0000040 "unitOfMeasureForThreshold" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A unit of measure for a threshold in a reactive infectious disease control strategy." xsd:string @@ -2401,7 +2457,7 @@ property_value: IAO:0000600 "A unit of measure for a threshold in a reactive inf id: APOLLO_SV:00000296 name: case definition def: "An information content entity that specifies the criteria that an organism must meet to be considered to be in some abnormal state." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "CaseDefinition" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A specification of the criteria an organism must meet to be considered to be in some abnormal state.\n\nThe abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.\n" xsd:string @@ -2419,8 +2475,6 @@ name: epidemic def: "A process whose beginning is demarcated by accelerating infection acquisition by one or more host species of a particular pathogen in a particular location and whose end is demarcated by the time when the rate of infection acquisition becomes constant." [] comment: An example of multiple host species is foot and mouth disease (such as the 2001 epidemic in the UK, see: http://www.sciencemag.org/content/292/5519/1155.long) and swine flu. The foot and mouth disease epidemic affected sheep, pigs, and cattle. is_a: APOLLO_SV:00000306 ! infection in ecosystem -relationship: BFO:0000118 APOLLO_SV:00000114 ! has proper occurrent part infection -relationship: BFO:0000118 APOLLO_SV:00000115 ! has proper occurrent part infection acquisition property_value: APOLLO_SV:0000040 "Epidemic" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "epidemic of infection" xsd:string @@ -2456,9 +2510,10 @@ property_value: IAO:0000600 "An immune resistance to infection that is causally id: APOLLO_SV:00000302 name: recovered organism def: "An organism that is the bearer of a naturally-acquired, active immune resistance to infection." [] -is_a: OBI:0100026 ! organism -intersection_of: OBI:0100026 ! organism -intersection_of: RO:0000053 APOLLO_SV:00000301 ! is bearer of naturally-acquired active immune resistance +is_a: APOLLO_SV:00000206 ! immune organism +intersection_of: OBI:0100026 +intersection_of: RO:0000053 APOLLO_SV:00000301 ! naturally-acquired active immune resistance +relationship: RO:0000053 APOLLO_SV:00000301 ! naturally-acquired active immune resistance property_value: APOLLO_SV:0000040 "recovered" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An organism that has recovered from infection with a particular pathogen, is no longer infectious to other organisms of any species, and is not able to be infected again with that pathogen." xsd:string @@ -2492,8 +2547,8 @@ id: APOLLO_SV:00000306 name: infection in ecosystem def: "A process comprised of numerous infections and infection acquisitions with a particular pathogen in one or more populations of hosts." [] is_a: BFO:0000015 -relationship: BFO:0000118 APOLLO_SV:00000114 ! has proper occurrent part infection -relationship: BFO:0000118 APOLLO_SV:00000115 ! has proper occurrent part infection acquisition +relationship: BFO:0000118 APOLLO_SV:00000114 ! infection +relationship: BFO:0000118 APOLLO_SV:00000115 ! infection acquisition property_value: IAO:0000111 "infection in an ecosystem" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A process of ongoing infection and infection acquisition in individuals in one or more populations in an ecosystem." xsd:string @@ -2511,6 +2566,7 @@ comment: Typically, the strategy is to limit the population of the second host s is_a: APOLLO_SV:00000086 ! infectious disease control strategy intersection_of: APOLLO_SV:00000086 ! infectious disease control strategy intersection_of: BFO:0000051 APOLLO_SV:00000310 ! vector control action specification +relationship: BFO:0000051 APOLLO_SV:00000310 ! vector control action specification property_value: APOLLO_SV:0000040 "VectorControlMeasure" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An infectious disease control strategy that attempts to reduce infections in a population of a particular host species by limiting infection acquisitions from a second host species, called the 'vector'." xsd:string @@ -2536,7 +2592,7 @@ property_value: IAO:0000600 "An action specification that is realized in reducin id: APOLLO_SV:00000311 name: Breteau Index def: "The average number of water containers testing positive for the presence of a particular mosquito species, typically Aedes aegyptii, per 100 households in the geographical region under surveillance." [] -is_a: OBI:0000679 ! average value +is_a: OBI:0000679 property_value: APOLLO_SV:0000040 "breteauIndex" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "The average number of containers positive (for presence of mosquito) per 100 households." xsd:string @@ -2545,9 +2601,10 @@ property_value: IAO:0000600 "The average number of containers positive (for pres id: APOLLO_SV:00000312 name: individual mosquito reproduction def: "A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157)" [] -is_a: GO:0032504 ! multicellular organism reproduction -intersection_of: GO:0032504 ! multicellular organism reproduction -intersection_of: RO:0002218 NCBITaxon:7157 ! has active participant Culicidae +is_a: GO:0032504 +intersection_of: GO:0032504 +intersection_of: RO:0002218 NCBITaxon:7157 +relationship: RO:0002218 NCBITaxon:7157 property_value: APOLLO_SV:0000040 "MosquitoReproduction" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Reproduction of a single mosquito" xsd:string @@ -2566,7 +2623,7 @@ property_value: IAO:0000600 "The duration of the gonotrophic cycle in a female m id: APOLLO_SV:00000314 name: gonotrophic cycle def: "The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition)." [] -is_a: GO:0008150 ! biological process +is_a: GO:0008150 property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition)." xsd:string @@ -2600,9 +2657,10 @@ property_value: IAO:0000600 "The period from onset of infection to onset of symp id: APOLLO_SV:00000318 name: drug treatment def: "A treatment with a drug product." [] -is_a: OGMS:0000090 ! treatment -intersection_of: OGMS:0000090 ! treatment -intersection_of: OBI:0000293 DRON:00000005 ! drug product +is_a: OGMS:0000090 +intersection_of: OGMS:0000090 +intersection_of: OBI:0000293 DRON:00000005 +relationship: OBI:0000293 DRON:00000005 property_value: APOLLO_SV:0000040 "DrugTreatment" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Treatment with a drug." xsd:string @@ -2628,7 +2686,7 @@ property_value: IAO:0000600 "An infectious disease conrol straegy that seeks to [Term] id: APOLLO_SV:00000326 name: epidemic investigation design -is_a: OBI:0500000 ! study design +is_a: OBI:0500000 property_value: IAO:0000111 "epidemic investigation study design" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A study design that specifies which epidemic(s) to investigate, how, and what information to output." xsd:string @@ -2656,7 +2714,7 @@ id: APOLLO_SV:00000330 name: colonization def: "a reproduction of a pathogen of a particular biological taxon inside a host organism of another taxon, without invasion of the tissues of the host." [] comment: Primary use case is colonization of humans, animals with Staph aureus, but it also covers bacteriuria, transient bactermia, and normal gut flora. -is_a: GO:0000003 ! reproduction +is_a: GO:0000003 property_value: APOLLO_SV:0000040 "Colonization" xsd:string property_value: IAO:0000111 "biological colonization" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -2677,7 +2735,7 @@ id: APOLLO_SV:00000332 name: colonization acquisition def: "a biological process where a pathogen organism of a particular biological taxon enters into a host organism of a particular taxon and begins to undergo reproduction in a location external to tissues of the host" [] comment: the host organism was not colonized wtih the pathogen prior to the colonization acquisition -is_a: GO:0044409 ! entry into host +is_a: GO:0044409 property_value: APOLLO_SV:0000040 "ColonizationAcquisition" xsd:string property_value: IAO:0000111 "colonization acquisition" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -2698,7 +2756,7 @@ property_value: IAO:0000600 "an indivdiual treatment control strategy that preve id: APOLLO_SV:00000334 name: infection acquistion from self colonization def: "An infection acquisition by which a pathogen organism from a particular biological taxon, which previously was participating in a colonization process in a host organism from another taxon, begins to invade the tissues of the same host organism and reproduce there." [] -is_a: GO:0044409 ! entry into host +is_a: GO:0044409 property_value: IAO:0000111 "establishment of infection from self colonization" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An infection acquisition by which a pathogen organism from a particular biological taxon, which previously was participating in a colonization process in a host organism from another taxon, begins to invade the tissues of the same host organism and reproduce there." xsd:string @@ -2709,7 +2767,6 @@ name: chemical resistance to infection def: "A resistance to infection that is conferred by the presence, in sufficient quantity, of a particular molecular entity that is not normally present in the organism." [] comment: As with all dispositions, chemical resistance need not be realized to exist. The presence of cholorquine confers this disposition even if the person is never bitten by a mosquito, let alone a malaria-laden mosquito. comment: Examples: chemoprophylaxis of malaria with chloroquine, treatment of infections with antibiotics, antiviral treatment -is_a: APOLLO_SV:00000145 ! resistance to infection property_value: IAO:0000111 "chemical resistance to infection" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "chemoprotection" xsd:string @@ -2846,6 +2903,7 @@ id: APOLLO_SV:00000348 name: ectosymbiotic commensalism def: "An ectosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms." [] is_a: APOLLO_SV:00000337 ! ectosymbiosis +relationship: BFO:0000051 APOLLO_SV:00000372 ! bodily benefit property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "ectocommensalism" xsd:string @@ -2881,6 +2939,7 @@ is_a: APOLLO_SV:00000337 ! ectosymbiosis intersection_of: APOLLO_SV:00000337 ! ectosymbiosis intersection_of: BFO:0000051 APOLLO_SV:00000372 ! bodily benefit intersection_of: BFO:0000051 APOLLO_SV:00000372 {all_only="true"} ! bodily benefit +relationship: BFO:0000051 APOLLO_SV:00000372 ! bodily benefit property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "ectomutualism" xsd:string @@ -3015,6 +3074,7 @@ id: APOLLO_SV:00000364 name: endosymbiotic commensalism def: "An endosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms." [] is_a: APOLLO_SV:00000354 ! endosymbiosis +relationship: BFO:0000051 APOLLO_SV:00000372 ! bodily benefit property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "endocommensalism" xsd:string @@ -3050,6 +3110,7 @@ is_a: APOLLO_SV:00000354 ! endosymbiosis intersection_of: APOLLO_SV:00000354 ! endosymbiosis intersection_of: BFO:0000051 APOLLO_SV:00000372 ! bodily benefit intersection_of: BFO:0000051 APOLLO_SV:00000372 {all_only="true"} ! bodily benefit +relationship: BFO:0000051 APOLLO_SV:00000372 ! bodily benefit property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "endomutualism" xsd:string @@ -3108,7 +3169,7 @@ property_value: IAO:0000600 "A process that facilitates the realization of one o id: APOLLO_SV:00000373 name: parasite def: "An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits." [] -is_a: OBI:0100026 ! organism +is_a: OBI:0100026 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits." xsd:string @@ -3117,7 +3178,7 @@ property_value: IAO:0000600 "An organism participating in an ectosymbiotic or en id: APOLLO_SV:00000374 name: parasitoid def: "An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits." [] -is_a: OBI:0100026 ! organism +is_a: OBI:0100026 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits." xsd:string @@ -3126,7 +3187,7 @@ property_value: IAO:0000600 "An organism participating in an ectosymbiotic or en id: APOLLO_SV:00000375 name: target population definition def: "An information content entity that is part of an infectious disease control strategy and that specifies the intended population to which one or more interventions in the control strategy will be applied." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "TargetPopulationDefinition" xsd:string property_value: IAO:0000600 "An information content entity that is part of an infectious disease control strategy and that specifies the intended population to which one or more interventions in the control strategy will be applied." xsd:string @@ -3144,7 +3205,7 @@ property_value: IAO:0000600 "An information content entity that designates a tem id: APOLLO_SV:00000377 name: location definition def: "An information content entity that specifies a geographical region by (1) listing the names of other geographical regions whose mereological sum constitutes it and optionally (2) listing the names of other geographical regions that are subsequently subtracted from the mereological sum." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "LocationDefinition" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3154,7 +3215,7 @@ property_value: IAO:0000600 "An information content entity that specifies a geog id: APOLLO_SV:00000378 name: treatment contraindication def: "A contraindication that increases the risk of a treatment." [] -is_a: OAE:0000055 ! contraindication +is_a: OAE:0000055 property_value: APOLLO_SV:0000040 "TreatmentContraindication" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3174,7 +3235,7 @@ property_value: IAO:0000600 "A duration that is specified as a probability distr id: APOLLO_SV:00000380 name: fraction of contaminated thing def: "A measurement datum that is the fraction of things of a particular type in a particular geographical region or site that are contaminated with a pathogen." [] -is_a: IAO:0000109 ! measurement datum +is_a: IAO:0000109 property_value: APOLLO_SV:0000040 "fractionContaminated" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3184,7 +3245,7 @@ property_value: IAO:0000600 "A measurement datum that is the fraction of things id: APOLLO_SV:00000381 name: specificity of case detection def: "The specificity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X." [] -is_a: STATO:0000134 ! true negative rate +is_a: STATO:0000134 property_value: APOLLO_SV:0000040 "specificityOfCaseDetection" xsd:string property_value: IAO:0000111 "specificity of case detection" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3194,7 +3255,7 @@ property_value: IAO:0000600 "The specificity of a process or system that detects id: APOLLO_SV:00000382 name: specificity of treatment detection def: "The specificity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment." [] -is_a: STATO:0000134 ! true negative rate +is_a: STATO:0000134 property_value: APOLLO_SV:0000040 "specificityOfTreatmentDetection" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "The specificity of the process or system that detects organisms that have undergone a particular treatment." xsd:string @@ -3203,7 +3264,7 @@ property_value: IAO:0000600 "The specificity of the process or system that detec id: APOLLO_SV:00000383 name: sensitivity of treatment detection def: "The sensitivity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment." [] -is_a: STATO:0000233 ! true positive rate +is_a: STATO:0000233 property_value: APOLLO_SV:0000040 "sensitivityOfTreatmentDetection" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "The sensitivity of the process or system that detects organisms that have undergone a particular treatment." xsd:string @@ -3233,7 +3294,7 @@ id: APOLLO_SV:00000387 name: census objective specification def: "An objective specification to observe and/or estimate all the organisms of a particular taxon in a particular geographical region or place and create a data set about them." [] comment: Today, census taking typically consist of some mixture of counting the number of individuals in a population and estimating the numbers of subpopulations that are prone to overcounting or undercounting. -is_a: IAO:0000005 ! objective specification +is_a: IAO:0000005 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An objective specification to observe all the organisms of a particular taxon in a particular geographical region or place and create a data set about them." xsd:string @@ -3242,7 +3303,7 @@ property_value: IAO:0000600 "An objective specification to observe all the organ id: APOLLO_SV:00000388 name: census plan specification def: "A plan specification with a census objective specification." [] -is_a: IAO:0000104 ! plan specification +is_a: IAO:0000104 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A plan specification with a census objective specification." xsd:string @@ -3251,7 +3312,7 @@ property_value: IAO:0000600 "A plan specification with a census objective specif id: APOLLO_SV:00000389 name: census taking def: "A planned process that realizes a census plan specification." [] -is_a: OBI:0000011 ! planned process +is_a: OBI:0000011 property_value: APOLLO_SV:0000040 "Census" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3291,7 +3352,7 @@ property_value: IAO:0000600 "A vector control strategy for mosquitoes that is re id: APOLLO_SV:00000393 name: treatment system logistics def: "An information content entity that specifies how many doses or courses of treatment, per a particular unit of time (typically one day), can be supplied for a given geographical region and/or how many of those doses or courses can subsequently be administered." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "TreatmentSystemLogistics" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3326,7 +3387,7 @@ property_value: IAO:0000600 "A population survey that assesses the presence (plu id: APOLLO_SV:00000397 name: infection case list def: "A data set that is a collection of case records." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 property_value: APOLLO_SV:0000040 "CaseList" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3336,7 +3397,7 @@ property_value: IAO:0000600 "A data set that is a collection of case records." x id: APOLLO_SV:00000398 name: infection case record def: "A data set whose data items are about a host and its participation in an infection and potentially other activities occuring in the same time interval as the infection." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 property_value: APOLLO_SV:0000040 "CaseRecord" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3365,7 +3426,7 @@ property_value: IAO:0000600 "The temporal interval occupied by an epidemic." xsd id: APOLLO_SV:00000401 name: individual mosquito behavior def: "An individual behavior of a mosquito (organism of family Culicidae)." [] -is_a: GO:0007610 ! behavior +is_a: GO:0007610 property_value: APOLLO_SV:0000040 "MosquitoBehavior" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3375,7 +3436,7 @@ property_value: IAO:0000600 "An individual behavior of a mosquito (organism of f id: APOLLO_SV:00000402 name: individual human behavior def: "An individual behavior of a human being." [] -is_a: GO:0007610 ! behavior +is_a: GO:0007610 property_value: APOLLO_SV:0000040 "HumanBehavior" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3387,7 +3448,7 @@ name: transmission tree def: "A data structure that represents, for a particular infection in ecosystem, a subset of infected organisms and for each infected organism in the subset except the first one infected temporally, its infection acquisition from an infected host as a machine-readable link to that infected host." [] comment: Because a set A is a subset of itself, we capture the possibility that all infected organisms in the epidemic are represented in the tree. comment: This definition allows for multiple trees in an epidemic because we did not require that the first case infected temporally be the index case, although the ideal situation is that there is one tree for the epidemic that includes the index case. -is_a: OBI:0000658 ! data representational model +is_a: OBI:0000658 property_value: APOLLO_SV:0000040 "TransmissionTree" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3400,8 +3461,9 @@ def: "A disposition inhering in an organism of a particular biological taxon tha comment: The disposition of Influenza A virus H3N2 subtype to infect human beings, the disposition of Plasmodium vivax to infect mosquitos and humans, the disposition of foot and mouth disease virus to infect cloven-hooved animals (sheep, cows, pigs, etc.). is_a: BFO:0000016 intersection_of: BFO:0000016 -intersection_of: BFO:0000054 APOLLO_SV:00000114 {all_only="true"} ! is realized by infection -intersection_of: RO:0000052 OBI:0100026 ! organism +intersection_of: BFO:0000054 APOLLO_SV:00000114 {all_only="true"} ! infection +intersection_of: RO:0000052 OBI:0100026 +relationship: RO:0000052 OBI:0100026 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 @@ -3410,7 +3472,7 @@ property_value: IAO:0000600 "A disposition inhering in an organism of a particul id: APOLLO_SV:00000405 name: potentially infectious contacting def: "A biological process that brings the organism into sufficiently close physical proximity to a pathogen population, either in or on a contaminated thing or an infectious host, such that the organism is likely but not certain to acquire an infection with the pathogen." [] -is_a: GO:0008150 ! biological process +is_a: GO:0008150 property_value: IAO:0000111 "potentially infectious contact process" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "potentially infectious contact" xsd:string @@ -3423,7 +3485,8 @@ def: "A role borne by an organism that is realized in a potentially infectious c comment: The organism bearing this role is the organism at risk for acquiring an infection when the role is realized. Also, this role differentiates participants in a process when there are two organisms participating, so it only begins to exist during its realization, justifying its existential restriction. is_a: BFO:0000023 intersection_of: BFO:0000023 -intersection_of: BFO:0000054 APOLLO_SV:00000405 ! is realized by potentially infectious contacting +intersection_of: BFO:0000054 APOLLO_SV:00000405 ! potentially infectious contacting +relationship: BFO:0000054 APOLLO_SV:00000405 ! potentially infectious contacting property_value: IAO:0000111 "potentially infectous contact role" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "contact role" xsd:string @@ -3434,9 +3497,10 @@ property_value: IAO:0000600 "A role borne by an organism that is realized in a p id: APOLLO_SV:00000407 name: contacted organism def: "An organism that is the bearer of a potentially infectious contact role during a potentially infectious contact process." [] -is_a: OBI:0100026 ! organism -intersection_of: OBI:0100026 ! organism -intersection_of: RO:0000053 APOLLO_SV:00000406 ! is bearer of potentially infectious contact role +is_a: OBI:0100026 +intersection_of: OBI:0100026 +intersection_of: RO:0000053 APOLLO_SV:00000406 ! potentially infectious contact role +relationship: RO:0000053 APOLLO_SV:00000406 ! potentially infectious contact role property_value: IAO:0000111 "potentially infectious contact organism" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An organism that has been exposed to a pathogen by coming into close physical proximity with either an infectious host or a contaminated thing." xsd:string @@ -3445,7 +3509,7 @@ property_value: IAO:0000600 "An organism that has been exposed to a pathogen by id: APOLLO_SV:00000408 name: contact definition def: "An information content entity that specifies which kinds of processes involving an interaction between a given organism and either (1) another, potentially infectious organism or (2) a contaminated environment have a sufficiently high probability of resultling in an infection acquisition by the organism to be of interest to an outbreak investigation." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "ContactDefinition" xsd:string property_value: IAO:0000111 "potentially infectious contact definition" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3485,7 +3549,7 @@ property_value: IAO:0000600 "A vector control action specification that specifie id: APOLLO_SV:00000412 name: leakage rate of Wolbachia infection in mosquito population infected with Wolbachia def: "The rate at which offspring of the Wolbachia-infected female mosquito subpopulation (of the overall mosquito population) are not infected with Wolbachia." [] -is_a: OBI:0001554 ! rate measurement datum +is_a: OBI:0001554 property_value: APOLLO_SV:0000040 "wolbachiaEffectOnLeakageRate" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3495,7 +3559,7 @@ property_value: IAO:0000600 "The rate at which offspring of the Wolbachia-infect id: APOLLO_SV:00000413 name: transmission rate of pathogen to human from Wolbachia-infected mosquito bites def: "The rate at which bites of mosquitoes infected with both Wolbachia and a particular pathogen such as dengue result in an infection in a susceptible human host." [] -is_a: OBI:0001554 ! rate measurement datum +is_a: OBI:0001554 property_value: APOLLO_SV:0000040 "wolbachiaEffectOnVectorialCapacity" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3534,7 +3598,7 @@ property_value: IAO:0000600 "An larvicide vector control strategy that is used p id: APOLLO_SV:00000417 name: life stages with duration and mortality def: "A data structure that refers to (1) a subpopulation of a population based on life stage, (2) the rate of mortality of that subpopulation, and (3) the average duration of time that the individuals in the subpopulation spend in that life stage." [] -is_a: OBI:0000658 ! data representational model +is_a: OBI:0000658 property_value: APOLLO_SV:0000040 "LifeStageWithDurationAndMortality" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3544,7 +3608,7 @@ property_value: IAO:0000600 "A data structure that refers to (1) a subpopulation id: APOLLO_SV:00000418 name: Wolbachia effect on egg mortality rate in mosquito population def: "A process of change in the egg mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population." [] -is_a: GO:0051701 ! interaction with host +is_a: GO:0051701 property_value: APOLLO_SV:0000040 "wolbachiaEffectOnEggMortalityRate" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3554,7 +3618,7 @@ property_value: IAO:0000600 "A process of change in the egg mortality rate of a id: APOLLO_SV:00000419 name: Wolbachia effect on adult mortality rate in mosquito population def: "A process of change in the adult mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population." [] -is_a: GO:0051701 ! interaction with host +is_a: GO:0051701 property_value: APOLLO_SV:0000040 "wolbachiaEffectOnAdultMortalityRate" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3564,7 +3628,7 @@ property_value: IAO:0000600 "A process of change in the adult mortality rate of id: APOLLO_SV:00000420 name: Wolbachia effect on larval mortality rate in mosquito population def: "A process of change in the larval mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population." [] -is_a: GO:0051701 ! interaction with host +is_a: GO:0051701 property_value: APOLLO_SV:0000040 "wolbachiaEffectOnLarvalMortalityRate" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3574,7 +3638,7 @@ property_value: IAO:0000600 "A process of change in the larval mortality rate of id: APOLLO_SV:00000421 name: Wolbachia effect on female fecundity in mosquito population def: "A process of change in fecundity of females in a mosquito population that is the outcome of an infection in that population with a Wolbachia bacteria population." [] -is_a: GO:0051701 ! interaction with host +is_a: GO:0051701 property_value: APOLLO_SV:0000040 "wolbachiaEffectOnFecundity" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3584,7 +3648,7 @@ property_value: IAO:0000600 "A process of change in fecundity of females in a mo id: APOLLO_SV:00000422 name: confidence interval def: "A data item that specifies both an interval estimate centered around some sample statistic, and the probability that the process/method of obtaining the interval estimate's range of values will generate an interval that contains some unobserved population parameter of interest." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3602,7 +3666,7 @@ property_value: IAO:0000600 "A seed release interval for a Wolbachia control mea id: APOLLO_SV:00000424 name: mean with confidence interval def: "A data structure that specifies both the sample mean and the confidence interval generated by the measurement process." [] -is_a: OBI:0000658 ! data representational model +is_a: OBI:0000658 property_value: APOLLO_SV:0000040 "MeanWithConfidenceInterval" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3611,7 +3675,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000425 name: mean with standard deviation def: "A data structure that specifies both the sample mean and the standard deviation generated by the measurement process." [] -is_a: OBI:0000658 ! data representational model +is_a: OBI:0000658 property_value: APOLLO_SV:0000040 "MeanWithStandardDeviation" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3640,7 +3704,7 @@ property_value: IAO:0000600 "An epidemic simulator action specification that whe id: APOLLO_SV:00000428 name: disease outcome with probability def: "A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism." [] -is_a: OBI:0302867 ! predicted data item +is_a: OBI:0302867 property_value: APOLLO_SV:0000040 "DiseaseOutcomeWithProbability" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3680,7 +3744,7 @@ property_value: IAO:0000600 "An epidemic simulator actions specification that sp id: APOLLO_SV:00000432 name: minimum value def: "A data item that specifies the smallest numerical value in a data set of scalar measurement data items." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "minimumValue" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3690,7 +3754,7 @@ property_value: IAO:0000600 "A data item that specifies the smallest numerical v id: APOLLO_SV:00000433 name: maximum value def: "A data item that specifies the largest numerical value in a data set of scalar measurement data itmes." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "maximumValue" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3700,7 +3764,7 @@ property_value: IAO:0000600 "A data item that specifies the largest numerical va id: APOLLO_SV:00000434 name: statistical confidence def: "A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest." [] -is_a: OBI:0302867 ! predicted data item +is_a: OBI:0302867 property_value: APOLLO_SV:0000040 "confidence" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3719,7 +3783,7 @@ is_obsolete: true id: APOLLO_SV:00000436 name: lower bound def: "An information content entity that delimits an interval data structure based on some value that is less than or equal to all other values within that data structure." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "lowerBound" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3729,7 +3793,7 @@ property_value: IAO:0000600 "An information content entity that delimits an inte id: APOLLO_SV:00000437 name: fraction of vector adults affected def: "A measurement datum that is the fraction of a particular adult vector population that have undergone 1) infection acquisition with a pathogen, and 2) have experienced some outcome of the resulting infection." [] -is_a: IAO:0000109 ! measurement datum +is_a: IAO:0000109 property_value: APOLLO_SV:0000040 "fractionOfVectorIndividualsAffected" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3739,7 +3803,7 @@ property_value: IAO:0000600 "A measurement datum that is the fraction of a parti id: APOLLO_SV:00000438 name: fraction reduction of eggs def: "A measurement datum that is the fraction of eggs laid by a particular host population that has been destroyed and thus will not develop into a new member of the population." [] -is_a: IAO:0000109 ! measurement datum +is_a: IAO:0000109 property_value: APOLLO_SV:0000040 "fractionReductionOfEggs" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3749,7 +3813,7 @@ property_value: IAO:0000600 "A measurement datum that is the fraction of eggs la id: APOLLO_SV:00000439 name: fraction reduction of larvae def: "A measurement datum that is the fraction of the larval subpopulation of a particular host population that has died due to some event in the population (e.g, due to a particular control measure)." [] -is_a: IAO:0000109 ! measurement datum +is_a: IAO:0000109 property_value: APOLLO_SV:0000040 "fractionReductionOfLarvae" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3779,7 +3843,7 @@ property_value: IAO:0000600 "A duration that measures the temporal interval betw id: APOLLO_SV:00000442 name: migration speed def: "A rate measurement datum of that divides the total distance traveled during some migration process by the duration of the temporal interval occupied by that process." [] -is_a: OBI:0001554 ! rate measurement datum +is_a: OBI:0001554 property_value: APOLLO_SV:0000040 "migrationSpeed" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3799,7 +3863,7 @@ property_value: IAO:0000600 "An information content entity that specifies the pr id: APOLLO_SV:00000444 name: movement speed def: "A rate measurement datum that specifies the ratio of distance travelled during a movement process to the duration of the time interval occupied by the process." [] -is_a: OBI:0001554 ! rate measurement datum +is_a: OBI:0001554 property_value: APOLLO_SV:0000040 "speedOfMovement" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3809,7 +3873,7 @@ property_value: IAO:0000600 "A rate measurement datum that specifies the ratio o id: APOLLO_SV:00000445 name: mortality rate def: "A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval." [] -is_a: OBI:0001554 ! rate measurement datum +is_a: OBI:0001554 property_value: APOLLO_SV:0000040 "mortalityRate" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3819,7 +3883,7 @@ property_value: IAO:0000600 "A rate measurement datum that specifies the percent id: APOLLO_SV:00000446 name: ratio of outdoor to indoor ovisites def: "A data item that specifies, as a ratio, the total count of oviposition sites located externally to all places in a geographic region relative to the total count of oviposition sites located internally to some place in that geographic region." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "ratioOfOutdoorToIndoorOvisites" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3829,7 +3893,7 @@ property_value: IAO:0000600 "A data item that specifies, as a ratio, the total c id: APOLLO_SV:00000447 name: upper bound def: "An information content entity that delimits an interval data structure based on some value that is greater than or equal to all other values within that data structure." [] -is_a: IAO:0000030 ! information content entity +is_a: IAO:0000030 property_value: APOLLO_SV:0000040 "upperBound" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3839,7 +3903,7 @@ property_value: IAO:0000600 "An information content entity that delimits an inte id: APOLLO_SV:00000448 name: standard deviation def: "A data item that specifies the dispersion of values around some parameter in a set of data, and whose values are standardized to express the same unit of measure as the parameter of interest." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "standardDeviation" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3890,7 +3954,7 @@ property_value: IAO:0000600 "An epidemic simulator action specification that spe id: APOLLO_SV:00000453 name: eggs per brood def: "An average value that specifies the number of eggs produced during one reproductive cycle for each individual female within a population." [] -is_a: OBI:0000679 ! average value +is_a: OBI:0000679 property_value: APOLLO_SV:0000040 "eggsPerBrood" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3980,7 +4044,7 @@ property_value: IAO:0000600 "An identifier that denotes a drug product." xsd:str id: APOLLO_SV:00000462 name: mean median minimum maximum summary statistics data structure def: "A data structure that holds the mean, median, minimum value, and maximum value of one set of measurement data." [] -is_a: OBI:0000658 ! data representational model +is_a: OBI:0000658 property_value: APOLLO_SV:0000040 "MeanMedianMinimumMaximum" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4061,7 +4125,7 @@ id: APOLLO_SV:00000470 name: probability def: "A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents." [] comment: The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'. -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "Probability" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4081,7 +4145,7 @@ property_value: IAO:0000600 "An epidemic simulator action specification that spe id: APOLLO_SV:00000472 name: age-dependent fecundity reduction def: "A rate measurement datum that measures the percentage decrease per unit time (typically per day) in the number of offspring to which a female mosquito passes an infection with a particular pathogen (e.g., Wolbachia)." [] -is_a: OBI:0001554 ! rate measurement datum +is_a: OBI:0001554 property_value: APOLLO_SV:0000040 "ageDependentFecundityReduction" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4151,7 +4215,7 @@ property_value: IAO:0000600 "A vector control strategy that has 1) an action spe id: APOLLO_SV:00000479 name: ovisite carrying capacity def: "A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining." [] -is_a: OBI:0302867 ! predicted data item +is_a: OBI:0302867 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining." xsd:string @@ -4160,7 +4224,7 @@ property_value: IAO:0000600 "A predicted data item that is the maximum value of id: APOLLO_SV:00000480 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 +is_a: GO:0007610 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "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." xsd:string @@ -4169,7 +4233,7 @@ property_value: IAO:0000600 "A behavior of one or more organisms that is charact id: APOLLO_SV:00000481 name: cut-off point specification def: "An action specification that delineates some minimum value or maximum value for some test statistic within a continuous probability distribution that is meant to serve as a lower bound or upper bound, respectively, for some population or sample of interest." [] -is_a: IAO:0000007 ! action specification +is_a: IAO:0000007 property_value: APOLLO_SV:0000040 "cutTailAt" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4344,7 +4408,7 @@ property_value: IAO:0000600 "An adult vector control strategy that has 1) an act id: APOLLO_SV:00000500 name: schedule def: "A plan specification that specifies 1) the quantity of which some material entity will be allocated to the eventual realization of some action specification, and 2) the temporal regions in which each action specification is to be realized." [] -is_a: IAO:0000104 ! plan specification +is_a: IAO:0000104 property_value: APOLLO_SV:0000040 "Schedule" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4385,7 +4449,7 @@ property_value: IAO:0000600 "A data set that comprises exactly one latitude meas id: APOLLO_SV:00000504 name: age in years datum def: "A time measurement datum that refers to the temporal interval occupied by the life course of some organism and that takes 'years' as its measurement unit label." [] -is_a: IAO:0000416 ! time measurement datum +is_a: IAO:0000416 property_value: APOLLO_SV:0000040 "ageInYears" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4462,7 +4526,7 @@ property_value: IAO:0000117 "Matthew Diller" xsd:string id: APOLLO_SV:00000512 name: rate of hydrological precipitation def: "A rate measurement datum that is the result of the measurement of the volume of water produced by some hydrological precipitation process at a particular geographical region divided by the number of temporal intervals of equal duration over which the precipitation occurred." [] -is_a: OBI:0001554 ! rate measurement datum +is_a: OBI:0001554 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4470,7 +4534,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000513 name: mean rate of hydrological precipitation def: "An average value that takes, as input, some set of rate of hydrological precipitation data that were recorded over a particular duration of time." [] -is_a: OBI:0000679 ! average value +is_a: OBI:0000679 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4478,7 +4542,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000514 name: mean air temperature def: "An average value that takes, as input, some set of air temperature measurement data that were recorded over a particular duration of time." [] -is_a: OBI:0000679 ! average value +is_a: OBI:0000679 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4486,7 +4550,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000515 name: potentially infectious sexual contacting def: "A sexual activity with at least one infectious host as participant where the infectious host(s) are infected with a pathogen that has a disposition to infect the tissues of the non-infected host that came into physical contact with the infectious host during the activity." [] -is_a: NBO:0000034 ! sexual activity +is_a: NBO:0000034 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4494,7 +4558,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000516 name: host population def: "A population of organisms some of which were susceptible to infection with a particular pathogen at some point in their lives." [] -is_a: PCO:0000001 ! population +is_a: PCO:0000001 property_value: IAO:0000111 "host population" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "population of host organisms" xsd:string @@ -4503,7 +4567,7 @@ property_value: IAO:0000118 "population of host organisms" xsd:string id: APOLLO_SV:00000517 name: prioritization scheme for control measure def: "An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure." [] -is_a: IAO:0000007 ! action specification +is_a: IAO:0000007 property_value: APOLLO_SV:0000040 "controlMeasureNamedPrioritizationScheme" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4514,7 +4578,7 @@ id: APOLLO_SV:00000518 name: one-way sensitivity analysis of a continuous variable def: "A data transformation that takes as its input exactly one continuous variable as a value and assesses whether any statistically significant change to that variable will produce some change to the model's output." [] comment: Class was originally created to correspond with a complex type from Apollo XSD v3.1.0. -is_a: OBI:0200000 ! data transformation +is_a: OBI:0200000 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A data transformation that takes as its input exactly one continuous variable as a value and assesses whether any statistically significant change to that variable will produce some change to the model's output." xsd:string @@ -4553,7 +4617,13 @@ property_value: IAO:0000600 "An infection acquisition from infectious host by an [Term] id: APOLLO_SV:00000522 name: source code repository -is_a: IAO:0000100 ! data set +def: "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc." [] +comment: Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based +is_a: IAO:0000100 +is_a: IAO:0000310 +relationship: BFO:0000051 IAO:0000096 +property_value: IAO:0000111 "software source code version control repository" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] id: APOLLO_SV:00000524 @@ -4561,7 +4631,7 @@ name: compiling software def: "A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions." [] comment: It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). comment: Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. -is_a: OBI:0000011 ! planned process +is_a: APOLLO_SV:00000008 ! software development property_value: IAO:0000111 "process of compiling software" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4569,7 +4639,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000525 name: compiled software code def: "A software that is the specified output of some compilation of software process" [] -is_a: IAO:0000010 ! software +is_a: IAO:0000010 property_value: IAO:0000111 "machine instructions compiled from software source code" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4577,7 +4647,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000526 name: scale-free network model def: "An algorithm that models some scale-free network." [] -is_a: IAO:0000064 ! algorithm +is_a: IAO:0000064 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4585,7 +4655,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000527 name: scale-free network def: "A graph of vertices in which, for some fraction of vertices, P(k), the number of connections, k, varies as a power of some parameter, γ. In other words, P(k) ~ k^(-γ), where 2 < γ < 3." [] -is_a: OBI:0000714 ! graph of vertices +is_a: OBI:0000714 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4594,8 +4664,8 @@ id: APOLLO_SV:00000528 name: synthetic ecosystem data set def: "A data set that represents 1) one or more collections of organisms at some time and some geographical region; and optionally 2) the school facilities, workplace facilities, and health care facilities in that region." [] comment: The interactions between each organism as they move between these facilities may also be included in the data set. -is_a: IAO:0000100 ! data set -relationship: IAO:0000136 APOLLO_SV:00000097 ! is about ecosystem +is_a: IAO:0000100 +relationship: IAO:0000136 APOLLO_SV:00000097 ! ecosystem property_value: APOLLO_SV:0000040 "SyntheticEcosystem" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4624,7 +4694,7 @@ property_value: IAO:0000600 "A conditional probability whose value is dependent id: APOLLO_SV:00000531 name: epidemic threshold def: "A data item that specifies the number of susceptible organisms necessary for an epidemic to occur within a population." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4648,7 +4718,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000534 name: human mobility data item def: "A data item that is about one or more instances of human travel, and that specifies the geographical start location, geographical end location, and the geographical regions visited throughout the process." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4695,7 +4765,7 @@ property_value: IAO:0000600 "An identifier that refers to all versions of a spec id: APOLLO_SV:00000539 name: software license URL def: "A unique resource locator that constitutes a reference to some software license." [] -is_a: OMIABIS:0000019 ! unique resource locator +is_a: OMIABIS:0000019 property_value: APOLLO_SV:0000040 "licenseLocation" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4715,7 +4785,7 @@ property_value: IAO:0000600 "An algorithm that simulates changes in the size and id: APOLLO_SV:00000541 name: disease surveillance objective specification def: "An objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval." [] -is_a: IAO:0000005 ! objective specification +is_a: IAO:0000005 property_value: IAO:0000111 "disease surveillance objective specification" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4725,8 +4795,8 @@ property_value: IAO:0000600 "An objective specification whose endpoint is human id: APOLLO_SV:00000542 name: mortality data def: "A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon." [] -is_a: IAO:0000100 ! data set -relationship: IAO:0000136 PCO:0000001 ! is about population +is_a: IAO:0000100 +relationship: IAO:0000136 PCO:0000001 property_value: IAO:0000111 "population mortality data set" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4746,7 +4816,7 @@ property_value: IAO:0000600 "Simulation software that simulates the evolution ov id: APOLLO_SV:00000545 name: disease surveillance def: "A planned process that is the realization of a disease surveillance objective specification." [] -is_a: OBI:0000011 ! planned process +is_a: OBI:0000011 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A planned process that is the realization of a disease surveillance objective specification." xsd:string @@ -4764,7 +4834,7 @@ property_value: IAO:0000600 "Individual human behavior that involves either 1) r id: APOLLO_SV:00000547 name: social interaction data item def: "A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s)." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s)." xsd:string @@ -4827,7 +4897,7 @@ property_value: IAO:0000600 "A Susceptible-Infected-Resistant model that represe id: APOLLO_SV:00000554 name: disease surveillance data def: "A data set that is about some disease surveillance." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 relationship: OBI:0000312 APOLLO_SV:00000545 ! disease surveillance property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4877,7 +4947,7 @@ property_value: IAO:0000600 "An investigation following a disease state study de id: APOLLO_SV:00000559 name: case series data set def: "A data set that is the output of a case series investigation." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 relationship: OBI:0000312 APOLLO_SV:00000558 ! case series property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4887,7 +4957,8 @@ property_value: IAO:0000600 "A data set that is the output of a case series inve id: APOLLO_SV:00000560 name: epidemic data set def: "A data set about an instance of an epidemic." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 +relationship: IAO:0000136 APOLLO_SV:00000298 ! epidemic property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A data set about an instance of an epidemic." xsd:string @@ -4937,8 +5008,8 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000566 name: data parsing def: "A data transformation that has a dataset, encoded in a particular data format specification, as input and extracts certain elements or parts of the dataset, typically into the volatile memory of a computer." [] -is_a: OBI:0200000 ! data transformation -relationship: OBI:0000293 IAO:0000100 ! data set +is_a: OBI:0200000 +relationship: OBI:0000293 IAO:0000100 property_value: IAO:0000111 "data parsing process" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "data reading process" xsd:string @@ -4949,7 +5020,7 @@ id: APOLLO_SV:00000567 name: synthetic ecosystem constructor def: "A software that when compiled and run, has specified output of an agent-level ecosystem data set." [] comment: example: Synthia, SPEW -is_a: IAO:0000010 ! software +is_a: IAO:0000010 property_value: IAO:0000111 "synthetic ecosystem constructor software" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "software for creating a synthetic ecosystem dataset" xsd:string @@ -4958,7 +5029,7 @@ property_value: IAO:0000118 "software for creating a synthetic ecosystem dataset id: APOLLO_SV:00000568 name: total fatal disease cases def: "A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "totalFatalCaseCount" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4969,6 +5040,7 @@ id: APOLLO_SV:00000569 name: total disease cases def: "A count of the total number of diseased indivduals in a population during a particular time interval." [] is_a: APOLLO_SV:00000617 ! population count +relationship: OBI:0000312 APOLLO_SV:00000155 ! population infection survey property_value: APOLLO_SV:0000040 "totalCaseCount" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4979,7 +5051,7 @@ id: APOLLO_SV:00000570 name: employment status data item def: "A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions." [] comment: If an individual is a member of the labor force, the criteria that this status is selected from includes whether they are in the armed forces, employed and working, employed but absent from work for a week, and unemployed. The criteria for those not in the labor force includes whether the individual is a houseworker, suffering from a physical impairment that prevents them from working, in school, or other miscellaneous reasons. -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 property_value: APOLLO_SV:0000040 "employmentStatus" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5017,7 +5089,7 @@ property_value: IAO:0000600 "An infectious disease control strategy that attempt id: APOLLO_SV:00000574 name: acute respiratory illness def: "A clinical phenotype that is causally preceded by some infection or some adverse drug reaction; and that is accompanied by a fever greater than or equal to 37.8 degrees Celsius, and a cough or sore throat." [] -is_a: OGMS:0000027 ! clinical phenotype +is_a: OGMS:0000027 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "influenza-like illness" xsd:string @@ -5044,7 +5116,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000577 name: epidemic peak intensity def: "A predicted data item that is about some aggregate of cases in an epidemic and whose value specification contains the maximum value in a data set that is about the epidemic." [] -is_a: OBI:0302867 ! predicted data item +is_a: OBI:0302867 property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5062,7 +5134,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000579 name: infectious disease forecast def: "A planned process that realizes some infectious disease forecasting software." [] -is_a: OBI:0000011 ! planned process +is_a: OBI:0000011 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5078,7 +5150,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000581 name: infectious disease forecast objective specification def: "An objective specification that is realized by the estimation of one or more predicted data items that are about 1) some infection in ecosystem and 2) potential changes to its number of participants (e.g., individuals within a host population, individuals within a vector population) relative to a particular temporal region; and is part of some infectious disease forecasting software." [] -is_a: IAO:0000005 ! objective specification +is_a: IAO:0000005 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5119,7 +5191,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000586 name: infectious disease forecast time specification def: "An action specification that specifies the duration of time that is to elapse between each calculation of each predicted data item that is the output of some infectious disease forecast." [] -is_a: IAO:0000007 ! action specification +is_a: IAO:0000007 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5127,13 +5199,13 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000587 name: intensive care unit encounter def: "An inpatient encounter in which the health care provider role is realized by some person employed by the intensive care department of some health care facility, and the patient role is realized by someone admitted to that intensive care department." [] -is_a: OGMS:0000100 ! inpatient encounter +is_a: OGMS:0000100 [Term] id: APOLLO_SV:00000588 name: data visualization objective specification def: "An objective specification that is realized when a diagram is drawn from one or more data sets." [] -is_a: IAO:0000005 ! objective specification +is_a: IAO:0000005 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5150,9 +5222,10 @@ property_value: IAO:0000600 "an individual treatment control strategy that is re id: APOLLO_SV:00000590 name: website with data comment: This class was created for use case for MIDAS Digital Repository to index websites that have useful data in them, albeit rarely as machine-interpretable, downloadable datasets. Much of the data are locked in PDF or other text-based formats. -is_a: FBcv:0000667 ! website -intersection_of: FBcv:0000667 ! website -intersection_of: BFO:0000111 IAO:0000027 ! data item +is_a: FBcv:0000667 +intersection_of: FBcv:0000667 +intersection_of: BFO:0000111 IAO:0000027 +relationship: BFO:0000111 IAO:0000027 property_value: IAO:0000111 "website that has data as a part" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5160,7 +5233,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000591 name: climate data set def: "A data set that is an aggregate of data items that are about an environmental system process (e.g., hydrological precipitation) or a participant in an environmental system process." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 property_value: IAO:0000111 "climate data set" xsd:string property_value: IAO:0000117 "Matt Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5178,7 +5251,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000593 name: abiotic ecosystem data set def: "A data set that is about some abiotic ecosystem or abiotic ecosystem element." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 property_value: IAO:0000111 "abiotic ecosystem data set" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "abiotic ecosystem dataset" xsd:string @@ -5199,7 +5272,6 @@ id: APOLLO_SV:00000595 name: treatment facility census def: "A census that counts the number of treatment facilities of some kind in a particular geographical region." [] comment: NOTE: this class counts the facilities themselves, not patients (people) in those facilities. For example, how many hospitals in a state. Not how many patients are in a hospital or hospitals in a state. -is_a: APOLLO_SV:00000173 ! census property_value: IAO:0000111 "census of treatment facility" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "census of treatment facilities" xsd:string @@ -5212,7 +5284,7 @@ id: APOLLO_SV:00000596 name: symbiosis def: "An interspecies interaction between two or more organisms in intimate association." [] comment: By "intimate interaction," we mean any interaction between two or more organisms that involves (1) physical contact or (2) multi-organism behavior in which all interacting organisms are participant. -is_a: GO:0044419 ! interspecies interaction between organisms +is_a: GO:0044419 property_value: IAO:0000111 "symbiosis" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5232,7 +5304,8 @@ name: disease identifier def: "an identifier that denotes a disease." [] is_a: IAO:0020000 intersection_of: IAO:0020000 -intersection_of: IAO:0000219 OGMS:0000031 ! disease +intersection_of: IAO:0000219 OGMS:0000031 +relationship: IAO:0000219 OGMS:0000031 property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017 property_value: http://purl.org/dc/elements/1.1/date "2021-03-16T16:01:41Z" xsd:dateTime @@ -5244,9 +5317,10 @@ id: APOLLO_SV:00000599 name: infection acquisition dataset def: "a dataset that is about infectious disease acquisitions at particular times and particular places." [] comment: The dataset may include sites (e.g. types of facilities, rooms), events (e.g., church service whether in or outdoors), dates, times, geographical regions, etc. in which the sites/events are located, and so on. -is_a: IAO:0000100 ! data set -intersection_of: IAO:0000100 ! data set -intersection_of: IAO:0000136 APOLLO_SV:00000115 ! is about infection acquisition +is_a: IAO:0000100 +intersection_of: IAO:0000100 +intersection_of: IAO:0000136 APOLLO_SV:00000115 ! infection acquisition +relationship: IAO:0000136 APOLLO_SV:00000115 ! infection acquisition property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017 property_value: http://purl.org/dc/elements/1.1/date "2021-03-16T16:16:26Z" xsd:dateTime property_value: IAO:0000111 "dataset about infectious disease acquisitions" xsd:string @@ -5258,7 +5332,7 @@ id: APOLLO_SV:00000600 name: hospital stay dataset def: "a dataset that is about two or more hospital stays involving two or more patients." [] comment: The dataset may be limited to stays in one hospital, but hospital discharge datasets as compiled by state departments of health typically contain stays from multiple hospitals (typically every hospital) in the geographical region over which they have jurisdiction -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017 property_value: http://purl.org/dc/elements/1.1/date "2021-03-16T16:20:48Z" xsd:dateTime property_value: IAO:0000111 "dataset about hospital stays" xsd:string @@ -5281,9 +5355,10 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000602 name: human daily movement data set def: "a data set that is about the human daily movement behavior of the individual huamns in a given population." [] -is_a: IAO:0000100 ! data set -intersection_of: IAO:0000100 ! data set -intersection_of: IAO:0000136 APOLLO_SV:00000601 ! is about human daily movement +is_a: IAO:0000100 +intersection_of: IAO:0000100 +intersection_of: IAO:0000136 APOLLO_SV:00000601 ! human daily movement +relationship: IAO:0000136 APOLLO_SV:00000601 ! human daily movement property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017 property_value: http://purl.org/dc/elements/1.1/date "2021-03-16T16:32:39Z" xsd:dateTime property_value: IAO:0000111 "human daily movement behavior data set" xsd:string @@ -5294,9 +5369,10 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000603 name: potentially infectious contact data set def: "a data set that is about one or more potentially infectious contact processes in a population of host organisms." [] -is_a: IAO:0000100 ! data set -intersection_of: IAO:0000100 ! data set -intersection_of: IAO:0000136 APOLLO_SV:00000405 ! is about potentially infectious contacting +is_a: IAO:0000100 +intersection_of: IAO:0000100 +intersection_of: IAO:0000136 APOLLO_SV:00000405 ! potentially infectious contacting +relationship: IAO:0000136 APOLLO_SV:00000405 ! potentially infectious contacting property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017 property_value: http://purl.org/dc/elements/1.1/date "2021-03-16T16:39:24Z" xsd:dateTime property_value: IAO:0000111 "potentially infectious contact process data set in a population" xsd:string @@ -5307,9 +5383,10 @@ property_value: IAO:0000118 "contact data set" xsd:string id: APOLLO_SV:00000604 name: control strategy census def: "a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem." [] -is_a: IAO:0000100 ! data set +is_a: APOLLO_SV:00000173 ! census intersection_of: APOLLO_SV:00000173 ! census -intersection_of: IAO:0000136 APOLLO_SV:00000086 ! is about infectious disease control strategy +intersection_of: IAO:0000136 APOLLO_SV:00000086 ! infectious disease control strategy +relationship: IAO:0000136 APOLLO_SV:00000086 ! infectious disease control strategy property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017 property_value: http://purl.org/dc/elements/1.1/date "2021-03-16T16:43:04Z" xsd:dateTime property_value: IAO:0000111 "infectious disease control strategy census" xsd:string @@ -5322,7 +5399,8 @@ def: "an infectious disease control strategy census that is about school closure comment: This class represents datasets about strategies for school closure. Datasets about individual actual school closures go elsewhere. is_a: APOLLO_SV:00000604 ! control strategy census intersection_of: APOLLO_SV:00000604 ! control strategy census -intersection_of: IAO:0000136 APOLLO_SV:00000123 ! is about school closure control strategy +intersection_of: IAO:0000136 APOLLO_SV:00000123 ! school closure control strategy +relationship: IAO:0000136 APOLLO_SV:00000123 ! school closure control strategy property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017 property_value: http://purl.org/dc/elements/1.1/date "2021-03-16T16:44:03Z" xsd:dateTime property_value: IAO:0000111 "school closure infectious disease control strategy census" xsd:string @@ -5334,7 +5412,8 @@ name: vaccination control strategy census comment: This class is an inventory of vaccination control strategies, not vaccinations themselves. So it should be a list of things like "Publix vaccination plan", "Alachua county vaccination plan", "Sam's Club vaccination plan", etc. And not a list of individual vaccinations given to actual patients (see population vaccination census) is_a: APOLLO_SV:00000604 ! control strategy census intersection_of: APOLLO_SV:00000604 ! control strategy census -intersection_of: IAO:0000136 APOLLO_SV:00000136 ! is about vaccination control strategy +intersection_of: IAO:0000136 APOLLO_SV:00000136 ! vaccination control strategy +relationship: IAO:0000136 APOLLO_SV:00000136 ! vaccination control strategy property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017 property_value: http://purl.org/dc/elements/1.1/date "2021-03-16T16:47:09Z" xsd:dateTime property_value: IAO:0000111 "vaccination infectious disease control strategy census" xsd:string @@ -5346,7 +5425,8 @@ name: vaccination administration census def: "a population treatment census that is about one or more vaccinations of organisms in a population." [] is_a: APOLLO_SV:00000187 ! population treatment census intersection_of: APOLLO_SV:00000187 ! population treatment census -intersection_of: IAO:0000136 APOLLO_SV:00000142 ! is about vaccination +intersection_of: IAO:0000136 APOLLO_SV:00000142 ! vaccination +relationship: IAO:0000136 APOLLO_SV:00000142 ! vaccination property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-9881-1017 property_value: http://purl.org/dc/elements/1.1/date "2021-03-16T16:48:42Z" xsd:dateTime property_value: IAO:0000111 "population vaccination census" xsd:string @@ -5392,7 +5472,7 @@ id: APOLLO_SV:00000611 name: parameter estimation model def: "An algoirthm that is used to estimate the \"true\" values of certain parameters of disease transmission and/or forecasting." [] comment: Examples of parameters estimated include R0, transmissibility, infectious period. -is_a: IAO:0000064 ! algorithm +is_a: IAO:0000064 property_value: http://purl.org/dc/elements/1.1/date "2022-09-18T17:51:00" xsd:string property_value: IAO:0000111 "model for disease transmission parameter estimation" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5402,7 +5482,7 @@ id: APOLLO_SV:00000612 name: network model def: "An algorithm that operates on a representation of some portion of reality and that representation has a structure with nodes that stand for certain entities and edges that state some direct or indirect relationship between pairs of entities." [] comment: The algorithm might involve also generating or creating the network structure in addition to operating on it. -is_a: IAO:0000064 ! algorithm +is_a: IAO:0000064 property_value: http://purl.org/dc/elements/1.1/date "2022-09-18T18:00:00" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5410,7 +5490,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000613 name: laboratory testing capacity def: "An action specification giving the number of laboratory tests of a certain type that it is possible to perform in a given population during a specific time interval." [] -is_a: IAO:0000007 ! action specification +is_a: IAO:0000007 property_value: http://purl.org/dc/elements/1.1/date "2022-09-18T18:21" xsd:string property_value: IAO:0000111 "laboratory testing capacity action specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5419,7 +5499,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000614 name: weather data set def: "A data set about the Earth's atmospheric weather" [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 property_value: http://purl.org/dc/elements/1.1/date "2022-09-18T18:34:00" xsd:string property_value: IAO:0000111 "data set about Earth's atmospheric weather" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5429,9 +5509,10 @@ id: APOLLO_SV:00000615 name: human monkeypox def: "A monkeypox disease inhering in a human being." [] comment: requested by MIDAS CC -is_a: DOID:3292 ! monkeypox -intersection_of: DOID:3292 ! monkeypox +is_a: DOID:3292 +intersection_of: DOID:3292 intersection_of: RO:0000052 NCBITaxon:9606 +relationship: RO:0000052 NCBITaxon:9606 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 @@ -5466,7 +5547,7 @@ property_value: IAO:0000118 "sewage surveillance data" xsd:string id: APOLLO_SV:00000619 name: population density datum def: "A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region." [] -is_a: IAO:0000032 ! scalar measurement datum +is_a: IAO:0000032 property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -5493,6 +5574,7 @@ 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 +is_a: APOLLO_SV:00000648 ! cumulative case count 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 @@ -5503,6 +5585,7 @@ def: "A count of cases in an epidemic that is about a proper part of the tempora 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 +is_a: APOLLO_SV:00000649 ! incident case count 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 @@ -5553,57 +5636,57 @@ property_value: IAO:0000600 "A count of infections in a population during a part [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 +def: "A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000642 ! cumulative infection count 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 +def: "An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval." [] +is_a: APOLLO_SV:00000643 ! incident infection count 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 +def: "A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000646 ! cumulative death count 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 +def: "An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." [] +is_a: APOLLO_SV:00000647 ! incident death count 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 +def: "A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000644 ! cumulative hospitalization count 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 +def: "An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." [] +is_a: APOLLO_SV:00000645 ! incident hospitalization count 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 +def: "A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000640 ! cumulative vaccination count 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 +def: "An incident vaccination count 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 reference interval." [] +is_a: APOLLO_SV:00000641 ! incident vaccination count property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] @@ -5629,17 +5712,116 @@ def: "A vaccination against respiratory syncytial virus via the administration o is_a: APOLLO_SV:00000142 ! vaccination property_value: IAO:0000117 "William R. Hogan" xsd:string +[Term] +id: APOLLO_SV:00000640 +name: cumulative vaccination count +def: "A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000641 +name: incident vaccination count +def: "A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000642 +name: cumulative infection count +def: "A count of infections in a population that is the total number of infections that occur during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000643 +name: incident infection count +def: "A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000644 +name: cumulative hospitalization count +def: "A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +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:00000645 +name: incident hospitalization count +def: "A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +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:00000646 +name: cumulative death count +def: "A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000647 +name: incident death count +def: "A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000648 +name: cumulative case count +def: "A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000497 ! count of disease cases +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000649 +name: incident case count +def: "A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000497 ! count of disease cases +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000650 +name: intent to have a ward vaccinated +def: "An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role." [] +comment: Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. +is_a: MF:0000073 +property_value: IAO:0000111 "guardian's intent to have a ward under their care vaccinated" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "The intent of a guardian to have a ward under their care vaccinated in the near future." xsd:string + +[Term] +id: APOLLO_SV:00000652 +name: intent to have a child vaccinated +def: "An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child." [] +comment: The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. +is_a: APOLLO_SV:00000650 ! intent to have a ward vaccinated +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "Intent to have one's child vaccinated." xsd:string + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification -is_a: IAO:0000007 ! action specification +is_a: IAO:0000007 property_value: IAO:0000111 "epidemic simulator action specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] id: APOLLO_SV:00000794 name: infectious disease control strategy action specification -is_a: IAO:0000007 ! action specification +is_a: IAO:0000007 property_value: IAO:0000111 "infectious disease control strategy action specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5654,9 +5836,10 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000796 name: dataset creating def: "A planned process that has a data set as its specified output." [] -is_a: OBI:0000011 ! planned process -intersection_of: OBI:0000011 ! planned process -intersection_of: OBI:0000299 IAO:0000100 ! data set +is_a: OBI:0000011 +intersection_of: OBI:0000011 +intersection_of: OBI:0000299 IAO:0000100 +relationship: OBI:0000299 IAO:0000100 property_value: IAO:0000111 "creating a data set" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "data set creation" xsd:string @@ -5667,9 +5850,10 @@ id: APOLLO_SV:00000797 name: creating a copyright license def: "A planned process that has a copyright license as its specified output." [] comment: Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time. -is_a: OBI:0000011 ! planned process -intersection_of: OBI:0000011 ! planned process +is_a: OBI:0000011 +intersection_of: OBI:0000011 intersection_of: OBI:0000299 APOLLO_SV:00000798 ! copyright license +relationship: OBI:0000299 APOLLO_SV:00000798 ! copyright license property_value: IAO:0000111 "creating a copyright license" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "copyright license creation" xsd:string @@ -5703,7637 +5887,49 @@ def: "A role borne by an organism in virtue of the fact that it is in intimate a is_a: BFO:0000023 property_value: IAO:0000111 "facultative role" xsd:string -[Term] -id: APOLLO_SV_00000001 -name: obsolete specificity of case detection -def: "The specificity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X." [] -comment: deprecated due to malformed URI and created anew. -property_value: APOLLO_SV:0000040 "specificityOfCaseDetection" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000600 "The specificity of a process or system that detects organisms who satisfy a case definition." xsd:string -is_obsolete: true - -[Term] -id: APOLLO_SV_00000002 -name: obsolete specificity of treatment detection -def: "the specificity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment" [] -comment: Deprecated due to malformed URI and created anew. -property_value: APOLLO_SV:0000040 "specificityOfTreatmentDetection" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000600 "the specificity of the process or system that detects organisms that have undergone a particular treatment" xsd:string +[Typedef] +id: APOLLO_SV:00000004 +name: basis of +is_a: ObsoleteProperty is_obsolete: true -[Term] -id: APOLLO_SV_00000003 -name: obsolete sensitivity of treatment detection -def: "the sensitivity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment" [] -comment: Deprecated due to malformed URI and created anew. -property_value: APOLLO_SV:0000040 "sensitivityOfTreatmentDetection" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000600 "the sensitivity of the process or system that detects organisms that have undergone a particular treatment" xsd:string +[Typedef] +id: APOLLO_SV:00000028 +name: obsolete is based on +comment: p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. +is_a: ObsoleteProperty is_obsolete: true -[Term] -id: BFO:0000027 -name: object_aggregate -comment: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries. -comment: Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital -comment: Synonyms: substance aggregate -is_a: BFO:0000040 - -[Term] -id: BFO:0000038 -property_value: APOLLO_SV:0000040 "Interval" xsd:string - -[Term] -id: BFO:0000182 -name: history -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 - -[Term] -id: CHEBI:36044 -name: antiviral drug -comment: The usage or intended usage of a drug product to act against a viral infection of a host. -is_a: BFO:0000023 - -[Term] -id: DOID:0060478 -name: Zika fever -def: "A viral infectious disease that has_material_basis in Zika virus, which is transmitted_by Aedes aegypti mosquitoes and targets neural progenitor cells and neuronal cells in all stages of maturity and has_symptom fever, has_symptom rash, has_symptom headaches and has_symptom joint pain." [] -synonym: "Zika virus disease" EXACT [] -xref: ICD10:U06 -xref: ICD10CM:A92.8 -xref: MESH:D000071243 -is_a: APOLLO_SV:00000239 ! infectious disease -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/doid.owl" xsd:string - -[Term] -id: DOID:12205 -name: dengue disease -namespace: disease_ontology -alt_id: DOID:0050142 -def: "A viral infectious disease that results_in infection, has_material_basis_in Dengue virus [NCBITaxon:12637] with four serotypes (Dengue virus 1, 2, 3 and 4), which are transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom severe headache, has_symptom severe pain behind the eyes, has_symptom joint pain, has_symptom muscle and bone pain, has_symptom rash, and has_symptom mild bleeding." [] -subset: zoonotic_infectious_disease -synonym: "breakbone fever" EXACT [] -synonym: "classic dengue" EXACT [] -synonym: "classical dengue" RELATED [] -synonym: "Dengue Fever" EXACT [] -xref: ICD10CM:A90 -xref: ICD9CM:061 -xref: MESH:D003715 -xref: NCI:C34528 -xref: SNOMEDCT_US_2016_03_01:154345006 -xref: SNOMEDCT_US_2016_03_01:266194002 -xref: SNOMEDCT_US_2016_03_01:38362002 -xref: UMLS_CUI:C0011311 -is_a: APOLLO_SV:00000239 ! infectious disease -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/doid.owl" xsd:string - -[Term] -id: DOID:12206 -name: dengue hemorrhagic fever -namespace: disease_ontology -def: "A dengue disease that occurs when a person experiences a second infection with a heterologous Dengue virus serotype, which is transmitted_by Aedes mosquito bite. The infection has_symptom hemorrhagic lesions of the skin, has_symptom thrombocytopenia, has_symptom reduction in the fluid part of the blood, and has_symptom high fever." [] -subset: zoonotic_infectious_disease -synonym: "Dengue haemorrhagic fever" RELATED [] -synonym: "DHF" EXACT [] -xref: ICD10CM:A91 -xref: MESH:D019595 -xref: NCI:C34683 -xref: SNOMEDCT_US_2016_03_01:186598001 -xref: SNOMEDCT_US_2016_03_01:186599009 -xref: SNOMEDCT_US_2016_03_01:20927009 -xref: UMLS_CUI:C0019100 -is_a: DOID:12205 ! dengue disease -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/doid.owl" xsd:string - -[Term] -id: DOID:3292 -name: monkeypox -namespace: disease_ontology -def: "A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus, which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy." [] -subset: NCIthesaurus -subset: zoonotic_infectious_disease -xref: GARD:10722 -xref: ICD10CM:B04 -xref: ICD9CM:059.01 -xref: MESH:D045908 -xref: NCI:C128421 -xref: SNOMEDCT_US_2021_09_01:240466002 -xref: UMLS_CUI:C0276180 -xref: url:http\://www.cdc.gov/ncidod/monkeypox/factsheet2.htm -is_a: APOLLO_SV:00000239 ! infectious disease -property_value: http://purl.org/dc/elements/1.1/type ECO:0007637 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl" xsd:string - -[Term] -id: DOID:8469 -name: influenza -namespace: disease_ontology -alt_id: DOID:8468 -def: "A viral infectious disease that results_in infection, located_in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness." [] -synonym: "flu" EXACT [] -synonym: "influenza with non-respiratory manifestation" EXACT [] -synonym: "Influenza with non-respiratory manifestation (disorder)" EXACT [] -synonym: "Influenza with other manifestations" EXACT [] -synonym: "Influenza with other manifestations (disorder)" EXACT [] -synonym: "Influenza with other manifestations NOS (disorder)" EXACT [] -xref: ICD10CM:J11.1 -xref: ICD9CM:487 -xref: MESH:D007251 -xref: NCI:C53482 -xref: SNOMEDCT_US_2016_03_01:155559006 -xref: SNOMEDCT_US_2016_03_01:155562009 -xref: SNOMEDCT_US_2016_03_01:195931008 -xref: SNOMEDCT_US_2016_03_01:266353003 -xref: SNOMEDCT_US_2016_03_01:266393000 -xref: SNOMEDCT_US_2016_03_01:6142004 -xref: UMLS_CUI:C0021400 -is_a: APOLLO_SV:00000239 ! infectious disease -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/doid.owl" xsd:string - -[Term] -id: DRON:00000005 -name: drug product -def: "a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role" [] -is_a: BFO:0000030 -property_value: http://purl.org/dc/elements/1.1/creator "William Hogan" xsd:string -property_value: IAO:0000117 "William Hogan" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/dron.owl" xsd:string - -[Term] -id: EFO:0004600 -name: genomic data -def: "Genomic data is data about the genomes of an organism." [] -is_a: IAO:0000100 ! data set -relationship: IAO:0000136 OBI:0100026 ! is about organism -property_value: IAO:0000117 "James Malone" xsd:string - -[Term] -id: ENVO:00010483 -name: environmental material -namespace: ENVO -def: "A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system." [] -comment: Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. -synonym: "portion of environmental material" EXACT [] -is_a: BFO:0000040 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo.owl" xsd:string - -[Term] -id: ENVO:01000203 -name: environmental condition -def: "An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system." [] -comment: A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional. -subset: envoPolar -xref: DOI:10.1186/2041-1480-4-43 -is_a: PATO:0001018 ! physical quality -property_value: IAO:0000114 IAO:0000121 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl" xsd:string -created_by: ORCID:0000-0002-4366-3088 -creation_date: 2013-04-07T14:35:18Z - -[Term] -id: ENVO:01000266 -name: water vapour -namespace: ENVO -def: "Water vapour is a vapour which is the gas phase of water." [] -comment: Perhaps a better relation between water vapour and water can be found in or added to RO? -synonym: "aqueous vapor" EXACT [] -synonym: "aqueous vapour" EXACT [] -synonym: "water vapor" EXACT [] -is_a: ENVO:01000797 ! gaseous environmental material -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo.owl" xsd:string -created_by: ORCID:0000-0002-4366-3088 -creation_date: 2013-10-10T07:58:18Z - -[Term] -id: ENVO:01000268 -name: atmospheric water vapour -namespace: ENVO -def: "Atmospheric water vapour is water vapour that is part of an atmosphere." [] -synonym: "atmospheric water vapor" EXACT [] -is_a: ENVO:01000266 ! water vapour -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo.owl" xsd:string -created_by: ORCID:0000-0002-4366-3088 -creation_date: 2013-10-10T08:22:07Z - -[Term] -id: ENVO:01000703 -name: hydrological precipitation process -def: "Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity." [] -comment: "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) -synonym: "precipitation" BROAD [] -is_a: ENVO:02500000 ! environmental system process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo.owl" xsd:string - -[Term] -id: ENVO:01000753 -name: air temperature -def: "A temperature that inheres in some portion of air." [] -is_a: ENVO:09200001 ! temperature of air -property_value: IAO:0000116 "Draft class. In discussion in Issue #278." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo.owl" xsd:string - -[Term] -id: ENVO:01000797 -name: gaseous environmental material -def: "A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely." [] -synonym: "gas" NARROW [] -is_a: ENVO:00010483 ! environmental material -property_value: IAO:0000116 "This class is to be populated by inference." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo.owl" xsd:string - -[Term] -id: ENVO:01001078 -name: weather -def: "Environmental variability which inheres in an astronomical body part or in outer space." [] -comment: This class refers to all weather, including atmospheric and space weather. Please use a subclass for more specificity. -xref: https://en.wikipedia.org/wiki/Space_weather -xref: https://en.wikipedia.org/wiki/Weather -is_a: ENVO:01001081 ! environmental variability -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl" xsd:string - -[Term] -id: ENVO:01001079 -name: atmospheric weather -def: "Weather which inheres in an atmosphere." [] -comment: This class refers to the common usage of "weather", referencing the state of a (part of) an astronomical body's atmosphere. -xref: https://en.wikipedia.org/wiki/Weather -is_a: ENVO:01001078 ! weather -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl" xsd:string - -[Term] -id: ENVO:01001081 -name: environmental variability -def: "A condition which inheres in an environmental system by virtue of that system undergoing variation in its composition, the distribution of the qualities its components bear, and/or in the processes which occur within it and which it participates in." [] -comment: This class is very general, but the nature of environmental variability is indeed quite variable. This class may be refined once we have more subclasses to consider. -is_a: ENVO:01000203 ! environmental condition -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl" xsd:string - -[Term] -id: ENVO:02500000 -name: environmental system process -comment: Should environmental feature become something more towards a disposition, the assert would be updated to something like "has participant (environmental system or (material entity and has disposition some environmental feature))". There are several issues surrounding the reconcilliation of environmental feature and environmental system, both theoretical and practical. -is_a: BFO:0000015 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo.owl" xsd:string - -[Term] -id: ENVO:09200000 -name: temperature of environmental material -def: "The temperature of a environmental material." [] -synonym: "environmental material temperature" EXACT [] -is_a: PATO:0000146 ! temperature -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo.owl" xsd:string - -[Term] -id: ENVO:09200001 -name: temperature of air -def: "The temperature of a air." [] -synonym: "air temperature" EXACT [] -is_a: ENVO:09200000 ! temperature of environmental material -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/envo.owl" xsd:string - -[Term] -id: ERO:0000657 -name: metagenomics analysis -def: "A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research." [] -is_a: OBI:0000011 ! planned process -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "PERSON: Nicole Vasilevsky" xsd:string -property_value: IAO:0000118 "community genomic analysis" xsd:string -property_value: IAO:0000118 "ecogenomic analysis" xsd:string -property_value: IAO:0000118 "environmental genomic analysis" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Metagenomics" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ero.owl" xsd:string - -[Term] -id: FBcv:0000667 -name: website -namespace: pub_type -def: "A set of related web pages containing content such as text, images, video, audio, etc., prepared and maintained as a collection of information on a particular subject." [] -is_a: IAO:0000310 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/fbcv.owl" xsd:string - -[Term] -id: FBcv:0000787 -name: journal -namespace: pub_type -def: "A publication issued on a regular, ongoing basis containing separate research articles and other writings such as reviews, comments and conference reports." [] -synonym: "Periodicals" RELATED [] -xref: MeSH:D020492 -is_a: IAO:0000030 ! information content entity -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/fbcv.owl" xsd:string -created_by: djs93 -creation_date: 2012-07-10T04:08:06Z - -[Term] -id: FBcv_0000209 -name: news article -namespace: pub_type -comment: Originally imported into Apollo-SV for purpose of indexing in OBC.ide news articles relevant to infectious disease epidemiology. -subset: camcur -is_a: IAO:0000310 -property_value: IAO:0000412 "http://purl.org/obo/owl/flybase_vocab" xsd:string - -[Term] -id: GEO:000000372 -def: "A site designated by some relative spatial orientation." [] -property_value: APOLLO_SV:0000040 "Location" xsd:string -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000600 "An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers." xsd:string - -[Term] -id: GO:0000003 -name: reproduction -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." [] -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.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:0006950 -name: response to stress -namespace: biological_process -def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [] -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 -subset: goslim_aspergillus -subset: goslim_candida -subset: goslim_chembl -subset: goslim_generic -subset: goslim_metagenomics -subset: goslim_plant -subset: gosubset_prok -synonym: "response to abiotic stress" RELATED [] -synonym: "response to biotic stress" RELATED [] -is_a: GO:0050896 ! response to stimulus -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0006952 -name: defense response -namespace: biological_process -alt_id: GO:0002217 -alt_id: GO:0042829 -def: "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [] -subset: gosubset_prok -synonym: "antimicrobial peptide activity" RELATED [] -synonym: "defence response" EXACT [] -synonym: "defense/immunity protein activity" RELATED [] -synonym: "physiological defense response" EXACT [] -is_a: GO:0006950 ! response to stress -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0006954 -name: inflammatory response -namespace: biological_process -def: "The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages." [] -comment: This term was improved by GO_REF:0000022. It was moved. -synonym: "Inflammation" BROAD [] -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:0007562 -name: eclose -name: eclosion -namespace: biological_process -def: "The emergence of an adult insect from a pupa case." [] -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 - -[Term] -id: GO:0007565 -name: female pregnancy -namespace: biological_process -def: "The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth." [] -subset: goslim_chembl -synonym: "carrying of young" RELATED [] -synonym: "gestation" EXACT [] -xref: Wikipedia:Gestation -is_a: GO:0044703 ! multi-organism reproductive process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0007567 -name: parturition -namespace: biological_process -def: "The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs." [] -synonym: "egg laying" NARROW [] -synonym: "giving birth" EXACT [] -is_a: GO:0044703 ! multi-organism reproductive process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0007568 -name: aging -namespace: biological_process -alt_id: GO:0016280 -subset: goslim_generic -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 - -[Term] -id: GO:0007610 -name: behavior -namespace: biological_process -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 -subset: goslim_plant -subset: gosubset_prok -synonym: "behavioral response to stimulus" EXACT [] -synonym: "behaviour" EXACT [] -synonym: "behavioural response to stimulus" EXACT [] -xref: Wikipedia:Behavior -is_a: GO:0008150 ! biological process -property_value: APOLLO_SV:0000040 "Behavior" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0007617 -name: mating behavior -namespace: biological_process -def: "The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes." [] -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 - -[Term] -id: GO:0008150 -name: biological process -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." [] -is_a: BFO:0000015 -property_value: IAO:0000111 "biological_process" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string - -[Term] -id: GO:0010259 -name: multicellular organismal aging -namespace: biological_process -def: "An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700)." [] -is_a: GO:0007568 ! aging -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0010941 -name: regulation of cell death -namespace: biological_process -def: "Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [] -is_a: GO:0050794 ! regulation of cellular process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0018991 -name: oviposition -namespace: biological_process -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 - -[Term] -id: GO:0019048 -name: modulation by virus of host morphology or physiology -namespace: biological_process -alt_id: GO:0044792 -def: "The process in which a virus effects a change in the structure or processes of its host organism." [] -subset: goslim_virus -subset: virus_checked -synonym: "host-virus interaction" EXACT [] -synonym: "modulation by virus of host anatomical structure or process" EXACT [] -synonym: "modulation by virus of host anatomy or process" EXACT [] -synonym: "viral interaction with host" EXACT [] -synonym: "viral-host process" EXACT [] -synonym: "virus-host interaction" BROAD [] -synonym: "virus-host process" EXACT [] -xref: Reactome:REACT_6323 -xref: VZ:886 -is_a: GO:0044003 ! modification by symbiont of host morphology or physiology -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0019051 -name: induction by virus of host apoptotic process -namespace: biological_process -def: "The set of viral processes that induce an apoptotic process in infected host cells, facilitating release and spread of progeny virions." [] -synonym: "activation by virus of host apoptosis" EXACT [] -synonym: "activation by virus of host apoptotic programmed cell death" EXACT [] -synonym: "activation of apoptosis in host by virus" EXACT [] -synonym: "induction by virus of host apoptosis" NARROW [] -synonym: "induction by virus of host apoptotic programmed cell death" EXACT [] -synonym: "induction of apoptosis in host by virus" EXACT [] -is_a: GO:0060139 ! positive regulation of apoptotic process by virus -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0019054 -name: modulation by virus of host process -namespace: biological_process -def: "The process in which a virus effects a change in the processes and activities of its host organism." [] -subset: virus_checked -synonym: "modification by virus of host cellular process" EXACT [] -synonym: "modulation of cellular process in host by virus" RELATED [] -synonym: "regulation by virus of host cellular process" EXACT [] -synonym: "regulation of cellular process in host by virus" EXACT [] -synonym: "regulation of host cellular process by virus" EXACT [] -synonym: "viral host cell process manipulation" EXACT [] -xref: Reactome:REACT_6222 -is_a: GO:0019048 ! modulation by virus of host morphology or physiology -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0019098 -name: reproductive behavior -namespace: biological_process -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 - -[Term] -id: GO:0022414 -name: reproductive process -namespace: biological_process -def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [] -subset: gosubset_prok -is_a: GO:0008150 ! biological process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0032502 -name: developmental process -namespace: biological_process -subset: goslim_aspergillus -subset: goslim_pir -subset: gosubset_prok -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 - -[Term] -id: GO:0032504 -name: multicellular organism reproduction -namespace: biological_process -def: "The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [] -is_a: GO:0000003 ! reproduction -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0033057 -name: multicellular organismal reproductive behavior -namespace: biological_process -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 - -[Term] -id: GO:0035176 -name: social behavior -namespace: biological_process -def: "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." [] -comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. -synonym: "cooperative behavior" RELATED [] -synonym: "social behaviour" EXACT [] -xref: Wikipedia:Social_behavior -is_a: GO:0044419 ! interspecies interaction between organisms -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0035821 -name: modification of morphology or physiology of other organism -namespace: biological_process -def: "The process in which an organism effects a change in the structure or processes of a second organism." [] -synonym: "regulation of morphology of other organism" NARROW [] -synonym: "regulation of morphology or physiology of other organism" RELATED [] -synonym: "regulation of physiological process of other organism" NARROW [] -synonym: "regulation of physiology of other organism" NARROW [] -is_a: GO:0065008 ! regulation of biological quality -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string -created_by: rfoulger -creation_date: 2011-04-21T01:31:51Z - -[Term] -id: GO:0039651 -name: induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process -namespace: biological_process -def: "Any process in which a virus increases the frequency, rate or extent of host cysteine-type endopeptidase activity (also called caspase activity) which contributes to the apoptotic process." [] -synonym: "activation of host caspases by virus" NARROW [] -synonym: "induction by virus of host caspase activity" NARROW [] -is_a: GO:0019051 ! induction by virus of host apoptotic process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string -created_by: rfoulger -creation_date: 2012-10-09T15:44:29Z - -[Term] -id: GO:0043067 -name: regulation of programmed cell death -namespace: biological_process -alt_id: GO:0043070 -def: "Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [] -synonym: "regulation of non-apoptotic programmed cell death" NARROW [] -is_a: GO:0010941 ! regulation of cell death -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0044003 -name: modification by symbiont of host morphology or physiology -namespace: biological_process -def: "The process in which a symbiont organism effects a change in the structure or processes of its host organism." [] -subset: gosubset_prok -is_a: GO:0051817 ! modification of morphology or physiology of other organism involved in symbiotic interaction -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -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 - -[Term] -id: GO:0044419 -name: interspecies interaction between organisms -def: "Any process in which an organism has an effect on an organism of a different species." [] -is_a: GO:0051704 ! multi-organism process - -[Term] -id: GO:0044531 -name: modulation of programmed cell death in other organism -namespace: biological_process -def: "A process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism." [] -is_a: GO:0043067 ! regulation of programmed cell death -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string -created_by: janelomax -creation_date: 2012-03-20T04:48:41Z - -[Term] -id: GO:0044703 -name: multi-organism reproductive process -namespace: biological_process -def: "A biological process that directly contributes to the process of producing new individuals, involving another organism." [] -is_a: GO:0022414 ! reproductive process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string -created_by: janelomax -creation_date: 2012-09-19T15:56:30Z - -[Term] -id: GO:0044705 -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 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string -created_by: janelomax -creation_date: 2012-09-19T16:02:12Z - -[Term] -id: GO:0048609 -name: multicellular organismal reproductive process -namespace: biological_process -def: "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs." [] -synonym: "organismal reproductive process" BROAD [] -synonym: "reproductive process in a multicellular organism" EXACT [] -is_a: GO:0022414 ! reproductive process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0050789 -name: regulation of biological process -namespace: biological_process -alt_id: GO:0050791 -def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [] -subset: goslim_aspergillus -subset: goslim_candida -subset: gosubset_prok -synonym: "regulation of physiological process" EXACT [] -is_a: GO:0065007 ! biological regulation -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0050794 -name: regulation of cellular process -namespace: biological_process -alt_id: GO:0051244 -def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [] -subset: gosubset_prok -synonym: "regulation of cellular physiological process" EXACT [] -is_a: GO:0050789 ! regulation of biological process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0050896 -name: response to stimulus -namespace: biological_process -alt_id: GO:0051869 -def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [] -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 -subset: goslim_pir -subset: gosubset_prok -synonym: "physiological response to stimulus" EXACT [] -is_a: GO:0008150 ! biological process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0051234 -name: establishment of localization -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 "http://purl.obolibrary.org/obo/ido.owl" xsd:string - -[Term] -id: GO:0051701 -name: interaction with host -namespace: biological_process -def: "An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism." [] -subset: gosubset_prok -is_a: GO:0044419 ! interspecies interaction between organisms -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -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 - -[Term] -id: GO:0051705 -name: multi-organism behavior -namespace: biological_process -alt_id: GO:0023032 -alt_id: GO:0044709 -def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [] -subset: goslim_pir -synonym: "behavioral interaction between organisms" EXACT [] -synonym: "behavioral interaction with other organism" EXACT [] -synonym: "behavioral signaling" NARROW [] -synonym: "behavioral signalling" NARROW [] -synonym: "behavioural interaction between organisms" EXACT [] -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/releases/2019-07-01/go.owl" xsd:string - -[Term] -id: GO:0051817 -name: modification of morphology or physiology of other organism involved in symbiotic interaction -namespace: biological_process -def: "The process in which an organism effects a change in the structure or processes of a second organism, where the two organisms are in a symbiotic interaction." [] -subset: gosubset_prok -synonym: "modification of morphology or physiology of other organism during symbiotic interaction" RELATED [] -synonym: "modulation of morphology or physiology of other organism during symbiotic interaction" RELATED [] -synonym: "regulation of morphology of other organism during symbiotic interaction" NARROW [] -synonym: "regulation of morphology or physiology of other organism during symbiotic interaction" RELATED [] -synonym: "regulation of physiological process in other organism during symbiotic interaction" NARROW [] -synonym: "regulation of physiology of other organism during symbiotic interaction" NARROW [] -is_a: GO:0035821 ! modification of morphology or physiology of other organism -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0052040 -name: modulation by symbiont of host programmed cell death -namespace: biological_process -alt_id: GO:0052152 -def: "Any process in which an organism modulates the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [] -subset: gosubset_prok -synonym: "modulation by symbiont of host non-apoptotic programmed cell death" NARROW [] -synonym: "modulation of host PCD" EXACT [] -is_a: GO:0052248 ! modulation of programmed cell death in other organism involved in symbiotic interaction -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0052042 -name: positive regulation by symbiont of host programmed cell death -namespace: biological_process -alt_id: GO:0012504 -alt_id: GO:0052044 -alt_id: GO:0052045 -alt_id: GO:0052153 -alt_id: GO:0052397 -alt_id: GO:0052400 -def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [] -subset: gosubset_prok -synonym: "activation by organism of host programmed cell death" EXACT [] -synonym: "activation by organism of non-apoptotic programmed cell death in other organism" NARROW [] -synonym: "activation by organism of programmed cell death in other organism during symbiotic interaction" EXACT [] -synonym: "activation by symbiont of host programmed cell death" NARROW [] -synonym: "enhancement of host programmed cell death" EXACT [] -synonym: "enhancement of host programmed cell death by organism" EXACT [] -synonym: "induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction" NARROW [] -synonym: "induction by organism of programmed cell death in other organism during symbiotic interaction" RELATED [] -synonym: "induction by organism of programmed cell death in other organism involved in symbiotic interaction" EXACT [] -synonym: "induction by symbiont of host programmed cell death" EXACT [] -synonym: "induction of non-apoptotic programmed cell death by other organism" RELATED [] -synonym: "positive regulation by symbiont of host non-apoptotic programmed cell death" NARROW [] -synonym: "stimulation by symbiont of host programmed cell death" NARROW [] -synonym: "upregulation by symbiont of host programmed cell death" EXACT [] -is_a: GO:0052040 ! modulation by symbiont of host programmed cell death -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0052151 -name: positive regulation by symbiont of host apoptotic process -namespace: biological_process -alt_id: GO:0033669 -alt_id: GO:0052030 -def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction." [] -comment: Note that term is to be used to annotate gene products in the symbiont. To annotate host gene products, consider the biological process term 'positive regulation of apoptosis ; GO:0043065'. -subset: gosubset_prok -synonym: "activation by organism of host apoptosis" EXACT [] -synonym: "activation by organism of host apoptotic programmed cell death" EXACT [] -synonym: "activation by symbiont of host apoptosis" NARROW [] -synonym: "induction by organism of host apoptotic programmed cell death" EXACT [] -synonym: "induction by symbiont of host apoptosis" EXACT [] -synonym: "positive regulation by organism of host apoptotic programmed cell death" EXACT [] -synonym: "positive regulation by symbiont of host apoptosis" NARROW [] -synonym: "stimulation by symbiont of host apoptosis" NARROW [] -synonym: "up regulation by organism of host apoptotic programmed cell death" EXACT [] -synonym: "up regulation by symbiont of host apoptosis" EXACT [] -synonym: "up-regulation by organism of host apoptotic programmed cell death" EXACT [] -synonym: "up-regulation by symbiont of host apoptosis" EXACT [] -synonym: "upregulation by organism of host apoptotic programmed cell death" EXACT [] -synonym: "upregulation by symbiont of host apoptosis" EXACT [] -is_a: GO:0052501 ! positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0052248 -name: modulation of programmed cell death in other organism involved in symbiotic interaction -namespace: biological_process -alt_id: GO:0052459 -def: "Any process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism, where the two organisms are in a symbiotic interaction." [] -subset: gosubset_prok -synonym: "modulation by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction" NARROW [] -synonym: "modulation of programmed cell death in other organism during symbiotic interaction" RELATED [] -is_a: GO:0044531 ! modulation of programmed cell death in other organism -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0052501 -name: positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction -namespace: biological_process -alt_id: GO:0052388 -def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism, where the two organisms are in a symbiotic interaction." [] -subset: gosubset_prok -synonym: "activation by organism of apoptosis in other organism during symbiotic interaction" NARROW [] -synonym: "activation by organism of apoptotic programmed cell death in other organism during symbiotic interaction" RELATED [] -synonym: "induction by organism of apoptosis in other organism during symbiotic interaction" RELATED [] -synonym: "induction by organism of apoptosis in other organism involved in symbiotic interaction" EXACT [] -synonym: "induction by organism of apoptotic programmed cell death in other organism during symbiotic interaction" RELATED [] -synonym: "positive regulation by organism of apoptosis in other organism during symbiotic interaction" RELATED [] -synonym: "positive regulation by organism of apoptosis in other organism involved in symbiotic interaction" NARROW [] -synonym: "positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction" NARROW [] -synonym: "positive regulation by organism of apoptotic programmed cell death in other organism during symbiotic interaction" RELATED [] -synonym: "stimulation by organism of apoptosis in other organism during symbiotic interaction" NARROW [] -synonym: "up regulation by organism of apoptosis in other organism during symbiotic interaction" RELATED [] -synonym: "up-regulation by organism of apoptosis in other organism during symbiotic interaction" RELATED [] -synonym: "upregulation by organism of apoptosis in other organism during symbiotic interaction" RELATED [] -is_a: GO:0052042 ! positive regulation by symbiont of host programmed cell death -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0060139 -name: positive regulation of apoptotic process by virus -namespace: biological_process -def: "Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process." [] -synonym: "positive regulation of apoptosis by virus" NARROW [] -is_a: GO:0052151 ! positive regulation by symbiont of host apoptotic process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0060153 -name: modulation by virus of host cell cycle -namespace: biological_process -def: "Any viral process that modulates the rate or extent of progression through the cell cycle." [] -subset: goslim_virus -synonym: "modulation of host cell cycle by virus" EXACT [] -synonym: "regulation by virus of host cell cycle" EXACT [] -synonym: "regulation of host cell cycle by virus" EXACT [] -synonym: "viral process regulating host cell cycle" EXACT [] -xref: VZ:1636 -is_a: GO:0019054 ! modulation by virus of host process -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0060403 -name: post-mating oviposition -namespace: biological_process -is_a: GO:0018991 ! oviposition -property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string - -[Term] -id: GO:0065007 -name: biological regulation -namespace: biological_process -def: "Any process that modulates a measurable attribute of any biological process, quality or function." [] -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" xsd:string - -[Term] -id: GO:0065008 -name: regulation of biological quality -namespace: biological_process -def: "Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." [] -subset: gosubset_prok -synonym: "regulation of biological attribute" EXACT [] -synonym: "regulation of biological characteristic" EXACT [] -is_a: GO:0065007 ! biological regulation -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string - -[Term] -id: GO:0071684 -name: organism emergence from protective structure -namespace: biological_process -is_a: GO:0008150 ! biological process -property_value: IAO:0000412 "http://purl.org/obo/owl/gene_ontology" xsd:string - -[Term] -id: IAO:0000001 -property_value: IAO:0000114 IAO:0000120 - -[Term] -id: IAO:0000003 -name: measurement unit label -def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." [] -is_a: IAO:0000009 -property_value: APOLLO_SV:0000040 "unitId" xsd:string -property_value: IAO:0000111 "measurement unit label" xsd:string -property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." xsd:string -property_value: IAO:0000116 "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string - -[Term] -id: IAO:0000005 -name: objective specification -def: "a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." [] -is_a: IAO:0000033 ! directive information entity -property_value: IAO:0000111 "objective specification" xsd:string -property_value: IAO:0000112 "purpose of a study; support of hypothesis, discovery of new information" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "2009-03-16: original definition when imported from OBI read: \"objective is an\nnon realizable information entity which can serve as that proper part\nof a plan towards which the realization of the plan is directed.\"" xsd:string -property_value: IAO:0000116 "Answers the question, why did you do this experiment?" xsd:string -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Barry Smith" xsd:string -property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string -property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string -property_value: IAO:0000119 "OBI Plan and Planned Process/Roles Branch" xsd:string -property_value: IAO:0000119 "OBI_0000217" xsd:string - -[Term] -id: IAO:0000007 -name: action specification -def: "a directive information entity that describes an action the bearer will take" [] -is_a: IAO:0000033 ! directive information entity -property_value: IAO:0000112 "Pour the contents of flask 1 into flask 2" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string - -[Term] -id: IAO:0000009 -def: "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" [] -property_value: APOLLO_SV:0000040 "label" xsd:string -property_value: IAO:0000111 "label" xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n" xsd:string -property_value: IAO:0000117 "GROUP: IAO" xsd:string - -[Term] -id: IAO:0000010 -name: software -def: "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." [] -is_a: IAO:0000104 ! plan specification -property_value: IAO:0000111 "software" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178" xsd:string -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string -property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string -property_value: IAO:0000119 "GROUP: OBI" xsd:string - -[Term] -id: IAO:0000027 -name: data item -def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] -property_value: IAO:0000111 "data item" xsd:string -property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string -property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string -property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string -property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string -property_value: IAO:0000118 "data" xsd:string - -[Term] -id: IAO:0000028 -name: symbol -def: "a smallish, word-like datum..." [] -property_value: IAO:0000111 "symbol" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "20091104, MC: this needs work and will most probably change" xsd:string -property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string - -[Term] -id: IAO:0000029 -property_value: IAO:0000114 IAO:0000123 - -[Term] -id: IAO:0000030 -name: information content entity -def: "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" [] -is_a: BFO:0000031 -property_value: IAO:0000111 "information content entity" xsd:string -property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string -property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000119 "OBI_0000142" xsd:string - -[Term] -id: IAO:0000032 -name: scalar measurement datum -def: "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." [] -is_a: IAO:0000109 ! measurement datum -property_value: IAO:0000112 "10 feet. 3 ml." xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" xsd:string -property_value: IAO:0000116 "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them." xsd:string -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string - -[Term] -id: IAO:0000033 -name: directive information entity -def: "An information content entity whose concretizations indicate to their bearer how to realize them in a process." [] -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be\nconcretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string -property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" xsd:string -property_value: IAO:0000116 "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan" xsd:string -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string - -[Term] -id: IAO:0000038 -property_value: IAO:0000114 IAO:0000125 - -[Term] -id: IAO:0000055 -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000114 IAO:0000124 - -[Term] -id: IAO:0000064 -name: algorithm -def: "A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] -is_a: IAO:0000104 ! plan specification -property_value: IAO:0000111 "algorithm" xsd:string -property_value: IAO:0000112 "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string -property_value: IAO:0000119 "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)" xsd:string -property_value: IAO:0000119 "OBI_0000270" xsd:string - -[Term] -id: IAO:0000100 -name: data set -def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." [] -property_value: APOLLO_SV:0000040 "dataSets" xsd:string -property_value: IAO:0000111 "data set" xsd:string -property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string -property_value: IAO:0000117 "person:Allyson Lister" xsd:string -property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string -property_value: IAO:0000119 "group:OBI" xsd:string -property_value: IAO:0000119 "OBI_0000042" xsd:string - -[Term] -id: IAO:0000104 -name: plan specification -def: "a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications." [] -comment: 2/3/2009 Comment from OBI review.\n \n Action specification not well enough specified.\n Conditional specification not well enough specified.\n Question whether all plan specifications have objective specifications.\n \n Request that IAO either clarify these or change definitions not to use them -is_a: IAO:0000033 ! directive information entity -relationship: BFO:0000051 IAO:0000005 ! objective specification -relationship: BFO:0000051 IAO:0000007 ! action specification -property_value: IAO:0000111 "plan specification" xsd:string -property_value: IAO:0000112 "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000116 "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string -property_value: IAO:0000116 "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved" xsd:string -property_value: IAO:0000117 "Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string -property_value: IAO:0000119 "OBI_0000344" xsd:string - -[Term] -id: IAO:0000109 -name: measurement datum -def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] -is_a: IAO:0000027 ! data item -property_value: IAO:0000111 "measurement datum" xsd:string -property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:string -property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string -property_value: IAO:0000119 "group:OBI" xsd:string -property_value: IAO:0000119 "OBI_0000305" xsd:string - -[Term] -id: IAO:0000129 -name: version number -def: "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name." [] -is_a: IAO:0000028 ! symbol -property_value: IAO:0000111 "version number" xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000114 IAO:0000124 -property_value: IAO:0000116 "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version" xsd:string -property_value: IAO:0000117 "GROUP: IAO" xsd:string - -[Term] -id: IAO:0000178 -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000114 IAO:0000122 - -[Term] -id: IAO:0000300 -property_value: IAO:0000114 IAO:0000123 - -[Term] -id: IAO:0000310 -property_value: IAO:0000114 IAO:0000120 - -[Term] -id: IAO:0000408 -property_value: IAO:0000114 IAO:0000123 - -[Term] -id: IAO:0000416 -name: time measurement datum -def: "A scalar measurement datum that is the result of measuring a temporal interval" [] -is_a: IAO:0000032 ! scalar measurement datum -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string -property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string - -[Term] -id: IAO:0000572 -property_value: IAO:0000114 IAO:0000125 - -[Term] -id: IAO:0000577 -property_value: IAO:0000114 IAO:0000120 - -[Term] -id: IAO:0000582 -name: time stamped measurement datum -is_a: IAO:0000109 ! measurement datum -relationship: IAO:0000581 IAO:0000416 ! has time stamp time measurement datum -relationship: IAO:0000583 IAO:0000109 ! has measurement datum measurement datum -property_value: IAO:0000114 IAO:0000123 - -[Term] -id: IAO:0000584 -name: time sampled measurement data set -def: "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time." [] -is_a: IAO:0000100 ! data set -relationship: BFO:0000051 IAO:0000582 ! time stamped measurement datum -property_value: IAO:0000112 "pmid:20604925 - time-lapse live cell microscopy" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Alan Ruttenberg" xsd:string -property_value: IAO:0000118 "experimental time series" xsd:string - -[Term] -id: IAO:0000594 -property_value: IAO:0000114 IAO:0000123 - -[Term] -id: IAO:0020000 -property_value: APOLLO_SV:0000040 "name" xsd:string - -[Term] -id: NBO:0000034 -name: sexual activity -is_a: GO:0019098 ! reproductive behavior -property_value: created:by "George Gkoutos" xsd:string -property_value: creation:date "2011-04-14T01:03:39Z" xsd:string -property_value: http://purl.obolibrary.org/obo/def "\"Behaviour related to the activity which primary purpose is the sexual reproduction.\" [NBO:GVG]" xsd:string -property_value: http://purl.obolibrary.org/obo/namespace "behavior_ontology" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/MF.owl" xsd:string - -[Term] -id: NCBITaxon:10090 -name: Mus musculus -is_a: NCBITaxon:2759 ! Eukaryota -property_value: IAO:0000111 "Mus musculus" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000118 "House mouse" xsd:string - -[Term] -id: NCBITaxon:10239 -name: Virus -is_a: OBI:0100026 ! organism - -[Term] -id: NCBITaxon:10240 -name: Poxviridae -is_a: NCBITaxon:35237 ! dsDNA virus, no RNA stage - -[Term] -id: NCBITaxon:10241 -name: Chordopoxvirinae -is_a: NCBITaxon:10240 ! Poxviridae - -[Term] -id: NCBITaxon:10242 -name: Orthopoxvirus -is_a: NCBITaxon:10241 ! Chordopoxvirinae - -[Term] -id: NCBITaxon:10244 -name: Monkeypox virus -is_a: NCBITaxon:10242 ! Orthopoxvirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "monkey pox virus" xsd:string - -[Term] -id: NCBITaxon:10255 -name: Variola virus -is_a: NCBITaxon:10242 ! Orthopoxvirus - -[Term] -id: NCBITaxon:102793 -name: H5N1 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H5N1 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:10292 -name: Herpesviridae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:548681 ! Herpesvirales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:10293 -name: Alphaherpesvirinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:10292 ! Herpesviridae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:10294 -name: Simplexvirus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:10293 ! Alphaherpesvirinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:10298 -name: Human alphaherpesvirus 1 -namespace: ncbi_taxonomy -synonym: "Herpes simplex virus 1" RELATED genbank_synonym [] -synonym: "herpes simplex virus 1 HSV-1" RELATED synonym [] -synonym: "herpes simplex virus HSV-1" RELATED synonym [] -synonym: "Herpes simplex virus type 1" EXACT genbank_common_name [] -synonym: "herpes simplex virus type 1 HSV-1" RELATED synonym [] -synonym: "herpes simplex virus type 1 HSV1" RELATED synonym [] -synonym: "herpes simplex virus type-1 HSV-1" RELATED synonym [] -synonym: "HSV-1" BROAD acronym [] -synonym: "HSV1" BROAD acronym [] -synonym: "Human herpesvirus 1" RELATED synonym [] -synonym: "Human herpesvirus type 1" RELATED synonym [] -synonym: "Human Herpesvirus-1" RELATED misspelling [] -xref: GC_ID:1 -is_a: NCBITaxon:10294 ! Simplexvirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:10310 -name: Human alphaherpesvirus 2 -namespace: ncbi_taxonomy -synonym: "Herpes simplex virus (type 2)" RELATED synonym [] -synonym: "Herpes simplex virus 2" RELATED genbank_synonym [] -synonym: "Herpes simplex virus II" RELATED synonym [] -synonym: "Herpes simplex virus type 2" RELATED synonym [] -synonym: "Herpes simplex virus type 2 (HSV-2)" EXACT equivalent_name [] -synonym: "herpes simplex virus type 2 HSV-2" RELATED synonym [] -synonym: "HSV2" BROAD acronym [] -synonym: "Human herpesvirus 2" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:10294 ! Simplexvirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:10319 -name: Varicellovirus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:10293 ! Alphaherpesvirinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:10335 -name: Human herpesvirus 3 -namespace: ncbi_taxonomy -synonym: "HHV-3" BROAD genbank_acronym [] -synonym: "Human alphaherpesvirus 3" RELATED synonym [] -synonym: "Human herpes virus 3" RELATED synonym [] -synonym: "Varicella Zoster Virus" RELATED synonym [] -synonym: "varicella zoster virus VZV" RELATED synonym [] -synonym: "Varicella-zoster virus" EXACT genbank_common_name [] -synonym: "varicella-zoster virus VZV" RELATED synonym [] -synonym: "VZV" BROAD acronym [] -xref: GC_ID:1 -is_a: NCBITaxon:10319 ! Varicellovirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:10345 -name: Suid herpesvirus 1 -namespace: ncbi_taxonomy -alt_id: NCBITaxon:44156 -synonym: "Alphaherpesvirus pseudorabies virus PRV" RELATED synonym [] -synonym: "Aujeszky's disease virus" RELATED synonym [] -synonym: "PRV" BROAD acronym [] -synonym: "Pseudorabies virus" EXACT genbank_common_name [] -synonym: "Pseudorabies Virus PRV" RELATED synonym [] -synonym: "Suid herpesvirus type 1" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:10319 ! Varicellovirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:10404 -name: Hepadnaviridae -namespace: ncbi_taxonomy -synonym: "hepatitis B-type viruses" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:35268 ! Retro-transcribing viruses -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:10405 -name: Orthohepadnavirus -namespace: ncbi_taxonomy -synonym: "mammalian hepatitis B-type viruses" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:10404 ! Hepadnaviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:10407 -name: Hepatitis B virus -namespace: ncbi_taxonomy -synonym: "HBV" BROAD acronym [] -synonym: "hepatitis B virus (HBV)" RELATED synonym [] -synonym: "hepatitis B virus HBV" RELATED synonym [] -synonym: "hepatitis B virus, HBV" RELATED synonym [] -synonym: "Human hepatitis B virus" RELATED synonym [] -synonym: "human hepatitis B virus HBV" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:10405 ! Orthohepadnavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1045010 -name: Escherichia coli O157 -namespace: ncbi_taxonomy -xref: GC_ID:11 -is_a: NCBITaxon:562 ! Escherichia coli - -[Term] -id: NCBITaxon:1056966 -name: Aedini -is_a: NCBITaxon:43817 ! Culicinae - -[Term] -id: NCBITaxon:106178 -name: canis group -namespace: ncbi_taxonomy -xref: GC_ID:11 -is_a: NCBITaxon:943 ! Ehrlichia -property_value: has_rank http://purl.obolibrary.org/obo/NCBITaxon_species_group - -[Term] -id: NCBITaxon:106179 -name: phagocytophilum group -namespace: ncbi_taxonomy -synonym: "phagocytophila group" EXACT equivalent_name [] -xref: GC_ID:11 -is_a: NCBITaxon:768 ! Anaplasma -property_value: has_rank http://purl.obolibrary.org/obo/NCBITaxon_species_group - -[Term] -id: NCBITaxon:10880 -name: Reoviridae -is_a: NCBITaxon:35325 ! dsRNA viruses -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:10912 -name: Rotavirus -is_a: NCBITaxon:689832 ! Sedoreovirinae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Rotaviruses" xsd:string - -[Term] -id: NCBITaxon:11018 -name: Togaviridae -is_a: NCBITaxon:35278 ! ssRNA positive-strand viruses, no DNA stage - -[Term] -id: NCBITaxon:11019 -name: Alphavirus -namespace: ncbi_taxonomy -synonym: "Alphaviridae" RELATED synonym [] -synonym: "arboviruses group A" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:11018 ! Togaviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:11020 -name: Barmah Forest virus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11019 ! Alphavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11021 -name: Eastern equine encephalitis virus -namespace: ncbi_taxonomy -synonym: "eastern equine encephalomyelitis EEE" RELATED synonym [] -synonym: "Eastern equine encephalomyelitis virus" RELATED synonym [] -synonym: "eastern equine encephalomyelitis virus EEEV" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:177873 ! EEEV complex -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11029 -name: Ross River virus -namespace: ncbi_taxonomy -synonym: "RRV" BROAD acronym [] -xref: GC_ID:1 -is_a: NCBITaxon:11019 ! Alphavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11039 -name: Western equine encephalitis virus -namespace: ncbi_taxonomy -synonym: "Western equine encephaliomyelitis virus" RELATED misspelling [] -synonym: "Western equine encephalomyelitis virus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:177874 ! WEEV complex -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11040 -name: Rubivirus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11018 ! Togaviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:11041 -name: Rubella virus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11040 ! Rubivirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11050 -name: Flaviviridae -is_a: NCBITaxon:35278 ! ssRNA positive-strand viruses, no DNA stage - -[Term] -id: NCBITaxon:11051 -name: Flavivirus -namespace: ncbi_taxonomy -synonym: "arboviruses group B" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:11050 ! Flaviviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:11052 -name: Dengue virus group -is_a: NCBITaxon:11051 ! Flavivirus - -[Term] -id: NCBITaxon:11053 -name: Dengue virus 1 -is_a: NCBITaxon:12637 ! Dengue virus - -[Term] -id: NCBITaxon:11060 -name: Dengue virus 2 -is_a: NCBITaxon:12637 ! Dengue virus - -[Term] -id: NCBITaxon:11069 -name: Dengue virus 3 -is_a: NCBITaxon:12637 ! Dengue virus - -[Term] -id: NCBITaxon:11070 -name: Dengue virus 4 -is_a: NCBITaxon:12637 ! Dengue virus - -[Term] -id: NCBITaxon:11071 -name: Japanese encephalitis virus group -namespace: ncbi_taxonomy -synonym: "Japanese encephalitis viruses" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:11051 ! Flavivirus -property_value: has_rank NCBITaxon:subgenus - -[Term] -id: NCBITaxon:11072 -name: Japanese encephalitis virus -namespace: ncbi_taxonomy -synonym: "Japanese encephalitis" RELATED misspelling [] -synonym: "Japanese encephalitis (JE) virus" RELATED synonym [] -synonym: "Japanese encephalitis virus JE" RELATED synonym [] -synonym: "Japanese encephalitis virus JEV" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:11071 ! Japanese encephalitis virus group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11079 -name: Murray Valley encephalitis virus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11071 ! Japanese encephalitis virus group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11080 -name: St. Louis encephalitis virus -namespace: ncbi_taxonomy -alt_id: NCBITaxon:64321 -synonym: "Saint Louis encephalitis virus" RELATED synonym [] -synonym: "St. Louis encephalitis virus SLEV" RELATED misnomer [] -xref: GC_ID:1 -is_a: NCBITaxon:11071 ! Japanese encephalitis virus group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11082 -name: West Nile virus -namespace: ncbi_taxonomy -synonym: "WNV" BROAD genbank_acronym [] -xref: GC_ID:1 -is_a: NCBITaxon:11071 ! Japanese encephalitis virus group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11083 -name: Powassan virus -namespace: ncbi_taxonomy -synonym: "Flavivirus powassan" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:29263 ! tick-borne encephalitis virus group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11089 -name: Yellow fever virus -namespace: ncbi_taxonomy -synonym: "Flavivirus febricis" RELATED synonym [] -synonym: "yellow fever virus YFV" RELATED synonym [] -synonym: "YFV" BROAD genbank_acronym [] -xref: GC_ID:1 -is_a: NCBITaxon:40005 ! Yellow fever virus group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11102 -name: Hepacivirus -is_a: NCBITaxon:11050 ! Flaviviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Hepatitis C virus group" xsd:string -property_value: IAO:0000118 "Hepatitis C viruses" xsd:string -property_value: IAO:0000118 "Hepatitis C-like viruses" xsd:string - -[Term] -id: NCBITaxon:11103 -name: Hepatitis C virus -is_a: NCBITaxon:11102 ! Hepacivirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "hepatitis C virus HCV" xsd:string -property_value: IAO:0000118 "human hepatitis C virus" xsd:string -property_value: IAO:0000118 "human hepatitis C virus HCV" xsd:string -property_value: IAO:0000118 "human hepatitis virus C HCV" xsd:string -property_value: IAO:0000118 "post-transfusion hepatitis non A non B virus" xsd:string - -[Term] -id: NCBITaxon:11118 -name: Coronaviridae -is_a: NCBITaxon:76804 ! Nidovirales -property_value: IAO:0000111 "Coronaviridae" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: NCBITaxon:1113537 -name: Chlamydia/Chlamydophila group -is_a: NCBITaxon:809 ! Chlamydiaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:111527 -name: pseudomallei group -namespace: ncbi_taxonomy -xref: GC_ID:11 -is_a: NCBITaxon:32008 ! Burkholderia -property_value: has_rank http://purl.obolibrary.org/obo/NCBITaxon_species_group - -[Term] -id: NCBITaxon:11157 -name: Mononegavirales -is_a: NCBITaxon:35301 ! ssRNA negative-strand virus - -[Term] -id: NCBITaxon:11158 -name: Paramyxoviridae -is_a: NCBITaxon:11157 ! Mononegavirales - -[Term] -id: NCBITaxon:11159 -name: Paramyxovirinae -is_a: NCBITaxon:11158 ! Paramyxoviridae - -[Term] -id: NCBITaxon:11161 -name: Mumps virus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:39744 ! Rubulavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11229 -name: Morbillivirus -is_a: NCBITaxon:11158 ! Paramyxoviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Morbilliviruses" xsd:string - -[Term] -id: NCBITaxon:11234 -name: Measles virus -is_a: NCBITaxon:11229 ! Morbillivirus - -[Term] -id: NCBITaxon:11244 -name: Pneumoviridae -is_a: NCBITaxon:11157 ! Mononegavirales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Pneumovirinae" xsd:string - -[Term] -id: NCBITaxon:11245 -name: Pneumovirus -is_a: NCBITaxon:11244 ! Pneumoviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:11266 -name: Filoviridae -is_a: NCBITaxon:11157 ! Mononegavirales - -[Term] -id: NCBITaxon:11269 -name: Marburg marburgvirus -namespace: ncbi_taxonomy -synonym: "Lake Victoria marburgvirus" RELATED synonym [] -synonym: "Marburg virus MBG" RELATED synonym [] -synonym: "MBG" BROAD acronym [] -xref: GC_ID:1 -is_a: NCBITaxon:186537 ! Marburgvirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11270 -name: Rhabdoviridae -is_a: NCBITaxon:11157 ! Mononegavirales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:11286 -name: Lyssavirus -is_a: NCBITaxon:11270 ! Rhabdoviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string +[Typedef] +id: APOLLO_SV:00000037 +name: commissions +def: "a commissions b, iff a does not participate in the creation or execution of b and participates in a legal agreement that c participates on the creation or execution of b and c getting something in exchange for that participation." [] +property_value: APOLLO_SV:0000040 "commissions" xsd:string +property_value: IAO:0000600 "A relation between two entities where the first entity formally requests a third party to create or execute the second entity." xsd:string -[Term] -id: NCBITaxon:11292 -name: Rabies lyssavirus -is_a: NCBITaxon:11286 ! Lyssavirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Rabies virus" xsd:string +[Typedef] +id: APOLLO_SV:00000057 +name: instantiates +def: "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. " [] +comment: Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222. -[Term] -id: NCBITaxon:11308 -name: Orthomyxoviridae -is_a: NCBITaxon:35301 ! ssRNA negative-strand virus +[Typedef] +id: APOLLO_SV:00000067 +name: simulates +def: "a simulates b, iff a is a purely intentional entity that is representing a fictional individual or fact b and a participates in a simulating." [] -[Term] -id: NCBITaxon:11320 -name: Influenza A virus -is_a: NCBITaxon:197911 ! Influenzavirus A +[Typedef] +id: APOLLO_SV:00000116 +name: causally_precedes +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string +is_a: ObsoleteProperty +is_obsolete: true -[Term] -id: NCBITaxon:114277 -name: spotted fever group -namespace: ncbi_taxonomy -xref: GC_ID:11 -xref: PMID:9734038 -is_a: NCBITaxon:780 ! Rickettsia -property_value: has_rank http://purl.obolibrary.org/obo/NCBITaxon_species_group - -[Term] -id: NCBITaxon:114292 -name: typhus group -namespace: ncbi_taxonomy -xref: GC_ID:11 -is_a: NCBITaxon:780 ! Rickettsia -property_value: has_rank http://purl.obolibrary.org/obo/NCBITaxon_species_group - -[Term] -id: NCBITaxon:114727 -name: H1N1 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H1N1 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:114729 -name: H2N2 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H2N2 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:11520 -name: Influenza B virus -is_a: NCBITaxon:197912 ! Influenzavirus B -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Influenza virus type B" xsd:string - -[Term] -id: NCBITaxon:11571 -name: Bunyaviridae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:35301 ! ssRNA negative-strand virus -property_value: has_rank NCBITaxon:family -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:11572 -name: Orthobunyavirus -namespace: ncbi_taxonomy -synonym: "Bunyavirus" RELATED synonym [] -synonym: "Bunyaviruses" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1980416 ! Peribunyaviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:11577 -name: La Crosse virus -namespace: ncbi_taxonomy -synonym: "Bunyavirus la crosse" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1933264 ! California encephalitis orthobunyavirus - -[Term] -id: NCBITaxon:11580 -name: Snowshoe hare virus -namespace: ncbi_taxonomy -synonym: "Bunyavirus snowshoe hare" RELATED synonym [] -synonym: "Snowshoe hare bunyavirus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1933264 ! California encephalitis orthobunyavirus - -[Term] -id: NCBITaxon:11584 -name: Phlebovirus -is_a: NCBITaxon:11571 ! Bunyaviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Phleboviruses" xsd:string - -[Term] -id: NCBITaxon:11588 -name: Rift Valley fever virus -is_a: NCBITaxon:1933187 ! Rift Valley fever phlebovirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:11598 -name: Hantavirus -namespace: ncbi_taxonomy -synonym: "Hantaviurs" RELATED misspelling [] -xref: GC_ID:1 -is_a: NCBITaxon:11571 ! Bunyaviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:11617 -name: Arenaviridae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:35301 ! ssRNA negative-strand virus -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:11619 -name: Junin mammarenavirus -namespace: ncbi_taxonomy -synonym: "Junin arenavirus" RELATED synonym [] -synonym: "Junin virus" RELATED synonym [] -synonym: "Junn mammarenavirus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1653394 ! Mammarenavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11620 -name: Lassa mammarenavirus -namespace: ncbi_taxonomy -synonym: "Lassa virus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1653394 ! Mammarenavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11628 -name: Machupo mammarenavirus -namespace: ncbi_taxonomy -synonym: "Machupo virus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1653394 ! Mammarenavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:11632 -name: Retroviridae -is_a: NCBITaxon:35268 ! Retro-transcribing viruses - -[Term] -id: NCBITaxon:11646 -name: Lentivirus -is_a: NCBITaxon:327045 ! Orthoretrovirinae -property_value: IAO:0000118 "Lentivirinae" xsd:string - -[Term] -id: NCBITaxon:11652 -name: Primate lentivirus group -is_a: NCBITaxon:11646 ! Lentivirus -property_value: IAO:0000118 "Primate immunodeficiency viruses" xsd:string - -[Term] -id: NCBITaxon:11676 -name: Human immunodeficiency virus 1 -is_a: NCBITaxon:11652 ! Primate lentivirus group -property_value: IAO:0000118 "HIV-1" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus 1 HIV-1" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus HIV-1" xsd:string -property_value: IAO:0000118 "Human immunodeficiency virus type 1" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus type 1 HIV 1" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus type 1 HIV-1" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus type 1 HIV1" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus type 1, HIV-1" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus type I HIV-1" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus type-1 HIV-1" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus-1 HIV-1" xsd:string - -[Term] -id: NCBITaxon:11709 -name: Human immunodeficiency virus 2 -is_a: NCBITaxon:11652 ! Primate lentivirus group -property_value: IAO:0000118 "HIV type 2" xsd:string -property_value: IAO:0000118 "HIV-2" xsd:string -property_value: IAO:0000118 "Human immunodeficiency virus type 2" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus type 2 HIV-2" xsd:string -property_value: IAO:0000118 "human immunodeficiency virus type 2, HIV-2" xsd:string -property_value: IAO:0000118 "Human immunodeficiency virus-2" xsd:string - -[Term] -id: NCBITaxon:117570 -name: Teleostomi -is_a: NCBITaxon:7776 ! Gnathostomata - -[Term] -id: NCBITaxon:117571 -name: Euteleostomi -is_a: NCBITaxon:117570 ! Teleostomi -property_value: IAO:0000118 "bony vertebrates" xsd:string - -[Term] -id: NCBITaxon:118882 -name: Brucellaceae -namespace: ncbi_taxonomy -synonym: "Brucellaceae Breed et al. 1957" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:356 ! Rhizobiales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:118968 -name: Coxiellaceae -namespace: ncbi_taxonomy -synonym: "Coxiella group" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:16280474 -is_a: NCBITaxon:118969 ! Legionellales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:118969 -name: Legionellales -namespace: ncbi_taxonomy -synonym: "Legionellaceae group" RELATED synonym [] -synonym: "Legionellales Garrity et al. 2005" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:16280474 -is_a: NCBITaxon:1236 ! Gammaproteobacteria -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:119060 -name: Burkholderiaceae -namespace: ncbi_taxonomy -alt_id: NCBITaxon:119063 -synonym: "Burkholderia group" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:16403855 -is_a: NCBITaxon:80840 ! Burkholderiales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:119088 -name: Enoplea -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6231 ! Nematoda -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:119089 -name: Chromadorea -namespace: ncbi_taxonomy -alt_id: NCBITaxon:27837 -synonym: "Adenophorea" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:6231 ! Nematoda -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:119210 -name: H3N2 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H3N2 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:119214 -name: H7N2 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H7N2 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:119218 -name: H7N7 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H7N7 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:119220 -name: H5N2 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H5N2 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:11974 -name: Caliciviridae -is_a: NCBITaxon:35278 ! ssRNA positive-strand viruses, no DNA stage -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:12058 -name: Picornaviridae -is_a: NCBITaxon:464095 ! Picornavirales - -[Term] -id: NCBITaxon:12059 -name: Enterovirus -is_a: NCBITaxon:12058 ! Picornaviridae - -[Term] -id: NCBITaxon:1206794 -name: Ecdysozoa -is_a: NCBITaxon:33317 ! Protostomia - -[Term] -id: NCBITaxon:12080 -name: Human poliovirus 1 -is_a: NCBITaxon:138950 ! Enterovirus C -property_value: IAO:0000118 "Human poliovirus type 1" xsd:string -property_value: IAO:0000118 "Poliovirus type 1" xsd:string -property_value: IAO:0000118 "poliovirus type 1 PV1" xsd:string - -[Term] -id: NCBITaxon:12086 -name: Human poliovirus 3 -is_a: NCBITaxon:138950 ! Enterovirus C -property_value: IAO:0000118 "Human poliovirus type 3" xsd:string -property_value: IAO:0000118 "Poliovirus type 3" xsd:string - -[Term] -id: NCBITaxon:12091 -name: Hepatovirus -is_a: NCBITaxon:12058 ! Picornaviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:12092 -name: Hepatovirus A -is_a: NCBITaxon:12091 ! Hepatovirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Hepatitis A virus" xsd:string - -[Term] -id: NCBITaxon:12109 -name: Aphthovirus -is_a: NCBITaxon:12058 ! Picornaviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:12110 -name: Foot-and-mouth disease virus -is_a: NCBITaxon:12109 ! Aphthovirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Foot and mouth disease virus" xsd:string -property_value: IAO:0000118 "foot and mouth disease virus FMDV" xsd:string -property_value: IAO:0000118 "foot-and-mouth disease virus FMDV" xsd:string - -[Term] -id: NCBITaxon:121791 -name: Nipah henipavirus -namespace: ncbi_taxonomy -synonym: "Nipah virus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:260964 ! Henipavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1224 -name: Proteobacteria -is_a: NCBITaxon:2 ! Bacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Alphaproteobacteraeota" xsd:string -property_value: IAO:0000118 "purple bacteria" xsd:string -property_value: IAO:0000118 "purple bacteria and relatives" xsd:string -property_value: IAO:0000118 "purple non-sulfur bacteria" xsd:string -property_value: IAO:0000118 "purple photosynthetic bacteria" xsd:string -property_value: IAO:0000118 "purple photosynthetic bacteria and relatives" xsd:string - -[Term] -id: NCBITaxon:1236 -name: Gammaproteobacteria -is_a: NCBITaxon:1224 ! Proteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "gamma proteobacteria" xsd:string -property_value: IAO:0000118 "gamma subdivision" xsd:string -property_value: IAO:0000118 "gamma subgroup" xsd:string -property_value: IAO:0000118 "Proteobacteria gamma subdivision" xsd:string -property_value: IAO:0000118 "Purple bacteria, gamma subdivision" xsd:string - -[Term] -id: NCBITaxon:1239 -name: Firmicutes -is_a: NCBITaxon:1783272 ! Terrabacteria group -property_value: IAO:0000118 "Gram-postive bacterium" xsd:string - -[Term] -id: NCBITaxon:12461 -name: Hepatitis E virus -namespace: ncbi_taxonomy -synonym: "Hepatitis E virus HEV" RELATED synonym [] -synonym: "HEV" BROAD acronym [] -xref: GC_ID:1 -is_a: NCBITaxon:1678143 ! Orthohepevirus A - -[Term] -id: NCBITaxon:12475 -name: Hepatitis delta virus -is_a: NCBITaxon:39759 ! Deltavirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Hepatitis D virus" xsd:string -property_value: IAO:0000118 "hepatitis delta virus HDV" xsd:string - -[Term] -id: NCBITaxon:12637 -name: Dengue virus -is_a: NCBITaxon:11052 ! Dengue virus group - -[Term] -id: NCBITaxon:1279 -name: Staphylococcus -is_a: NCBITaxon:90964 ! Staphylococcaceae -property_value: IAO:0000111 "Staphylococcus" xsd:string -property_value: IAO:0000118 "Aurococcus" xsd:string - -[Term] -id: NCBITaxon:127906 -name: Vibrio cholerae O1 -is_a: NCBITaxon:666 ! Vibrio cholerae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Vibrio cholerae serogroup O1" xsd:string - -[Term] -id: NCBITaxon:1280 -name: Staphylococcus aureus -is_a: NCBITaxon:1279 ! Staphylococcus -property_value: IAO:0000111 "Staphylococcus aureus" xsd:string -property_value: IAO:0000118 "Micrococcus aureus" xsd:string -property_value: IAO:0000118 "Micrococcus pyogenes" xsd:string -property_value: IAO:0000118 "Staphlococcus pyogenes citreus" xsd:string -property_value: IAO:0000118 "Staphylococcus pyogenes aureus" xsd:string -property_value: IAO:0000118 "Streptococcus aureus" xsd:string - -[Term] -id: NCBITaxon:1280412 -name: Conoidasida -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:5794 ! Apicomplexa - -[Term] -id: NCBITaxon:12814 -name: Respiratory syncytial virus -is_a: NCBITaxon:11245 ! Pneumovirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "respiratory syncytial virus RS" xsd:string -property_value: IAO:0000118 "respiratory syncytial virus RS virus" xsd:string -property_value: IAO:0000118 "respiratory syncytial virus RSV" xsd:string - -[Term] -id: NCBITaxon:1300 -name: Streptococcaceae -is_a: NCBITaxon:186826 ! Lactobacillales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:1301 -name: Streptococcus -is_a: NCBITaxon:1300 ! Streptococcaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:131221 -name: Streptophytina -namespace: ncbi_taxonomy -synonym: "Charophyta/Embryophyta group" RELATED synonym [] -synonym: "charophyte/embryophyte group" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:35493 ! Streptophyta -property_value: has_rank NCBITaxon:subphylum - -[Term] -id: NCBITaxon:1313 -name: Streptococcus pneumoniae -is_a: NCBITaxon:1301 ! Streptococcus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Diplococcus pneumoniae" xsd:string -property_value: IAO:0000118 "Micrococcus pneumoniae" xsd:string - -[Term] -id: NCBITaxon:1329799 -name: Archelosauria -namespace: ncbi_taxonomy -synonym: "Archosauria-Testudines" RELATED synonym [] -synonym: "Testudines + Archosauria group" RELATED synonym [] -xref: GC_ID:1 -xref: PMID:22839753 -xref: PMID:25450099 -is_a: NCBITaxon:32561 ! Sauria - -[Term] -id: NCBITaxon:1335626 -name: Middle East respiratory syndrome coronavirus -is_a: NCBITaxon:694002 ! Betacoronavirus - -[Term] -id: NCBITaxon:1338369 -name: Dipnotetrapodomorpha -is_a: NCBITaxon:8287 ! Sarcopterygii - -[Term] -id: NCBITaxon:135623 -name: Vibrionales -is_a: NCBITaxon:1236 ! Gammaproteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Vibrionaceae group" xsd:string - -[Term] -id: NCBITaxon:135625 -name: Pasteurellales -is_a: NCBITaxon:1236 ! Gammaproteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Pasteruellaceae group" xsd:string - -[Term] -id: NCBITaxon:136 -name: Spirochaetales -namespace: ncbi_taxonomy -synonym: "spirochetes" RELATED blast_name [] -xref: GC_ID:11 -xref: PMID:11075904 -xref: PMID:11542017 -xref: PMID:16558735 -xref: PMID:1917844 -xref: PMID:23908650 -is_a: NCBITaxon:203692 ! Spirochaetia -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:137 -name: Spirochaetaceae -namespace: ncbi_taxonomy -synonym: "Treponemataceae" RELATED in_part [] -xref: GC_ID:11 -xref: PMID:23908650 -is_a: NCBITaxon:136 ! Spirochaetales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:138 -name: Borrelia -namespace: ncbi_taxonomy -synonym: "Relapsing Fever Borrelia" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:24744012 -xref: PMID:8863409 -xref: PMID:8863416 -is_a: NCBITaxon:1643685 ! Borreliaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:1385 -name: Bacillales -is_a: NCBITaxon:91061 ! Bacilli - -[Term] -id: NCBITaxon:1386 -name: Bacillus -is_a: NCBITaxon:186817 ! Bacillaceae - -[Term] -id: NCBITaxon:138948 -name: Enterovirus A -is_a: NCBITaxon:12059 ! Enterovirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Coxsackievirus A" xsd:string -property_value: IAO:0000118 "Enterovirus EV-A" xsd:string -property_value: IAO:0000118 "Human coxsackievirus A" xsd:string -property_value: IAO:0000118 "Human enterovirus A" xsd:string - -[Term] -id: NCBITaxon:138950 -name: Enterovirus C -is_a: NCBITaxon:12059 ! Enterovirus -property_value: IAO:0000118 "Enterovirus EV-C" xsd:string -property_value: IAO:0000118 "Human enterovirus C" xsd:string -property_value: IAO:0000118 "Poliovirus" xsd:string - -[Term] -id: NCBITaxon:138951 -name: Enterovirus D -is_a: NCBITaxon:12059 ! Enterovirus - -[Term] -id: NCBITaxon:1392 -name: Bacillus anthracis -is_a: NCBITaxon:86661 ! Bacillus cereus group -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "anthrax" xsd:string -property_value: IAO:0000118 "anthrax bacterium" xsd:string -property_value: IAO:0000118 "Bacillus cereus var. anthracis" xsd:string -property_value: IAO:0000118 "Bacteridium anthracis" xsd:string - -[Term] -id: NCBITaxon:142786 -name: Norovirus -is_a: NCBITaxon:11974 ! Caliciviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Norwalk-like viruses" xsd:string - -[Term] -id: NCBITaxon:1437010 -name: Boreoeutheria -namespace: ncbi_taxonomy -synonym: "Boreotheria" RELATED synonym [] -xref: GC_ID:1 -xref: PMID:11743200 -xref: PMID:11791233 -is_a: NCBITaxon:9347 ! Eutheria - -[Term] -id: NCBITaxon:144512 -name: Trichinella murrelli -namespace: ncbi_taxonomy -alt_id: NCBITaxon:92178 -synonym: "Trichinella sp. T5" EXACT equivalent_name [] -synonym: "Trichinella T5" EXACT equivalent_name [] -xref: GC_ID:1 -xref: PMID:10701576 -is_a: NCBITaxon:6333 ! Trichinella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1457286 -name: Dorylaimia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:119088 ! Enoplea -property_value: has_rank NCBITaxon:subclass - -[Term] -id: NCBITaxon:147537 -name: Saccharomycotina -namespace: ncbi_taxonomy -synonym: "true yeasts" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:716545 ! saccharomyceta -property_value: has_rank NCBITaxon:subphylum - -[Term] -id: NCBITaxon:147538 -name: Pezizomycotina -namespace: ncbi_taxonomy -synonym: "Euascomycota" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:716545 ! saccharomyceta -property_value: has_rank NCBITaxon:subphylum - -[Term] -id: NCBITaxon:147545 -name: Eurotiomycetes -namespace: ncbi_taxonomy -alt_id: NCBITaxon:147540 -synonym: "bitunicate ascomycetes" RELATED in_part [] -synonym: "Loculoascomycetes" RELATED in_part [] -synonym: "Plectomycetes" RELATED in_part [] -xref: GC_ID:1 -is_a: NCBITaxon:716546 ! leotiomyceta -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:147711 -name: Rhinovirus A -is_a: NCBITaxon:12059 ! Enterovirus -property_value: IAO:0000111 "Rhinovirus A" xsd:string - -[Term] -id: NCBITaxon:1485 -name: Clostridium -namespace: ncbi_taxonomy -alt_id: NCBITaxon:69207 -synonym: "Anaerobacter" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:26643615 -is_a: NCBITaxon:31979 ! Clostridiaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:1491 -name: Clostridium botulinum -namespace: ncbi_taxonomy -alt_id: NCBITaxon:29368 -synonym: "Bacillus botulinus" RELATED synonym [] -synonym: "Bacillus putrificus" RELATED synonym [] -synonym: "Botulobacillus botulinus" RELATED synonym [] -synonym: "Clostridium putrificum" RELATED synonym [] -synonym: "Ermengemillus botulinus" RELATED synonym [] -synonym: "Pacinia putrifica" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:10028279 -xref: PMID:15244052 -is_a: NCBITaxon:1485 ! Clostridium -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1496 -name: Clostridioides difficile -is_a: NCBITaxon:1870884 ! Clostridioides -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bacillus difficilis" xsd:string -property_value: IAO:0000118 "Clostridium difficile" xsd:string -property_value: IAO:0000118 "Peptoclostridium difficile" xsd:string - -[Term] -id: NCBITaxon:1513 -name: Clostridium tetani -namespace: ncbi_taxonomy -synonym: "Bacillus tetani" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:1485 ! Clostridium -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1540022 -name: Clavispora/Candida clade -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:36910 ! Clavispora - -[Term] -id: NCBITaxon:1549675 -name: Galloanserae -namespace: ncbi_taxonomy -synonym: "ducks, geese, chickens, fowl, quail, currasows and allies" EXACT equivalent_name [] -synonym: "Galloanseri" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:8825 ! Neognathae - -[Term] -id: NCBITaxon:157 -name: Treponema -namespace: ncbi_taxonomy -synonym: "Microspironema" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:23961314 -xref: PMID:9019153 -xref: PMID:9734025 -is_a: NCBITaxon:137 ! Spirochaetaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:1593277 -name: Onygenales incertae sedis -namespace: ncbi_taxonomy -alt_id: NCBITaxon:34383 -xref: GC_ID:1 -is_a: NCBITaxon:33183 ! Onygenales - -[Term] -id: NCBITaxon:160 -name: Treponema pallidum -namespace: ncbi_taxonomy -synonym: "Microspironema pallidum" RELATED synonym [] -synonym: "Spirillum pallidum" RELATED synonym [] -synonym: "Spirochaeta pallida" RELATED synonym [] -synonym: "Spironema pallidum" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:157 ! Treponema -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:161 -name: Treponema pallidum subsp. pallidum -namespace: ncbi_taxonomy -synonym: "syphilis treponeme" EXACT genbank_common_name [] -synonym: "Treponema pallidum pallidum" EXACT equivalent_name [] -xref: GC_ID:11 -is_a: NCBITaxon:160 ! Treponema pallidum -property_value: has_rank NCBITaxon:subspecies - -[Term] -id: NCBITaxon:1637 -name: Listeria -namespace: ncbi_taxonomy -synonym: "Listerella" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:10408878 -xref: PMID:15709360 -xref: PMID:1713054 -xref: PMID:1899799 -xref: PMID:8427807 -xref: PMID:8782674 -xref: PMID:9226919 -xref: PMID:9542083 -is_a: NCBITaxon:186820 ! Listeriaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:1638 -name: Listeria ivanovii -namespace: ncbi_taxonomy -synonym: "Listeria bulgarica" RELATED synonym [] -synonym: "Listeria monocytogenes subsp. perhaemolytica" RELATED synonym [] -synonym: "Listeria perhaemolytica" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:8782698 -is_a: NCBITaxon:1637 ! Listeria -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1639 -name: Listeria monocytogenes -namespace: ncbi_taxonomy -alt_id: NCBITaxon:1634566 -synonym: "Bacterium monocytogenes" RELATED synonym [] -synonym: "Bacterium monocytogenes hominis" RELATED synonym [] -synonym: "Corynebacterium infantisepticum" RELATED synonym [] -synonym: "Corynebacterium parvulum" RELATED synonym [] -synonym: "Erysipelothrix monocytogenes" RELATED synonym [] -synonym: "Listerella hepatolytica" RELATED synonym [] -synonym: "Listeria momocytogenes" RELATED misspelling [] -synonym: "Lysteria monocytogenes" RELATED misspelling [] -xref: GC_ID:11 -xref: PMID:17773427 -xref: PMID:1906732 -xref: PMID:8782698 -is_a: NCBITaxon:1637 ! Listeria -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1639119 -name: Plasmodiidae -is_a: NCBITaxon:5819 ! Haemosporida -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:1641 -name: Listeria grayi -namespace: ncbi_taxonomy -alt_id: NCBITaxon:1644 -alt_id: NCBITaxon:47986 -synonym: "Listeria grayi grayi" EXACT equivalent_name [] -synonym: "Listeria grayi murrayi" RELATED synonym [] -synonym: "Listeria grayi subsp. grayi" RELATED synonym [] -synonym: "Listeria murrayi" RELATED synonym [] -synonym: "Murraya grayi" RELATED synonym [] -synonym: "Murraya grayi subsp. grayi" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:1736964 -is_a: NCBITaxon:1637 ! Listeria -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1643685 -name: Borreliaceae -namespace: ncbi_taxonomy -xref: GC_ID:11 -xref: PMID:23908650 -is_a: NCBITaxon:136 ! Spirochaetales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:1643688 -name: Leptospirales -namespace: ncbi_taxonomy -synonym: "Leptospiriales" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:23908650 -is_a: NCBITaxon:203692 ! Spirochaetia - -[Term] -id: NCBITaxon:1649845 -name: Yersinia pseudotuberculosis complex -namespace: ncbi_taxonomy -xref: GC_ID:11 -is_a: NCBITaxon:629 ! Yersinia -property_value: has_rank http://purl.obolibrary.org/obo/NCBITaxon_species_group - -[Term] -id: NCBITaxon:1653 -name: Corynebacteriaceae -namespace: ncbi_taxonomy -synonym: "Coryneform bacteria" EXACT genbank_common_name [] -xref: GC_ID:11 -xref: PMID:19244447 -is_a: NCBITaxon:85007 ! Corynebacteriales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:1653394 -name: Mammarenavirus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11617 ! Arenaviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:1678141 -name: Orthohepevirus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:291484 ! Hepeviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:1678143 -name: Orthohepevirus A -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1678141 ! Orthohepevirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:170 -name: Leptospiraceae -namespace: ncbi_taxonomy -synonym: "Treponemataceae" RELATED in_part [] -xref: GC_ID:11 -xref: PMID:16014471 -is_a: NCBITaxon:1643688 ! Leptospirales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:171 -name: Leptospira -namespace: ncbi_taxonomy -alt_id: NCBITaxon:29512 -alt_id: NCBITaxon:29514 -alt_id: NCBITaxon:29516 -synonym: "Ancona" RELATED misnomer [] -synonym: "Canela" RELATED misnomer [] -synonym: "Jequitaia" RELATED misnomer [] -xref: GC_ID:11 -xref: PMID:10425768 -xref: PMID:1581182 -xref: PMID:19868121 -xref: PMID:9103653 -is_a: NCBITaxon:170 ! Leptospiraceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:1716 -name: Corynebacterium -namespace: ncbi_taxonomy -xref: GC_ID:11 -xref: PMID:10425754 -xref: PMID:19661509 -xref: PMID:7547284 -xref: PMID:7547291 -xref: PMID:7547293 -is_a: NCBITaxon:1653 ! Corynebacteriaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:1717 -name: Corynebacterium diphtheriae -namespace: ncbi_taxonomy -synonym: "Bacillus diphtheriae" RELATED synonym [] -synonym: "Bacterium diphtheriae" RELATED synonym [] -synonym: "Microsporon diphthericum" RELATED synonym [] -synonym: "Microsporon diphtheriticum" RELATED synonym [] -synonym: "Mycobacterium diphtheriae" RELATED synonym [] -synonym: "Pacinia loeffleri" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:7729671 -is_a: NCBITaxon:1716 ! Corynebacterium -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1760 -name: Actinobacteria -is_a: NCBITaxon:201174 ! Actinobacteria -property_value: IAO:0000118 "Actinomycetes" xsd:string -property_value: IAO:0000118 "High GC gram-positive bacteria" xsd:string - -[Term] -id: NCBITaxon:1762 -name: Mycobacteriaceae -is_a: NCBITaxon:85007 ! Corynebacteriales - -[Term] -id: NCBITaxon:1763 -name: Mycobacterium -is_a: NCBITaxon:1762 ! Mycobacteriaceae -property_value: IAO:0000118 "Mycobacterium Lehmann and Neumann 1896" xsd:string - -[Term] -id: NCBITaxon:1769 -name: Mycobacterium leprae -namespace: ncbi_taxonomy -synonym: "Bacillus leprae" RELATED synonym [] -synonym: "Mycoplasma leprae" RELATED misnomer [] -xref: GC_ID:11 -is_a: NCBITaxon:1763 ! Mycobacterium -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1773 -name: Mycobacterium tuberculosis -is_a: NCBITaxon:77643 ! Mycobacterium tuberculosis complex -property_value: IAO:0000118 "Bacillus tuberculosis" xsd:string -property_value: IAO:0000118 "Bacterium tuberculosis" xsd:string -property_value: IAO:0000118 "Mycobacterium tuberculosis typus humanus" xsd:string -property_value: IAO:0000118 "Mycobacterium tuberculosis var. hominis" xsd:string - -[Term] -id: NCBITaxon:177873 -name: EEEV complex -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11019 ! Alphavirus - -[Term] -id: NCBITaxon:177874 -name: WEEV complex -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11019 ! Alphavirus - -[Term] -id: NCBITaxon:177875 -name: SFV complex -is_a: NCBITaxon:11019 ! Alphavirus - -[Term] -id: NCBITaxon:1783257 -name: PVC group -is_a: NCBITaxon:2 ! Bacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:1783272 -name: Terrabacteria group -is_a: NCBITaxon:2 ! Bacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:186536 -name: Ebolavirus -is_a: NCBITaxon:11266 ! Filoviridae -property_value: IAO:0000118 "Ebola-like virus" xsd:string - -[Term] -id: NCBITaxon:186537 -name: Marburgvirus -namespace: ncbi_taxonomy -synonym: "Marburg-like viruses" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:11266 ! Filoviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:186538 -name: Zaire ebolavirus -is_a: NCBITaxon:186536 ! Ebolavirus - -[Term] -id: NCBITaxon:186539 -name: Reston ebolavirus -is_a: NCBITaxon:186536 ! Ebolavirus -property_value: IAO:0000118 "Ebola virus Reston" xsd:string -property_value: IAO:0000118 "REBOV" xsd:string -property_value: IAO:0000118 "Reston Ebola virus" xsd:string - -[Term] -id: NCBITaxon:186540 -name: Sudan ebolavirus -is_a: NCBITaxon:186536 ! Ebolavirus -property_value: IAO:0000118 "Ebolavirus Sudan" xsd:string -property_value: IAO:0000118 "SEBOV" xsd:string -property_value: IAO:0000118 "Sudan Ebola virus" xsd:string - -[Term] -id: NCBITaxon:186541 -name: Tai Forest ebolavirus -is_a: NCBITaxon:186536 ! Ebolavirus -property_value: IAO:0000118 "CIEBOV" xsd:string -property_value: IAO:0000118 "Côte d'Ivoire Ebola virus" xsd:string -property_value: IAO:0000118 "Côte d'Ivoire ebolavirus" xsd:string -property_value: IAO:0000118 "Ivory Coast ebolavirus" xsd:string - -[Term] -id: NCBITaxon:186801 -name: Clostridia -is_a: NCBITaxon:1239 ! Firmicutes -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:186802 -name: Clostridiales -is_a: NCBITaxon:186801 ! Clostridia -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:186804 -name: Peptostreptococcaceae -is_a: NCBITaxon:186802 ! Clostridiales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Clostridium cluster XI" xsd:string - -[Term] -id: NCBITaxon:186817 -name: Bacillaceae -is_a: NCBITaxon:1385 ! Bacillales - -[Term] -id: NCBITaxon:186820 -name: Listeriaceae -namespace: ncbi_taxonomy -xref: GC_ID:11 -xref: PMID:20212322 -is_a: NCBITaxon:1385 ! Bacillales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:186826 -name: Lactobacillales -is_a: NCBITaxon:91061 ! Bacilli -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:1870884 -name: Clostridioides -is_a: NCBITaxon:186804 ! Peptostreptococcaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:1903411 -name: Yersiniaceae -namespace: ncbi_taxonomy -xref: GC_ID:11 -xref: PMID:27620848 -is_a: NCBITaxon:91347 ! Enterobacterales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:1933187 -name: Rift Valley fever phlebovirus -is_a: NCBITaxon:11584 ! Phlebovirus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:1933264 -name: California encephalitis orthobunyavirus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11572 ! Orthobunyavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:1933274 -name: Guaroa orthobunyavirus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11572 ! Orthobunyavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:194 -name: Campylobacter -namespace: ncbi_taxonomy -synonym: "Ampylobacter" RELATED misspelling [] -xref: GC_ID:11 -xref: PMID:11542086 -xref: PMID:12361288 -xref: PMID:16627635 -xref: PMID:1704793 -xref: PMID:19801389 -is_a: NCBITaxon:72294 ! Campylobacteraceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:197562 -name: Pancrustacea -is_a: NCBITaxon:197563 ! Mandibulata - -[Term] -id: NCBITaxon:197563 -name: Mandibulata -is_a: NCBITaxon:6656 ! Arthropoda - -[Term] -id: NCBITaxon:197911 -name: Influenzavirus A -is_a: NCBITaxon:11308 ! Orthomyxoviridae - -[Term] -id: NCBITaxon:197912 -name: Influenzavirus B -is_a: NCBITaxon:11308 ! Orthomyxoviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:1980410 -name: Bunyavirales -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:35301 ! ssRNA negative-strand virus -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:1980415 -name: Nairoviridae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1980410 ! Bunyavirales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:1980416 -name: Peribunyaviridae -namespace: ncbi_taxonomy -alt_id: NCBITaxon:11571 -synonym: "Bunyaviridae" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1980410 ! Bunyavirales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:1980517 -name: Orthonairovirus -namespace: ncbi_taxonomy -alt_id: NCBITaxon:11592 -synonym: "Nairovirus" RELATED synonym [] -synonym: "Nairoviruses" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1980415 ! Nairoviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:1980519 -name: Crimean-Congo hemorrhagic fever orthonairovirus -namespace: ncbi_taxonomy -alt_id: NCBITaxon:11593 -synonym: "CCHFV" BROAD acronym [] -synonym: "Crimean Congo Hemorrhagic Fever virus" RELATED misspelling [] -synonym: "Crimean-Congo haemorrhagic fever virus" RELATED synonym [] -synonym: "Crimean-Congo hemorrhagic fever nairovirus" RELATED synonym [] -synonym: "Crimean-Congo hemorrhagic fever virus" RELATED synonym [] -synonym: "Crimean-Congo hemorrhagic virus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1980517 ! Orthonairovirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:199306 -name: Coccidioides posadasii -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:5500 ! Coccidioides -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:2 -name: Bacteria -is_a: OBI:0100026 ! organism - -[Term] -id: NCBITaxon:201174 -name: Actinobacteria -is_a: NCBITaxon:1783272 ! Terrabacteria group -property_value: IAO:0000118 "'Actinobacteria'" xsd:string -property_value: IAO:0000118 "not Actinobacteria Cavalier-Smith 2002" xsd:string - -[Term] -id: NCBITaxon:203691 -name: Spirochaetes -namespace: ncbi_taxonomy -synonym: "Spirochaetae" RELATED synonym [] -synonym: "Spirochaetaeota" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:11837318 -xref: PMID:26654112 -is_a: NCBITaxon:2 ! Bacteria -property_value: has_rank NCBITaxon:phylum - -[Term] -id: NCBITaxon:203692 -name: Spirochaetia -namespace: ncbi_taxonomy -synonym: "Spirochaetes" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:11837318 -xref: PMID:25288668 -xref: PMID:26654112 -is_a: NCBITaxon:203691 ! Spirochaetes -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:204428 -name: Chlamydiae -is_a: NCBITaxon:1783257 ! PVC group -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Chlamydaeota" xsd:string - -[Term] -id: NCBITaxon:204429 -name: Chlamydiia -is_a: NCBITaxon:204428 ! Chlamydiae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Chlamydiae" xsd:string - -[Term] -id: NCBITaxon:206351 -name: Neisseriales -is_a: NCBITaxon:28216 ! Betaproteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:207245 -name: Fornicata -namespace: ncbi_taxonomy -synonym: "Diplomonadida group" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:2759 ! Eukaryota - -[Term] -id: NCBITaxon:209 -name: Helicobacter -is_a: NCBITaxon:72293 ! Helicobacteraceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:210 -name: Helicobacter pylori -is_a: NCBITaxon:209 ! Helicobacter -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Campylobacter pylori" xsd:string -property_value: IAO:0000118 "Campylobacter pylori subsp. pylori" xsd:string -property_value: IAO:0000118 "Campylobacter pyloridis" xsd:string -property_value: IAO:0000118 "Helicobacter nemestrinae" xsd:string - -[Term] -id: NCBITaxon:213849 -name: Campylobacterales -is_a: NCBITaxon:29547 ! Epsilonproteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:223472 -name: Psoroptidia -namespace: ncbi_taxonomy -alt_id: NCBITaxon:261182 -synonym: "Sarcoptidia" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:6951 ! Astigmata - -[Term] -id: NCBITaxon:227859 -name: SARS coronavirus -is_a: NCBITaxon:694002 ! Betacoronavirus - -[Term] -id: NCBITaxon:232441 -name: H5N8 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H5N8 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:234 -name: Brucella -namespace: ncbi_taxonomy -synonym: "Brucella Meyer and Shaw 1920" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:8573514 -is_a: NCBITaxon:118882 ! Brucellaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:235 -name: Brucella abortus -namespace: ncbi_taxonomy -synonym: "Bacterium abortus" RELATED synonym [] -synonym: "Brucella melitensis biovar Abortus" RELATED genbank_synonym [] -synonym: "Brucella melitensis bv. Abortus" EXACT equivalent_name [] -xref: GC_ID:11 -is_a: NCBITaxon:234 ! Brucella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:237895 -name: Cryptosporidium hominis -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:5806 ! Cryptosporidium -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:260964 -name: Henipavirus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11158 ! Paramyxoviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:262 -name: Francisella -namespace: ncbi_taxonomy -xref: GC_ID:11 -xref: PMID:19783615 -xref: PMID:8123561 -is_a: NCBITaxon:34064 ! Francisellaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:263 -name: Francisella tularensis -namespace: ncbi_taxonomy -synonym: "Bacterium tularense" RELATED synonym [] -synonym: "Brucella tularensis" RELATED synonym [] -synonym: "Francisella tularense" RELATED synonym [] -synonym: "Pasteurella tularensis" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:262 ! Francisella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:27319 -name: Metschnikowiaceae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:4892 ! Saccharomycetales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:2759 -name: Eukaryota -is_a: OBI:0100026 ! organism - -[Term] -id: NCBITaxon:27592 -name: Bovinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9895 ! Bovidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:28211 -name: Alphaproteobacteria -namespace: ncbi_taxonomy -synonym: "a-proteobacteria" RELATED blast_name [] -synonym: "alpha proteobacteria" RELATED synonym [] -synonym: "alpha subdivision" RELATED synonym [] -synonym: "alpha subgroup" RELATED synonym [] -synonym: "Alphabacteria" RELATED synonym [] -synonym: "Proteobacteria alpha subdivision" RELATED synonym [] -synonym: "Purple bacteria, alpha subdivision" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:11541974 -xref: PMID:11837318 -xref: PMID:16166687 -xref: PMID:16403855 -xref: PMID:19060069 -is_a: NCBITaxon:1224 ! Proteobacteria -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:28216 -name: Betaproteobacteria -is_a: NCBITaxon:1224 ! Proteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "beta proteobacteria" xsd:string -property_value: IAO:0000118 "beta subdivision" xsd:string -property_value: IAO:0000118 "beta subgroup" xsd:string -property_value: IAO:0000118 "Proteobacteria beta subdivision" xsd:string -property_value: IAO:0000118 "Purple bacteria, beta subdivision" xsd:string - -[Term] -id: NCBITaxon:28295 -name: Porcine epidemic diarrhea virus -is_a: NCBITaxon:693996 ! Alphacoronavirus -property_value: IAO:0000118 "PEDV" xsd:string - -[Term] -id: NCBITaxon:28450 -name: Burkholderia pseudomallei -namespace: ncbi_taxonomy -alt_id: NCBITaxon:1435366 -alt_id: NCBITaxon:1435368 -alt_id: NCBITaxon:1435988 -alt_id: NCBITaxon:1439853 -alt_id: NCBITaxon:1487954 -alt_id: NCBITaxon:1487955 -synonym: "Bacillus pseudomallei" RELATED synonym [] -synonym: "Bacterium whitmori" RELATED synonym [] -synonym: "Burkholderia pseudomallai" RELATED misspelling [] -synonym: "Burkholderia pseudomallei MSHR4009" RELATED misspelling [] -synonym: "Burkholderia pseudomallei MSHR4018" RELATED misspelling [] -synonym: "Burkholderia pseudomallei MSHR44" RELATED misspelling [] -synonym: "Burkholderia pseudomallei MSHR7839" RELATED misspelling [] -synonym: "Burkholderia sp. MSHR7839" RELATED misspelling [] -synonym: "Loefflerella pseudomallei" RELATED synonym [] -synonym: "Malleomyces pseudomallei" RELATED synonym [] -synonym: "Pseudomonas pseudomallei" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:12734250 -xref: PMID:1283774 -is_a: NCBITaxon:111527 ! pseudomallei group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:28901 -name: Salmonella enterica -is_a: NCBITaxon:590 ! Salmonella -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bacillus cholerae-suis" xsd:string -property_value: IAO:0000118 "Salmonella cholerae-suis" xsd:string -property_value: IAO:0000118 "Salmonella choleraesuis" xsd:string -property_value: IAO:0000118 "Salmonella enterica ser. choleraesuis" xsd:string - -[Term] -id: NCBITaxon:291484 -name: Hepeviridae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:35278 ! ssRNA positive-strand viruses, no DNA stage -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:29169 -name: Ancylostoma -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:53469 ! Ancylostomatinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:29170 -name: Ancylostoma caninum -namespace: ncbi_taxonomy -synonym: "dog hookworm" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:29169 ! Ancylostoma -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:29263 -name: tick-borne encephalitis virus group -namespace: ncbi_taxonomy -synonym: "Tick-borne encephalitis viruses" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:11051 ! Flavivirus -property_value: has_rank NCBITaxon:subgenus - -[Term] -id: NCBITaxon:29459 -name: Brucella melitensis -namespace: ncbi_taxonomy -synonym: "Micrococcus melitensis" RELATED synonym [] -synonym: "Streptococcus Miletensis" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:8573514 -is_a: NCBITaxon:234 ! Brucella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:29461 -name: Brucella suis -namespace: ncbi_taxonomy -synonym: "Brucella melitensis biovar Suis" RELATED genbank_synonym [] -synonym: "Brucella melitensis bv. Suis" EXACT equivalent_name [] -xref: GC_ID:11 -is_a: NCBITaxon:234 ! Brucella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:29547 -name: Epsilonproteobacteria -is_a: NCBITaxon:68525 ! delta/epsilon subdivisions -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "epsilon proteobacteria" xsd:string -property_value: IAO:0000118 "epsilon subdivision" xsd:string -property_value: IAO:0000118 "epsilon subgroup" xsd:string -property_value: IAO:0000118 "not Epsilobacteria" xsd:string -property_value: IAO:0000118 "Proteobacteria epsilon subdivision" xsd:string -property_value: IAO:0000118 "Purple bacteria, epsilon subdivision" xsd:string - -[Term] -id: NCBITaxon:297696 -name: Spondweni virus group -is_a: NCBITaxon:11051 ! Flavivirus -property_value: IAO:0000111 "Spondweni virus group" xsd:string - -[Term] -id: NCBITaxon:31244 -name: Schistosomatoidea -is_a: NCBITaxon:6180 ! Strigeidida -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:31245 -name: Schistosomatidae -is_a: NCBITaxon:31244 ! Schistosomatoidea -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "blood flukes" xsd:string - -[Term] -id: NCBITaxon:314145 -name: Laurasiatheria -namespace: ncbi_taxonomy -xref: GC_ID:1 -xref: PMID:11214318 -xref: PMID:11214319 -xref: PMID:12878460 -is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder - -[Term] -id: NCBITaxon:314146 -name: Euarchontoglires -is_a: NCBITaxon:1437010 ! Boreoeutheria - -[Term] -id: NCBITaxon:314293 -name: Simiiformes -is_a: NCBITaxon:376913 ! Haplorrhini -property_value: IAO:0000118 "Anthropoidea" xsd:string - -[Term] -id: NCBITaxon:314294 -name: Cercopithecoidea -is_a: NCBITaxon:9526 ! Catarrhini - -[Term] -id: NCBITaxon:31704 -name: Coxsackievirus A16 -namespace: ncbi_taxonomy -synonym: "Coxsackie A virus type 16" RELATED synonym [] -synonym: "CV-A16" BROAD genbank_acronym [] -synonym: "CVA-16" BROAD acronym [] -synonym: "CVA16" BROAD acronym [] -synonym: "Human coxsackievirus A16" RELATED synonym [] -synonym: "Human enterovirus CVA16" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:138948 ! Enterovirus A - -[Term] -id: NCBITaxon:3193 -name: Embryophyta -namespace: ncbi_taxonomy -synonym: "higher plants" EXACT common_name [] -synonym: "land plants" EXACT common_name [] -synonym: "land plants" RELATED blast_name [] -synonym: "plants" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:131221 ! Streptophytina - -[Term] -id: NCBITaxon:31979 -name: Clostridiaceae -namespace: ncbi_taxonomy -xref: GC_ID:11 -is_a: NCBITaxon:186802 ! Clostridiales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:32008 -name: Burkholderia -namespace: ncbi_taxonomy -synonym: "Pseudomonas RNA homology group II" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:10555347 -xref: PMID:1283774 -xref: PMID:25566316 -is_a: NCBITaxon:119060 ! Burkholderiaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:32523 -name: Tetrapoda -is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: IAO:0000118 "tetrapods" xsd:string - -[Term] -id: NCBITaxon:32524 -name: Amniota -namespace: ncbi_taxonomy -synonym: "amniotes" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:32523 ! Tetrapoda -property_value: IAO:0000118 "amniotes" xsd:string - -[Term] -id: NCBITaxon:32525 -name: Theria -comment: authority: Theria Parker & Haswell, 1897 -is_a: NCBITaxon:40674 ! Mammalia - -[Term] -id: NCBITaxon:32561 -name: Sauria -namespace: ncbi_taxonomy -synonym: "Diapsida" RELATED synonym [] -synonym: "diapsids" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:8457 ! Sauropsida - -[Term] -id: NCBITaxon:327045 -name: Orthoretrovirinae -is_a: NCBITaxon:11632 ! Retroviridae - -[Term] -id: NCBITaxon:329376 -name: H5N6 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H5N6 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:33084 -name: Entamoebidae -namespace: ncbi_taxonomy -synonym: "Entamoebida" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:555406 ! Archamoebae - -[Term] -id: NCBITaxon:33090 -name: Viridiplantae -namespace: ncbi_taxonomy -synonym: "Chlorobionta" RELATED synonym [] -synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] -synonym: "chlorophyte/embryophyte group" RELATED synonym [] -synonym: "green plants" EXACT common_name [] -synonym: "green plants" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:kingdom - -[Term] -id: NCBITaxon:33154 -name: Opisthokonta -namespace: ncbi_taxonomy -synonym: "Fungi/Metazoa group" RELATED synonym [] -synonym: "opisthokonts" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:2759 ! Eukaryota - -[Term] -id: NCBITaxon:33183 -name: Onygenales -namespace: ncbi_taxonomy -alt_id: NCBITaxon:259362 -alt_id: NCBITaxon:36053 -alt_id: NCBITaxon:5102 -synonym: "Gymnoascales" RELATED synonym [] -xref: GC_ID:1 -xref: PMID:17486980 -is_a: NCBITaxon:451871 ! Eurotiomycetidae -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:33208 -name: Metazoa -is_a: NCBITaxon:33154 ! Opisthokonta - -[Term] -id: NCBITaxon:33213 -name: Bilateria -is_a: NCBITaxon:6072 ! Eumetazoa - -[Term] -id: NCBITaxon:33277 -name: Ancylostomatoidea -namespace: ncbi_taxonomy -synonym: "hookworms" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:6308 ! Strongylida -property_value: has_rank NCBITaxon:superfamily - -[Term] -id: NCBITaxon:33278 -name: Ancylostomatidae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33277 ! Ancylostomatoidea -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:33317 -name: Protostomia -is_a: NCBITaxon:33213 ! Bilateria - -[Term] -id: NCBITaxon:333278 -name: H7N9 subtype -is_a: NCBITaxon:11320 ! Influenza A virus -property_value: IAO:0000111 "H7N9 subtype of Influenza A virus" xsd:string - -[Term] -id: NCBITaxon:33340 -name: Neoptera -is_a: NCBITaxon:7496 ! Pterygota - -[Term] -id: NCBITaxon:33392 -name: Endopterygota -is_a: NCBITaxon:33340 ! Neoptera - -[Term] -id: NCBITaxon:33511 -name: Deuterostomia -is_a: NCBITaxon:33213 ! Bilateria -property_value: IAO:0000118 "deuterostomes" xsd:string - -[Term] -id: NCBITaxon:33554 -name: Carnivora -namespace: ncbi_taxonomy -synonym: "carnivores" EXACT genbank_common_name [] -synonym: "carnivores" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:314145 ! Laurasiatheria -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:33630 -name: Alveolata -is_a: NCBITaxon:2759 ! Eukaryota -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000118 "alveolates" xsd:string - -[Term] -id: NCBITaxon:33682 -name: Euglenozoa -is_a: NCBITaxon:2759 ! Eukaryota -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Euglenozoans" xsd:string - -[Term] -id: NCBITaxon:33988 -name: Rickettsieae -namespace: ncbi_taxonomy -synonym: "Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:11760958 -xref: PMID:8240958 -is_a: NCBITaxon:775 ! Rickettsiaceae -property_value: has_rank NCBITaxon:tribe - -[Term] -id: NCBITaxon:34064 -name: Francisellaceae -namespace: ncbi_taxonomy -synonym: "Francisella group" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:16280474 -xref: PMID:22939414 -xref: PMID:26747442 -is_a: NCBITaxon:72273 ! Thiotrichales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:35082 -name: Cryptosporidiidae -namespace: ncbi_taxonomy -synonym: "Cryptosporidae" RELATED misspelling [] -synonym: "Cryptosporiidae" RELATED misspelling [] -xref: GC_ID:1 -is_a: NCBITaxon:423054 ! Eimeriorina -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:35237 -name: dsDNA virus, no RNA stage -name: dsDNA viruses, no RNA stage -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:10239 ! Virus - -[Term] -id: NCBITaxon:35268 -name: Retro-transcribing viruses -is_a: NCBITaxon:10239 ! Virus -property_value: IAO:0000118 "Retroid viruses" xsd:string - -[Term] -id: NCBITaxon:35278 -name: ssRNA positive-strand viruses, no DNA stage -is_a: NCBITaxon:439488 ! ssRNA virus -property_value: IAO:0000111 "ssRNA positive-strand viruses, no DNA stage" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: NCBITaxon:35301 -name: ssRNA negative-strand virus -is_a: NCBITaxon:439488 ! ssRNA virus - -[Term] -id: NCBITaxon:35305 -name: California encephalitis virus -namespace: ncbi_taxonomy -alt_id: NCBITaxon:35512 -synonym: "California bunyavirus group" RELATED synonym [] -synonym: "California encephalitis virus group" RELATED synonym [] -synonym: "California serogroup" RELATED synonym [] -synonym: "California virus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1933264 ! California encephalitis orthobunyavirus - -[Term] -id: NCBITaxon:35325 -name: dsRNA viruses -is_a: NCBITaxon:10239 ! Virus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "dsRNA nonenveloped viruses" xsd:string - -[Term] -id: NCBITaxon:35493 -name: Streptophyta -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33090 ! Viridiplantae -property_value: has_rank NCBITaxon:phylum - -[Term] -id: NCBITaxon:35497 -name: Suina -namespace: ncbi_taxonomy -synonym: "Artiodactyla" RELATED in_part [] -synonym: "Suiformes" RELATED in_part [] -xref: GC_ID:1 -is_a: NCBITaxon:91561 ! Cetartiodactyla -property_value: has_rank NCBITaxon:infraorder - -[Term] -id: NCBITaxon:35500 -name: Pecora -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9845 ! Ruminantia -property_value: has_rank NCBITaxon:infraorder - -[Term] -id: NCBITaxon:35510 -name: Equus -namespace: ncbi_taxonomy -synonym: "Equus" EXACT scientific_name [] -synonym: "Equus subg. Equus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:9789 ! Equus -property_value: has_rank NCBITaxon:subgenus - -[Term] -id: NCBITaxon:35511 -name: Jamestown Canyon virus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1933264 ! California encephalitis orthobunyavirus - -[Term] -id: NCBITaxon:356 -name: Rhizobiales -namespace: ncbi_taxonomy -synonym: "alpha-2 proteobacteria" RELATED in_part [] -synonym: "rhizobacteria" EXACT genbank_common_name [] -synonym: "Rhizobiaceae group" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:16403855 -xref: PMID:1854635 -is_a: NCBITaxon:28211 ! Alphaproteobacteria -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:36330 -name: Plasmodium ovale -is_a: NCBITaxon:418103 ! Plasmodium (Plasmodium) -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000118 "malaria parasite p. ovale" xsd:string - -[Term] -id: NCBITaxon:36470 -name: Streptococcus sp. 'group A' -namespace: ncbi_taxonomy -synonym: "group A streptococci" RELATED synonym [] -synonym: "group A streptococcus" RELATED synonym [] -synonym: "Streptococcus sp. (group A)" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:1301 ! Streptococcus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:36855 -name: Brucella canis -namespace: ncbi_taxonomy -synonym: "Brucella melitensis biovar Canis" RELATED genbank_synonym [] -synonym: "Brucella melitensis bv. Canis" EXACT equivalent_name [] -xref: GC_ID:11 -is_a: NCBITaxon:234 ! Brucella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:36910 -name: Clavispora -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:27319 ! Metschnikowiaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:37124 -name: Chikungunya virus -is_a: NCBITaxon:177875 ! SFV complex - -[Term] -id: NCBITaxon:376913 -name: Haplorrhini -is_a: NCBITaxon:9443 ! Primates - -[Term] -id: NCBITaxon:379584 -name: Caniformia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33554 ! Carnivora -property_value: has_rank NCBITaxon:suborder - -[Term] -id: NCBITaxon:39054 -name: Enterovirus A71 -namespace: ncbi_taxonomy -synonym: "Enterovirus 71" RELATED synonym [] -synonym: "Enterovirus EV-A71" RELATED synonym [] -synonym: "enterovirus type 71" RELATED synonym [] -synonym: "EV-71" BROAD acronym [] -synonym: "EV-A71" BROAD genbank_acronym [] -synonym: "EV71" BROAD acronym [] -synonym: "Human enterovirus 71" RELATED synonym [] -synonym: "Human enterovirus A71" RELATED synonym [] -synonym: "Human enterovirus type 71" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:138948 ! Enterovirus A - -[Term] -id: NCBITaxon:39744 -name: Rubulavirus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11158 ! Paramyxoviridae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:39759 -name: Deltavirus -is_a: NCBITaxon:10239 ! Virus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:39824 -name: Klebsiella granulomatis -namespace: ncbi_taxonomy -synonym: "Calymmatobacterium granulomatis" RELATED synonym [] -synonym: "Donovania granulomatis" RELATED synonym [] -synonym: "Encapsulatus inguinalis" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:10555350 -is_a: NCBITaxon:570 ! Klebsiella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:40005 -name: Yellow fever virus group -namespace: ncbi_taxonomy -synonym: "Yellow fever viruses" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:11051 ! Flavivirus -property_value: has_rank NCBITaxon:subgenus - -[Term] -id: NCBITaxon:40674 -name: Mammalia -is_a: NCBITaxon:32524 ! Amniota -property_value: IAO:0000118 "mammals" xsd:string - -[Term] -id: NCBITaxon:418103 -name: Plasmodium (Plasmodium) -is_a: NCBITaxon:5820 ! Plasmodium -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000118 "plasmodium" xsd:string - -[Term] -id: NCBITaxon:418107 -name: Plasmodium (Laverania) -is_a: NCBITaxon:5820 ! Plasmodium -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000118 "laverania" xsd:string - -[Term] -id: NCBITaxon:41827 -name: Culicoidea -is_a: NCBITaxon:43786 ! Culicomorpha - -[Term] -id: NCBITaxon:422676 -name: Aconoidasida -is_a: NCBITaxon:5794 ! Apicomplexa -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000118 "hematozoa" xsd:string - -[Term] -id: NCBITaxon:423054 -name: Eimeriorina -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:75739 ! Eucoccidiorida -property_value: has_rank NCBITaxon:suborder - -[Term] -id: NCBITaxon:42789 -name: Enterovirus D68 -is_a: NCBITaxon:138951 ! Enterovirus D - -[Term] -id: NCBITaxon:436486 -name: Dinosauria -namespace: ncbi_taxonomy -synonym: "dinosaur" EXACT common_name [] -synonym: "dinosaurs" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:8492 ! Archosauria - -[Term] -id: NCBITaxon:436489 -name: Saurischia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:436486 ! Dinosauria - -[Term] -id: NCBITaxon:436491 -name: Theropoda -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:436489 ! Saurischia - -[Term] -id: NCBITaxon:436492 -name: Coelurosauria -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:436491 ! Theropoda - -[Term] -id: NCBITaxon:43786 -name: Culicomorpha -is_a: NCBITaxon:7148 ! Nematocera - -[Term] -id: NCBITaxon:43816 -name: Anophelinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7157 ! Culicidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:43817 -name: Culicinae -is_a: NCBITaxon:7157 ! Culicidae - -[Term] -id: NCBITaxon:439488 -name: ssRNA virus -is_a: NCBITaxon:10239 ! Virus - -[Term] -id: NCBITaxon:44025 -name: Koutango virus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:11071 ! Japanese encephalitis virus group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:444 -name: Legionellaceae -namespace: ncbi_taxonomy -synonym: "Legionellaceae Brenner et al. 1979" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:434652 -is_a: NCBITaxon:118969 ! Legionellales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:44417 -name: Cyclospora -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:5799 ! Eimeriidae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:44482 -name: Anopheles -namespace: ncbi_taxonomy -synonym: "Anopheles" EXACT scientific_name [] -xref: GC_ID:1 -is_a: NCBITaxon:7164 ! Anopheles -property_value: has_rank NCBITaxon:subgenus - -[Term] -id: NCBITaxon:445 -name: Legionella -namespace: ncbi_taxonomy -alt_id: NCBITaxon:29550 -xref: GC_ID:11 -xref: PMID:16166707 -xref: PMID:434652 -xref: PMID:8573522 -xref: PMID:9734026 -is_a: NCBITaxon:444 ! Legionellaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:451864 -name: Dikarya -namespace: ncbi_taxonomy -xref: GC_ID:1 -xref: PMID:15689432 -xref: PMID:16151185 -xref: PMID:17010206 -xref: PMID:17051209 -xref: PMID:17572334 -is_a: NCBITaxon:4751 ! Fungi -property_value: has_rank NCBITaxon:subkingdom - -[Term] -id: NCBITaxon:451871 -name: Eurotiomycetidae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:147545 ! Eurotiomycetes -property_value: has_rank NCBITaxon:subclass - -[Term] -id: NCBITaxon:45219 -name: Guanarito mammarenavirus -namespace: ncbi_taxonomy -synonym: "GTOV" BROAD acronym [] -synonym: "Guanarito arenavirus" RELATED synonym [] -synonym: "Guanarito virus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1653394 ! Mammarenavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:45269 -name: Inkoo virus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1933264 ! California encephalitis orthobunyavirus - -[Term] -id: NCBITaxon:45270 -name: Tahyna virus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1933264 ! California encephalitis orthobunyavirus - -[Term] -id: NCBITaxon:45709 -name: Sabia mammarenavirus -namespace: ncbi_taxonomy -synonym: "Sabi mammarenavirus" RELATED synonym [] -synonym: "Sabia arenavirus" RELATED synonym [] -synonym: "Sabia virus" RELATED synonym [] -synonym: "Sabio virus" RELATED misspelling [] -xref: GC_ID:1 -is_a: NCBITaxon:1653394 ! Mammarenavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:45882 -name: Trichinella britovi -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6333 ! Trichinella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:464095 -name: Picornavirales -is_a: NCBITaxon:35278 ! ssRNA positive-strand viruses, no DNA stage - -[Term] -id: NCBITaxon:466544 -name: Perdicinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9005 ! Phasianidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:466552 -name: Meleagridinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9005 ! Phasianidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:468 -name: Moraxellaceae -is_a: NCBITaxon:72274 ! Pseudomonadales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Acinetobacteraceae" xsd:string -property_value: IAO:0000118 "Branhamaceae" xsd:string - -[Term] -id: NCBITaxon:469 -name: Acinetobacter -is_a: NCBITaxon:468 ! Moraxellaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:470 -name: Acinetobacter baumannii -is_a: NCBITaxon:909768 ! Acinetobacter calcoaceticus/baumannii complex -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Acinetobacter genomosp. 2" xsd:string -property_value: IAO:0000118 "Acinetobacter genomospecies 2" xsd:string -property_value: IAO:0000118 "Bacterium anitratum" xsd:string - -[Term] -id: NCBITaxon:474019 -name: Sarcoptinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:52281 ! Sarcoptidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:4751 -name: Fungi -namespace: ncbi_taxonomy -synonym: "fungi" EXACT genbank_common_name [] -synonym: "fungi" RELATED blast_name [] -xref: GC_ID:1 -xref: PMID:11062127 -xref: PMID:12684019 -is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom - -[Term] -id: NCBITaxon:47570 -name: Schizotrypanum -is_a: NCBITaxon:5690 ! Trypanosoma -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:480418 -name: Mycobacterium lepromatosis -namespace: ncbi_taxonomy -xref: GC_ID:11 -xref: PMID:19019760 -xref: PMID:25831531 -is_a: NCBITaxon:1763 ! Mycobacterium -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:481 -name: Neisseriaceae -is_a: NCBITaxon:206351 ! Neisseriales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:482 -name: Neisseria -is_a: NCBITaxon:481 ! Neisseriaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "\"Gonococcus\" Lindau 1898" xsd:string -property_value: IAO:0000118 "\"Merismopedia\" Zopf 1885" xsd:string -property_value: IAO:0000118 "Gonococcus" xsd:string - -[Term] -id: NCBITaxon:485 -name: Neisseria gonorrhoeae -is_a: NCBITaxon:482 ! Neisseria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Diplococcus gonorrhoeae" xsd:string -property_value: IAO:0000118 "Gonococcus neisseri" xsd:string -property_value: IAO:0000118 "Merismopedia gonorrhoeae" xsd:string -property_value: IAO:0000118 "Micrococcus der gonorrhoe" xsd:string -property_value: IAO:0000118 "Micrococcus gonococcus" xsd:string -property_value: IAO:0000118 "Micrococcus gonorrhoeae" xsd:string - -[Term] -id: NCBITaxon:487 -name: Neisseria meningitidis -is_a: NCBITaxon:482 ! Neisseria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Diplokokkus intracellularis meningitidis" xsd:string -property_value: IAO:0000118 "Micrococcus intracellularis" xsd:string -property_value: IAO:0000118 "Micrococcus meningitidis" xsd:string -property_value: IAO:0000118 "Micrococcus meningitidis cerebrospinalis" xsd:string -property_value: IAO:0000118 "Neisseria weichselbaumii" xsd:string - -[Term] -id: NCBITaxon:4890 -name: Ascomycota -namespace: ncbi_taxonomy -synonym: "ascomycetes" EXACT genbank_common_name [] -synonym: "ascomycetes" RELATED blast_name [] -synonym: "sac fungi" EXACT common_name [] -xref: GC_ID:1 -xref: PMID:17572334 -is_a: NCBITaxon:451864 ! Dikarya -property_value: has_rank NCBITaxon:phylum - -[Term] -id: NCBITaxon:4891 -name: Saccharomycetes -namespace: ncbi_taxonomy -synonym: "Hemiascomycetes" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:147537 ! Saccharomycotina -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:4892 -name: Saccharomycetales -namespace: ncbi_taxonomy -synonym: "budding yeasts" EXACT genbank_common_name [] -synonym: "Endomycetales" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:4891 ! Saccharomycetes -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:498019 -name: Candida auris -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1540022 ! Clavispora/Candida clade -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:50557 -name: Insecta -is_a: NCBITaxon:6960 ! Hexapoda - -[Term] -id: NCBITaxon:506 -name: Alcaligenaceae -is_a: NCBITaxon:80840 ! Burkholderiales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:51022 -name: Ancylostoma duodenale -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:29169 ! Ancylostoma -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:51291 -name: Chlamydiales -is_a: NCBITaxon:204429 ! Chlamydiia -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:517 -name: Bordetella -is_a: NCBITaxon:506 ! Alcaligenaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:518105 -name: Culex pipiens complex -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:53527 ! Culex - -[Term] -id: NCBITaxon:520 -name: Bordetella pertussis -is_a: NCBITaxon:517 ! Bordetella -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bacterium tussis-convulsivae" xsd:string -property_value: IAO:0000118 "Hemophilus pertussis" xsd:string -property_value: IAO:0000118 "Microbe de la coqueluche" xsd:string - -[Term] -id: NCBITaxon:52281 -name: Sarcoptidae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:83158 ! Sarcoptoidea -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:52282 -name: Sarcoptes -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:474019 ! Sarcoptinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:52283 -name: Sarcoptes scabiei -namespace: ncbi_taxonomy -alt_id: NCBITaxon:197185 -alt_id: NCBITaxon:198574 -alt_id: NCBITaxon:268761 -alt_id: NCBITaxon:268762 -alt_id: NCBITaxon:268763 -alt_id: NCBITaxon:337908 -synonym: "Sarcoptes scabiei type canis" RELATED synonym [] -synonym: "Sarcoptes scabiei type chimp" RELATED synonym [] -synonym: "Sarcoptes scabiei type hominis" RELATED synonym [] -synonym: "Sarcoptes scabiei type suis" RELATED synonym [] -synonym: "Sarcoptes scabiei type wallaby" RELATED synonym [] -synonym: "Sarcoptes scabiei type wombati" RELATED synonym [] -synonym: "Sarcoptes scabiei var. canis" RELATED synonym [] -synonym: "Sarcoptes scabiei var. chimp" RELATED synonym [] -synonym: "Sarcoptes scabiei var. hominis" RELATED synonym [] -synonym: "Sarcoptes scabiei var. nyctereutis" RELATED synonym [] -synonym: "Sarcoptes scabiei var. suis" RELATED synonym [] -synonym: "Sarcoptes scabiei var. wallaby" RELATED synonym [] -synonym: "Sarcoptes scabiei var. wombati" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:52282 ! Sarcoptes -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:53469 -name: Ancylostomatinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33278 ! Ancylostomatidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:53527 -name: Culex -namespace: ncbi_taxonomy -synonym: "Culex" EXACT scientific_name [] -xref: GC_ID:1 -is_a: NCBITaxon:7174 ! Culex -property_value: has_rank NCBITaxon:subgenus - -[Term] -id: NCBITaxon:53541 -name: Stegomyia -is_a: NCBITaxon:7158 ! Aedes - -[Term] -id: NCBITaxon:53550 -name: Culicini -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43817 ! Culicinae -property_value: has_rank NCBITaxon:tribe - -[Term] -id: NCBITaxon:543 -name: Enterobacteriaceae -is_a: NCBITaxon:91347 ! Enterobacterales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Enterobacteraceae" xsd:string - -[Term] -id: NCBITaxon:54388 -name: Salmonella enterica subsp. enterica serovar Paratyphi A -is_a: NCBITaxon:59201 ! Salmonella enterica subsp. enterica -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bacterium paratyphi" xsd:string -property_value: IAO:0000118 "Bacterium paratyphi typhus A" xsd:string -property_value: IAO:0000118 "Salmonella choleraesuis choleraesuis (serotype paratyphi A)" xsd:string -property_value: IAO:0000118 "Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A" xsd:string -property_value: IAO:0000118 "Salmonella paratyphi" xsd:string -property_value: IAO:0000118 "Salmonella paratyphi A" xsd:string -property_value: IAO:0000118 "Salmonella paratyphi-a" xsd:string - -[Term] -id: NCBITaxon:54736 -name: Salmonella bongori -namespace: ncbi_taxonomy -alt_id: NCBITaxon:59206 -synonym: "Salmonella cholerae-suis subsp. bongori" RELATED synonym [] -synonym: "Salmonella choleraesuis subsp. bongori" RELATED synonym [] -synonym: "Salmonella enterica subsp. bongori" RELATED synonym [] -synonym: "Salmonella enterica subsp. V" RELATED synonym [] -synonym: "Salmonella enterica V" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:15653929 -xref: PMID:15653930 -xref: PMID:2915026 -xref: PMID:4011990 -xref: PMID:7149525 -is_a: NCBITaxon:590 ! Salmonella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:548681 -name: Herpesvirales -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:35237 ! dsDNA virus, no RNA stage -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:5500 -name: Coccidioides -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1593277 ! Onygenales incertae sedis -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:5501 -name: Coccidioides immitis -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:5500 ! Coccidioides -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:554915 -name: Amoebozoa -namespace: ncbi_taxonomy -xref: GC_ID:1 -xref: PMID:23020233 -is_a: NCBITaxon:2759 ! Eukaryota - -[Term] -id: NCBITaxon:555406 -name: Archamoebae -namespace: ncbi_taxonomy -xref: GC_ID:1 -xref: PMID:23020233 -is_a: NCBITaxon:554915 ! Amoebozoa - -[Term] -id: NCBITaxon:561 -name: Escherichia -is_a: NCBITaxon:543 ! Enterobacteriaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:562 -name: Escherichia coli -is_a: NCBITaxon:561 ! Escherichia -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bacillus coli" xsd:string -property_value: IAO:0000118 "Bacterium coli" xsd:string -property_value: IAO:0000118 "Bacterium coli commune" xsd:string -property_value: IAO:0000118 "E. coli" xsd:string -property_value: IAO:0000118 "Enterococcus coli" xsd:string - -[Term] -id: NCBITaxon:5653 -name: Kinetoplastida -is_a: NCBITaxon:33682 ! Euglenozoa -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Kinetoplastea" xsd:string -property_value: IAO:0000118 "kinetoplasts" xsd:string -property_value: IAO:0000118 "Protomonadida" xsd:string - -[Term] -id: NCBITaxon:5654 -name: Trypanosomatidae -is_a: NCBITaxon:5653 ! Kinetoplastida -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:565995 -name: Bundibugyo ebolavirus -is_a: NCBITaxon:186536 ! Ebolavirus -property_value: IAO:0000118 "Ebolavirus bundibugyo" xsd:string - -[Term] -id: NCBITaxon:5690 -name: Trypanosoma -is_a: NCBITaxon:5654 ! Trypanosomatidae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:5693 -name: Trypanosoma cruzi -is_a: NCBITaxon:47570 ! Schizotrypanum -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:570 -name: Klebsiella -namespace: ncbi_taxonomy -alt_id: NCBITaxon:39823 -synonym: "Hyalococcus" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:10555350 -xref: PMID:11411716 -xref: PMID:12635932 -is_a: NCBITaxon:543 ! Enterobacteriaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:5738 -name: Diplomonadida -namespace: ncbi_taxonomy -synonym: "diplomonads" EXACT common_name [] -synonym: "diplomonads" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:207245 ! Fornicata - -[Term] -id: NCBITaxon:5739 -name: Hexamitidae -namespace: ncbi_taxonomy -xref: GC_ID:6 -is_a: NCBITaxon:5738 ! Diplomonadida -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:5740 -name: Giardia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:68459 ! Giardiinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:5741 -name: Giardia intestinalis -namespace: ncbi_taxonomy -synonym: "Giardia duodenalis" RELATED synonym [] -synonym: "Giardia lamblia" RELATED genbank_synonym [] -synonym: "Lamblia intestinalis" RELATED synonym [] -xref: GC_ID:1 -xref: PMID:11432808 -xref: PMID:19135417 -is_a: NCBITaxon:5740 ! Giardia -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:5758 -name: Entamoeba -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33084 ! Entamoebidae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:5794 -name: Apicomplexa -is_a: NCBITaxon:33630 ! Alveolata -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000118 "apicomplexans" xsd:string - -[Term] -id: NCBITaxon:5796 -name: Coccidia -namespace: ncbi_taxonomy -synonym: "coccidians" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1280412 ! Conoidasida -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:5799 -name: Eimeriidae -namespace: ncbi_taxonomy -synonym: "Eimeriids" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:423054 ! Eimeriorina -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:5806 -name: Cryptosporidium -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:35082 ! Cryptosporidiidae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:5807 -name: Cryptosporidium parvum -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:5806 ! Cryptosporidium -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:5819 -name: Haemosporida -is_a: NCBITaxon:422676 ! Aconoidasida -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000118 "haemosporidians" xsd:string -property_value: IAO:0000118 "haemosporina" xsd:string - -[Term] -id: NCBITaxon:5820 -name: Plasmodium -is_a: NCBITaxon:1639119 ! Plasmodiidae -property_value: IAO:0000117 "Matthew Diller" xsd:string - -[Term] -id: NCBITaxon:5833 -name: Plasmodium falciparum -is_a: NCBITaxon:418107 ! Plasmodium (Laverania) -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "malaria parasite P. falciparum" xsd:string -property_value: IAO:0000118 "plasmodium (laverania) falciparum" xsd:string - -[Term] -id: NCBITaxon:5855 -name: Plasmodium vivax -is_a: NCBITaxon:418103 ! Plasmodium (Plasmodium) -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000118 "malaria parasite p. vivax" xsd:string - -[Term] -id: NCBITaxon:5858 -name: Plasmodium malariae -is_a: NCBITaxon:418103 ! Plasmodium (Plasmodium) -property_value: IAO:0000117 "Matthew Diller" xsd:string - -[Term] -id: NCBITaxon:590 -name: Salmonella -is_a: NCBITaxon:543 ! Enterobacteriaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:59201 -name: Salmonella enterica subsp. enterica -is_a: NCBITaxon:28901 ! Salmonella enterica -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Salmonella cholerae-suis subsp. cholerae-suis" xsd:string -property_value: IAO:0000118 "Salmonella choleraesuis subsp. choleraesuis" xsd:string -property_value: IAO:0000118 "Salmonella enterica I" xsd:string -property_value: IAO:0000118 "Salmonella enterica subsp. I" xsd:string - -[Term] -id: NCBITaxon:6072 -name: Eumetazoa -is_a: NCBITaxon:33208 ! Metazoa - -[Term] -id: NCBITaxon:6157 -name: Platyhelminthes -is_a: NCBITaxon:33213 ! Bilateria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "flatworms" xsd:string - -[Term] -id: NCBITaxon:6178 -name: Trematoda -is_a: NCBITaxon:6157 ! Platyhelminthes -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:6179 -name: Digenea -is_a: NCBITaxon:6178 ! Trematoda -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "flukes" xsd:string - -[Term] -id: NCBITaxon:6180 -name: Strigeidida -is_a: NCBITaxon:6179 ! Digenea -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:6181 -name: Schistosoma -is_a: NCBITaxon:31245 ! Schistosomatidae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:6183 -name: Schistosoma mansoni -is_a: NCBITaxon:6181 ! Schistosoma -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:6185 -name: Schistosoma haematobium -is_a: NCBITaxon:6181 ! Schistosoma -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:620 -name: Shigella -namespace: ncbi_taxonomy -xref: GC_ID:11 -xref: PMID:26834722 -is_a: NCBITaxon:543 ! Enterobacteriaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:622 -name: Shigella dysenteriae -namespace: ncbi_taxonomy -synonym: "Bacillus dysenteriae" RELATED synonym [] -synonym: "Bacillus dysentericus" RELATED synonym [] -synonym: "Bacillus shigae" RELATED synonym [] -synonym: "Eberthella dysenteriae" RELATED synonym [] -synonym: "Escherichia/Shigella dysenteriae" EXACT equivalent_name [] -synonym: "Shigella shigae" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:12054222 -is_a: NCBITaxon:620 ! Shigella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:623 -name: Shigella flexneri -namespace: ncbi_taxonomy -synonym: "Escherichia/Shigella flexneri" EXACT equivalent_name [] -synonym: "Shigella paradysenteriae" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:620 ! Shigella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:6231 -name: Nematoda -namespace: ncbi_taxonomy -synonym: "Nemata" RELATED synonym [] -synonym: "nematode" EXACT common_name [] -synonym: "nematodes" EXACT common_name [] -synonym: "nematodes" RELATED blast_name [] -synonym: "roundworm" EXACT common_name [] -synonym: "roundworms" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:1206794 ! Ecdysozoa -property_value: has_rank NCBITaxon:phylum - -[Term] -id: NCBITaxon:6236 -name: Rhabditida -namespace: ncbi_taxonomy -alt_id: NCBITaxon:33251 -xref: GC_ID:1 -is_a: NCBITaxon:119089 ! Chromadorea -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:624 -name: Shigella sonnei -namespace: ncbi_taxonomy -synonym: "Bacterium sonnei" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:620 ! Shigella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:629 -name: Yersinia -namespace: ncbi_taxonomy -synonym: "Yersinia" EXACT scientific_name [] -xref: GC_ID:11 -is_a: NCBITaxon:1903411 ! Yersiniaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:630 -name: Yersinia enterocolitica -namespace: ncbi_taxonomy -synonym: "Bacterium enterocoliticum" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:629 ! Yersinia -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:6308 -name: Strongylida -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6236 ! Rhabditida -property_value: has_rank NCBITaxon:suborder - -[Term] -id: NCBITaxon:632 -name: Yersinia pestis -namespace: ncbi_taxonomy -synonym: "Bacillus pestis" RELATED synonym [] -synonym: "Bacterium pestis" RELATED synonym [] -synonym: "Pasteurella pestis" RELATED synonym [] -synonym: "Pestisella pestis" RELATED synonym [] -synonym: "Yersinia pseudotuberculosis subsp. pestis" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:15084509 -is_a: NCBITaxon:1649845 ! Yersinia pseudotuberculosis complex -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:6329 -name: Trichocephalida -namespace: ncbi_taxonomy -alt_id: NCBITaxon:36085 -alt_id: NCBITaxon:6331 -xref: GC_ID:1 -is_a: NCBITaxon:1457286 ! Dorylaimia -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:6332 -name: Trichinellidae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6329 ! Trichocephalida -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:6333 -name: Trichinella -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6332 ! Trichinellidae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:6334 -name: Trichinella spiralis -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6333 ! Trichinella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:6335 -name: Trichinella nativa -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6333 ! Trichinella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:6336 -name: Trichinella nelsoni -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6333 ! Trichinella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:641 -name: Vibrionaceae -is_a: NCBITaxon:135623 ! Vibrionales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:64320 -name: Zika virus -is_a: NCBITaxon:297696 ! Spondweni virus group -property_value: IAO:0000111 "Zika virus" xsd:string - -[Term] -id: NCBITaxon:649188 -name: Lujo mammarenavirus -namespace: ncbi_taxonomy -synonym: "Lujo virus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1653394 ! Mammarenavirus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:662 -name: Vibrio -is_a: NCBITaxon:641 ! Vibrionaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Beneckea" xsd:string -property_value: IAO:0000118 "Listonella" xsd:string -property_value: IAO:0000118 "Microspira" xsd:string -property_value: IAO:0000118 "Pacinia" xsd:string - -[Term] -id: NCBITaxon:6656 -name: Arthropoda -is_a: NCBITaxon:88770 ! Panarthropoda - -[Term] -id: NCBITaxon:666 -name: Vibrio cholerae -is_a: NCBITaxon:662 ! Vibrio -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bacillo virgola del Koch" xsd:string -property_value: IAO:0000118 "Bacillus cholerae" xsd:string -property_value: IAO:0000118 "Bacillus cholerae-asiaticae" xsd:string -property_value: IAO:0000118 "Kommabacillus" xsd:string -property_value: IAO:0000118 "Liquidivibrio cholerae" xsd:string -property_value: IAO:0000118 "Microspira comma" xsd:string -property_value: IAO:0000118 "Pacinia cholerae-asiaticae" xsd:string -property_value: IAO:0000118 "Spirillum cholerae" xsd:string -property_value: IAO:0000118 "Spirillum cholerae-asiaticae" xsd:string -property_value: IAO:0000118 "Vibrio cholera" xsd:string -property_value: IAO:0000118 "Vibrio cholerae Pacini 1854" xsd:string -property_value: IAO:0000118 "Vibrio cholerae-asiaticae" xsd:string -property_value: IAO:0000118 "Vibrio comma" xsd:string - -[Term] -id: NCBITaxon:670 -name: Vibrio parahaemolyticus -namespace: ncbi_taxonomy -synonym: "Beneckea parahaemolytica" RELATED synonym [] -synonym: "Oceanomonas parahaemolytica" RELATED synonym [] -synonym: "Pasteurella parahaemolytica" RELATED synonym [] -synonym: "Vibrio parahemolyticus" RELATED misspelling [] -xref: GC_ID:11 -xref: PMID:14071901 -xref: PMID:4935323 -is_a: NCBITaxon:717610 ! Vibrio harveyi group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:672 -name: Vibrio vulnificus -namespace: ncbi_taxonomy -synonym: "Beneckea vulnifica" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:1015934 -xref: PMID:8186099 -is_a: NCBITaxon:662 ! Vibrio -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:6843 -name: Chelicerata -namespace: ncbi_taxonomy -synonym: "chelicerates" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:6656 ! Arthropoda -property_value: has_rank NCBITaxon:subphylum - -[Term] -id: NCBITaxon:68459 -name: Giardiinae -namespace: ncbi_taxonomy -xref: GC_ID:6 -is_a: NCBITaxon:5739 ! Hexamitidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:68525 -name: delta/epsilon subdivisions -is_a: NCBITaxon:1224 ! Proteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "not Thiobacteria" xsd:string - -[Term] -id: NCBITaxon:6854 -name: Arachnida -namespace: ncbi_taxonomy -synonym: "arachnids" EXACT genbank_common_name [] -synonym: "arachnids" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:6843 ! Chelicerata -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:689832 -name: Sedoreovirinae -is_a: NCBITaxon:10880 ! Reoviridae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:6933 -name: Acari -namespace: ncbi_taxonomy -synonym: "Acarina" RELATED synonym [] -synonym: "mites & ticks" RELATED blast_name [] -synonym: "mites and ticks" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:6854 ! Arachnida -property_value: has_rank NCBITaxon:subclass - -[Term] -id: NCBITaxon:693995 -name: Coronavirinae -is_a: NCBITaxon:11118 ! Coronaviridae - -[Term] -id: NCBITaxon:693996 -name: Alphacoronavirus -is_a: NCBITaxon:693995 ! Coronavirinae -property_value: IAO:0000118 "Coronavirus group 1" xsd:string -property_value: IAO:0000118 "Group 1 species" xsd:string - -[Term] -id: NCBITaxon:694002 -name: Betacoronavirus -is_a: NCBITaxon:693995 ! Coronavirinae - -[Term] -id: NCBITaxon:6946 -name: Acariformes -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6933 ! Acari -property_value: has_rank NCBITaxon:superorder - -[Term] -id: NCBITaxon:6951 -name: Astigmata -namespace: ncbi_taxonomy -alt_id: NCBITaxon:41437 -alt_id: NCBITaxon:41440 -alt_id: NCBITaxon:41441 -xref: GC_ID:1 -is_a: NCBITaxon:83137 ! Sarcoptiformes -property_value: has_rank NCBITaxon:suborder - -[Term] -id: NCBITaxon:6960 -name: Hexapoda -is_a: NCBITaxon:197562 ! Pancrustacea - -[Term] -id: NCBITaxon:712 -name: Pasteurellaceae -is_a: NCBITaxon:135625 ! Pasteurellales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:7147 -name: Diptera -is_a: NCBITaxon:33392 ! Endopterygota - -[Term] -id: NCBITaxon:7148 -name: Nematocera -is_a: NCBITaxon:7147 ! Diptera - -[Term] -id: NCBITaxon:7157 -name: Culicidae -is_a: NCBITaxon:41827 ! Culicoidea -property_value: IAO:0000118 "mosquitos" xsd:string - -[Term] -id: NCBITaxon:7158 -name: Aedes -is_a: NCBITaxon:1056966 ! Aedini - -[Term] -id: NCBITaxon:7159 -name: Aedes aegypti -is_a: NCBITaxon:53541 ! Stegomyia -property_value: IAO:0000118 "Stegomyia aegypti" xsd:string - -[Term] -id: NCBITaxon:7160 -name: Aedes albopictus -is_a: NCBITaxon:53541 ! Stegomyia -property_value: IAO:0000118 "forest day mosquito" xsd:string -property_value: IAO:0000118 "Stegomyia albopicta" xsd:string - -[Term] -id: NCBITaxon:7164 -name: Anopheles -namespace: ncbi_taxonomy -synonym: "Anopheles" EXACT scientific_name [] -xref: GC_ID:1 -is_a: NCBITaxon:43816 ! Anophelinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:716545 -name: saccharomyceta -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:4890 ! Ascomycota - -[Term] -id: NCBITaxon:716546 -name: leotiomyceta -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:147538 ! Pezizomycotina - -[Term] -id: NCBITaxon:7174 -name: Culex -namespace: ncbi_taxonomy -alt_id: NCBITaxon:44555 -synonym: "Culex" EXACT scientific_name [] -xref: GC_ID:1 -is_a: NCBITaxon:53550 ! Culicini -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:7176 -name: Culex quinquefasciatus -namespace: ncbi_taxonomy -synonym: "Culex fatigan" RELATED misspelling [] -synonym: "Culex fatigans" RELATED synonym [] -synonym: "Culex pipiens fatigans" RELATED synonym [] -synonym: "Culex pipiens quinquefasciatus" RELATED synonym [] -synonym: "Culex pipiens quiquefasciatus" RELATED misspelling [] -synonym: "Culex quinquifasciatus" RELATED misspelling [] -synonym: "Culex quinquifasiatus" RELATED misspelling [] -synonym: "Culex quiquefasciatus" RELATED misspelling [] -synonym: "southern house mosquito" EXACT genbank_common_name [] -xref: GC_ID:1 -xref: PMID:12597651 -is_a: NCBITaxon:518105 ! Culex pipiens complex -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:717610 -name: Vibrio harveyi group -namespace: ncbi_taxonomy -synonym: "Vibrio harveyi clade" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:17704223 -is_a: NCBITaxon:662 ! Vibrio -property_value: has_rank http://purl.obolibrary.org/obo/NCBITaxon_species_group - -[Term] -id: NCBITaxon:72273 -name: Thiotrichales -namespace: ncbi_taxonomy -synonym: "Thiomicrospira group" RELATED synonym [] -synonym: "Thiothrix/Francisella group" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:16280474 -is_a: NCBITaxon:1236 ! Gammaproteobacteria -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:72274 -name: Pseudomonadales -is_a: NCBITaxon:1236 ! Gammaproteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Pseudomonaceae/Moraxellaceae group" xsd:string - -[Term] -id: NCBITaxon:72293 -name: Helicobacteraceae -is_a: NCBITaxon:213849 ! Campylobacterales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Helicobacter group" xsd:string - -[Term] -id: NCBITaxon:72294 -name: Campylobacteraceae -namespace: ncbi_taxonomy -synonym: "Campylobacter group" RELATED synonym [] -synonym: "Campylobacteraceae Vandamme and De Ley 1991" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:213849 ! Campylobacterales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:724 -name: Haemophilus -is_a: NCBITaxon:712 ! Pasteurellaceae -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:727 -name: Haemophilus influenzae -is_a: NCBITaxon:724 ! Haemophilus -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bacterium influenzae" xsd:string -property_value: IAO:0000118 "Coccobacillus pfeifferi" xsd:string -property_value: IAO:0000118 "Haemophilus meningitidis" xsd:string -property_value: IAO:0000118 "Influenza-bacillus" xsd:string -property_value: IAO:0000118 "Mycobacterium influenzae" xsd:string - -[Term] -id: NCBITaxon:730 -name: [Haemophilus] ducreyi -namespace: ncbi_taxonomy -synonym: "Bacillus ulceris cancrosi" RELATED synonym [] -synonym: "Coccobacillus ducreyi" RELATED synonym [] -synonym: "Haemophilus ducreyi" EXACT equivalent_name [] -xref: GC_ID:11 -is_a: NCBITaxon:724 ! Haemophilus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:7496 -name: Pterygota -is_a: NCBITaxon:85512 ! Dicondylia - -[Term] -id: NCBITaxon:75739 -name: Eucoccidiorida -namespace: ncbi_taxonomy -synonym: "Eucoccidiida" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:5796 ! Coccidia -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:766 -name: Rickettsiales -namespace: ncbi_taxonomy -synonym: "alpha-1 proteobacteria" RELATED in_part [] -synonym: "Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993" RELATED synonym [] -synonym: "Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001" RELATED synonym [] -synonym: "rickettsias" EXACT genbank_common_name [] -xref: GC_ID:11 -xref: PMID:11760958 -xref: PMID:8240958 -is_a: NCBITaxon:28211 ! Alphaproteobacteria -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:768 -name: Anaplasma -namespace: ncbi_taxonomy -synonym: "Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:11760958 -is_a: NCBITaxon:942 ! Anaplasmataceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:76804 -name: Nidovirales -is_a: NCBITaxon:35278 ! ssRNA positive-strand viruses, no DNA stage -property_value: IAO:0000111 "Nidovirales" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: NCBITaxon:7711 -name: Chordata -is_a: NCBITaxon:33511 ! Deuterostomia -property_value: IAO:0000118 "chordates" xsd:string - -[Term] -id: NCBITaxon:7742 -name: Vertebrata -comment: authority: Vertebrata Cuvier, 1812 -is_a: NCBITaxon:89593 ! Craniata -property_value: IAO:0000118 "vertebrates" xsd:string - -[Term] -id: NCBITaxon:775 -name: Rickettsiaceae -namespace: ncbi_taxonomy -synonym: "Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Brenner et al. 1993" RELATED synonym [] -synonym: "Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Dumler et al. 2001" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:11760958 -xref: PMID:2592342 -xref: PMID:8240958 -is_a: NCBITaxon:766 ! Rickettsiales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:776 -name: Coxiella -namespace: ncbi_taxonomy -synonym: "Burnetia" RELATED synonym [] -synonym: "Coxiella" EXACT scientific_name [] -xref: GC_ID:11 -is_a: NCBITaxon:118968 ! Coxiellaceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:77643 -name: Mycobacterium tuberculosis complex -is_a: NCBITaxon:1763 ! Mycobacterium - -[Term] -id: NCBITaxon:777 -name: Coxiella burnetii -namespace: ncbi_taxonomy -synonym: "Coxiella burnetii8" RELATED misspelling [] -synonym: "Rickettsia burneti" RELATED synonym [] -synonym: "Rickettsia diaporica" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:9226923 -is_a: NCBITaxon:776 ! Coxiella -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:7776 -name: Gnathostomata -is_a: NCBITaxon:7742 ! Vertebrata -property_value: IAO:0000118 "jawed vertebrates" xsd:string - -[Term] -id: NCBITaxon:780 -name: Rickettsia -namespace: ncbi_taxonomy -synonym: "Rickettsia da Rocha-Lima 1916" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:10939649 -xref: PMID:11491333 -xref: PMID:9103608 -is_a: NCBITaxon:33988 ! Rickettsieae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:782 -name: Rickettsia prowazekii -namespace: ncbi_taxonomy -xref: GC_ID:11 -xref: PMID:15879256 -is_a: NCBITaxon:114292 ! typhus group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:783 -name: Rickettsia rickettsii -namespace: ncbi_taxonomy -synonym: "\"Dermacentroxenus rickettsii\" Wolbach 1919" RELATED synonym [] -synonym: "Dermacentroxenus rickettsii" RELATED synonym [] -synonym: "Rickettsia rickettsii (Wolbach 1919) Brumpt 1922" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:114277 ! spotted fever group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:785 -name: Rickettsia typhi -namespace: ncbi_taxonomy -synonym: "Dermacentroxenus typhi" RELATED synonym [] -synonym: "Rickettsia mooseri" RELATED synonym [] -xref: GC_ID:11 -is_a: NCBITaxon:114292 ! typhus group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:80840 -name: Burkholderiales -is_a: NCBITaxon:28216 ! Betaproteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Burkholderia/Oxalobacter/Ralstonia group" xsd:string - -[Term] -id: NCBITaxon:809 -name: Chlamydiaceae -is_a: NCBITaxon:51291 ! Chlamydiales -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:80941 -name: Guaroa virus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1933274 ! Guaroa orthobunyavirus - -[Term] -id: NCBITaxon:810 -name: Chlamydia -is_a: NCBITaxon:1113537 ! Chlamydia/Chlamydophila group -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bedsonia" xsd:string -property_value: IAO:0000118 "Chlamydophila" xsd:string -property_value: IAO:0000118 "Miyagawanella" xsd:string -property_value: IAO:0000118 "Rakeia" xsd:string -property_value: IAO:0000118 "Rickettsiaformis" xsd:string - -[Term] -id: NCBITaxon:813 -name: Chlamydia trachomatis -is_a: NCBITaxon:810 ! Chlamydia -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Chlamydozoon trachomatis" xsd:string -property_value: IAO:0000118 "Rickettsia trachomae" xsd:string -property_value: IAO:0000118 "Rickettsia trachomatis" xsd:string - -[Term] -id: NCBITaxon:8287 -name: Sarcopterygii -is_a: NCBITaxon:117571 ! Euteleostomi - -[Term] -id: NCBITaxon:83137 -name: Sarcoptiformes -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6946 ! Acariformes -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:83158 -name: Sarcoptoidea -namespace: ncbi_taxonomy -synonym: "Listrophoroidea" RELATED synonym [] -synonym: "Psoroptoidea" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:223472 ! Psoroptidia -property_value: has_rank NCBITaxon:superfamily - -[Term] -id: NCBITaxon:83554 -name: Chlamydia psittaci -namespace: ncbi_taxonomy -alt_id: NCBITaxon:812 -synonym: "Chlamydia psitacci" RELATED misspelling [] -synonym: "Chlamydophila psittaci" RELATED genbank_synonym [] -synonym: "Chlamydozoon psittaci" RELATED synonym [] -synonym: "Ehrlichia psittaci" RELATED synonym [] -synonym: "Rickettsia psittaci" RELATED synonym [] -synonym: "Rickettsiaformis psittacosis" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:10319462 -xref: PMID:12807198 -xref: PMID:8102247 -xref: PMID:8347519 -is_a: NCBITaxon:810 ! Chlamydia -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:8457 -name: Sauropsida -namespace: ncbi_taxonomy -synonym: "sauropsids" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:32524 ! Amniota - -[Term] -id: NCBITaxon:8492 -name: Archosauria -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1329799 ! Archelosauria - -[Term] -id: NCBITaxon:85007 -name: Corynebacteriales -is_a: NCBITaxon:1760 ! Actinobacteria -property_value: IAO:0000118 "Corynebacterineae" xsd:string - -[Term] -id: NCBITaxon:85512 -name: Dicondylia -is_a: NCBITaxon:50557 ! Insecta - -[Term] -id: NCBITaxon:86661 -name: Bacillus cereus group -is_a: NCBITaxon:1386 ! Bacillus - -[Term] -id: NCBITaxon:8782 -name: Aves -namespace: ncbi_taxonomy -synonym: "birds" EXACT genbank_common_name [] -synonym: "birds" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:436492 ! Coelurosauria -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:8825 -name: Neognathae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:8782 ! Aves -property_value: has_rank NCBITaxon:superorder - -[Term] -id: NCBITaxon:8826 -name: Anseriformes -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1549675 ! Galloanserae -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:8830 -name: Anatidae -namespace: ncbi_taxonomy -synonym: "waterfowl" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:8826 ! Anseriformes -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:88456 -name: Cyclospora cayetanensis -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:44417 ! Cyclospora -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:88770 -name: Panarthropoda -is_a: NCBITaxon:1206794 ! Ecdysozoa - -[Term] -id: NCBITaxon:89593 -name: Craniata -is_a: NCBITaxon:7711 ! Chordata - -[Term] -id: NCBITaxon:8976 -name: Galliformes -namespace: ncbi_taxonomy -synonym: "fowls" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:1549675 ! Galloanserae -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:9005 -name: Phasianidae -namespace: ncbi_taxonomy -alt_id: NCBITaxon:9099 -synonym: "turkeys" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:8976 ! Galliformes -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:9030 -name: Gallus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9072 ! Phasianinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:9031 -name: Gallus gallus -namespace: ncbi_taxonomy -synonym: "bantam" EXACT common_name [] -synonym: "chicken" EXACT genbank_common_name [] -synonym: "chickens" EXACT common_name [] -synonym: "Gallus domesticus" RELATED misnomer [] -synonym: "Gallus gallus domesticus" RELATED misnomer [] -xref: GC_ID:1 -is_a: NCBITaxon:9030 ! Gallus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:90370 -name: Salmonella enterica subsp. enterica serovar Typhi -is_a: NCBITaxon:59201 ! Salmonella enterica subsp. enterica -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bacillus typhi" xsd:string -property_value: IAO:0000118 "Bacterium (subgen. Eberthella) typhi" xsd:string -property_value: IAO:0000118 "Salmonella choleraesuis serovar Typhi" xsd:string -property_value: IAO:0000118 "Salmonella choleraesuis typhi" xsd:string -property_value: IAO:0000118 "Salmonella enterica ser. typhi" xsd:string -property_value: IAO:0000118 "Salmonella enterica serotype Typhi" xsd:string -property_value: IAO:0000118 "Salmonella enterica serovar Typhi" xsd:string -property_value: IAO:0000118 "Salmonella typhi" xsd:string - -[Term] -id: NCBITaxon:9072 -name: Phasianinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9005 ! Phasianidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:9090 -name: Coturnix -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:466544 ! Perdicinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:90964 -name: Staphylococcaceae -is_a: NCBITaxon:1385 ! Bacillales -property_value: IAO:0000111 "Staphylococcaceae" xsd:string -property_value: IAO:0000118 "Staphylococcus group" xsd:string - -[Term] -id: NCBITaxon:909768 -name: Acinetobacter calcoaceticus/baumannii complex -is_a: NCBITaxon:469 ! Acinetobacter -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string - -[Term] -id: NCBITaxon:9102 -name: Meleagris -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:466552 ! Meleagridinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:9103 -name: Meleagris gallopavo -namespace: ncbi_taxonomy -synonym: "common turkey" EXACT common_name [] -synonym: "turkey" EXACT genbank_common_name [] -synonym: "wild turkey" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:9102 ! Meleagris -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:91061 -name: Bacilli -is_a: NCBITaxon:1239 ! Firmicutes -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Bacillus/Lactobacillus/Strptococcus group" xsd:string -property_value: IAO:0000118 "Firmibacteria" xsd:string - -[Term] -id: NCBITaxon:91347 -name: Enterobacterales -is_a: NCBITaxon:1236 ! Gammaproteobacteria -property_value: IAO:0000117 "Mirela L Vasconcelos" xsd:string -property_value: IAO:0000118 "Enterobacteriaceae and related endosymbionts" xsd:string -property_value: IAO:0000118 "Enterobacteriaceae group" xsd:string -property_value: IAO:0000118 "Enterobacteriales" xsd:string - -[Term] -id: NCBITaxon:91561 -name: Cetartiodactyla -namespace: ncbi_taxonomy -synonym: "even-toed ungulates" RELATED blast_name [] -synonym: "whales, hippos, ruminants, pigs, camels etc." EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:314145 ! Laurasiatheria - -[Term] -id: NCBITaxon:9347 -name: Eutheria -is_a: NCBITaxon:32525 ! Theria -property_value: IAO:0000118 "eutherian mammals" xsd:string -property_value: IAO:0000118 "placental mammals" xsd:string -property_value: IAO:0000118 "Placentalia" xsd:string -property_value: IAO:0000118 "placentals" xsd:string - -[Term] -id: NCBITaxon:93934 -name: Coturnix japonica -namespace: ncbi_taxonomy -synonym: "Coturnix coturnix japanica" RELATED synonym [] -synonym: "Coturnix coturnix japonica" RELATED synonym [] -synonym: "Coturnix coturnix Japonicus" RELATED synonym [] -synonym: "Coturnix japonica japonica" RELATED synonym [] -synonym: "Japanese quail" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:9090 ! Coturnix -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:942 -name: Anaplasmataceae -namespace: ncbi_taxonomy -synonym: "Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001" RELATED synonym [] -synonym: "Ehrlichiae" RELATED misspelling [] -xref: GC_ID:11 -xref: PMID:11760958 -is_a: NCBITaxon:766 ! Rickettsiales -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:943 -name: Ehrlichia -namespace: ncbi_taxonomy -alt_id: NCBITaxon:778 -synonym: "\"Ehrlichia (subgen. Cowdria)\" Moshkovski 1945" RELATED synonym [] -synonym: "\"Kurlovia\" Zhdanov 1953" RELATED synonym [] -synonym: "\"Nicollea\" (in part) Macchiavello 1947" RELATED synonym [] -synonym: "\"Nicollea\" Macchiavello 1947" RELATED synonym [] -synonym: "\"Rickettsia (subgen. Ehrlichia)\" Moshkovski 1937" RELATED synonym [] -synonym: "Cowdria" RELATED synonym [] -synonym: "Cowdria Moshkovski 1947" RELATED synonym [] -synonym: "Ehrlichia (subgen. Cowdria)" RELATED synonym [] -synonym: "Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001" RELATED synonym [] -synonym: "Kurlovia" RELATED synonym [] -synonym: "Nicollea" RELATED synonym [] -synonym: "possibly \"Donatienella\" Rousselot 1948" RELATED synonym [] -synonym: "Rickettsia (subgen. Ehrlichia)" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:11414267 -xref: PMID:11760958 -is_a: NCBITaxon:942 ! Anaplasmataceae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:9443 -name: Primates -is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: IAO:0000118 "Primata" xsd:string -property_value: IAO:0000118 "primate" xsd:string -property_value: IAO:0000118 "primates" xsd:string - -[Term] -id: NCBITaxon:945 -name: Ehrlichia chaffeensis -namespace: ncbi_taxonomy -synonym: "Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001" RELATED synonym [] -synonym: "Ehrlichia chaffensis" RELATED misspelling [] -xref: GC_ID:11 -xref: PMID:11760958 -xref: PMID:1757557 -is_a: NCBITaxon:106178 ! canis group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:948 -name: Anaplasma phagocytophilum -namespace: ncbi_taxonomy -alt_id: NCBITaxon:59888 -alt_id: NCBITaxon:75053 -alt_id: NCBITaxon:75115 -alt_id: NCBITaxon:946 -synonym: "agent of human granulocytic ehrlichiosis" EXACT common_name [] -synonym: "Anaplasma phagocytophila" RELATED synonym [] -synonym: "Cytoecetes bovis" RELATED synonym [] -synonym: "Cytoecetes phagocytophila" RELATED synonym [] -synonym: "Ehrlichia equi" RELATED synonym [] -synonym: "Ehrlichia phagocytophila" RELATED synonym [] -synonym: "Ehrlichia sp. 'HGE agent'" RELATED synonym [] -synonym: "HGE agent" RELATED synonym [] -synonym: "human granulocytic Ehrlichia" RELATED synonym [] -synonym: "Rickettsia phagocytophila" RELATED synonym [] -synonym: "Rickettsia phagocytophila ovis" RELATED synonym [] -xref: GC_ID:11 -xref: PMID:1115421 -xref: PMID:11760958 -xref: PMID:8195363 -is_a: NCBITaxon:106179 ! phagocytophilum group -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:9526 -name: Catarrhini -is_a: NCBITaxon:314293 ! Simiiformes - -[Term] -id: NCBITaxon:9527 -name: Cercopithecidae -is_a: NCBITaxon:314294 ! Cercopithecoidea -property_value: IAO:0000118 "monkey" xsd:string -property_value: IAO:0000118 "monkeys" xsd:string -property_value: IAO:0000118 "Old World monkeys" xsd:string - -[Term] -id: NCBITaxon:9528 -name: Cercopithecinae -is_a: NCBITaxon:9527 ! Cercopithecidae - -[Term] -id: NCBITaxon:9539 -name: Macaca -is_a: NCBITaxon:9528 ! Cercopithecinae -property_value: IAO:0000118 "macaque" xsd:string -property_value: IAO:0000118 "macaques" xsd:string - -[Term] -id: NCBITaxon:9541 -name: Macaca fascicularis -namespace: ncbi_taxonomy -alt_id: NCBITaxon:36519 -synonym: "crab eating macaque" EXACT common_name [] -synonym: "crab-eating macaque" EXACT genbank_common_name [] -synonym: "cynomolgus macaque" RELATED synonym [] -synonym: "cynomolgus monkey" EXACT common_name [] -synonym: "cynomolgus monkeys" EXACT common_name [] -synonym: "long-tailed macaque" EXACT common_name [] -synonym: "Macaca cynomolgus" RELATED synonym [] -synonym: "Macaca irus" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:9539 ! Macaca -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:9544 -name: Macaca mulatta -is_a: NCBITaxon:9539 ! Macaca -property_value: IAO:0000118 "rhesus macaque" xsd:string -property_value: IAO:0000118 "rhesus macaques" xsd:string -property_value: IAO:0000118 "Rhesus monkey" xsd:string -property_value: IAO:0000118 "rhesus monkeys" xsd:string - -[Term] -id: NCBITaxon:9606 -is_a: NCBITaxon:2759 ! Eukaryota -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - -[Term] -id: NCBITaxon:9608 -name: Canidae -namespace: ncbi_taxonomy -synonym: "dog, coyote, wolf, fox" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:379584 ! Caniformia -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:9611 -name: Canis -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9608 ! Canidae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:9612 -name: Canis lupus -namespace: ncbi_taxonomy -synonym: "gray wolf" EXACT genbank_common_name [] -synonym: "grey wolf" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:9611 ! Canis -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:9615 -name: Canis lupus familiaris -namespace: ncbi_taxonomy -synonym: "Canis canis" RELATED synonym [] -synonym: "Canis domesticus" RELATED synonym [] -synonym: "Canis familiaris" RELATED synonym [] -synonym: "dog" EXACT genbank_common_name [] -synonym: "dogs" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:9612 ! Canis lupus -property_value: has_rank NCBITaxon:subspecies - -[Term] -id: NCBITaxon:9787 -name: Perissodactyla -namespace: ncbi_taxonomy -synonym: "odd-toed ungulates" EXACT genbank_common_name [] -synonym: "odd-toed ungulates" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:314145 ! Laurasiatheria -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:9788 -name: Equidae -namespace: ncbi_taxonomy -synonym: "horses" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:9787 ! Perissodactyla -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:9789 -name: Equus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9788 ! Equidae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:9796 -name: Equus caballus -namespace: ncbi_taxonomy -synonym: "domestic horse" EXACT common_name [] -synonym: "equine" EXACT common_name [] -synonym: "Equus ferus caballus" RELATED synonym [] -synonym: "Equus przewalskii f. caballus" RELATED synonym [] -synonym: "Equus przewalskii forma caballus" RELATED synonym [] -synonym: "horse" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:35510 ! Equus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:9821 -name: Suidae -namespace: ncbi_taxonomy -alt_id: NCBITaxon:39423 -synonym: "boars" EXACT common_name [] -synonym: "pigs" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:35497 ! Suina -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:9822 -name: Sus -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9821 ! Suidae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:9823 -name: Sus scrofa -namespace: ncbi_taxonomy -synonym: "pig" EXACT genbank_common_name [] -synonym: "pigs" EXACT common_name [] -synonym: "Sus scrofus" RELATED misspelling [] -synonym: "swine" EXACT common_name [] -synonym: "wild boar" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:9822 ! Sus -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:9845 -name: Ruminantia -namespace: ncbi_taxonomy -synonym: "Artiodactyla" RELATED in_part [] -xref: GC_ID:1 -is_a: NCBITaxon:91561 ! Cetartiodactyla -property_value: has_rank NCBITaxon:suborder - -[Term] -id: NCBITaxon:9895 -name: Bovidae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:35500 ! Pecora -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:9903 -name: Bos -namespace: ncbi_taxonomy -synonym: "oxen, cattle" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:27592 ! Bovinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:9913 -name: Bos taurus -namespace: ncbi_taxonomy -alt_id: NCBITaxon:272461 -synonym: "Bos bovis" RELATED synonym [] -synonym: "Bos primigenius taurus" RELATED synonym [] -synonym: "Bos Tauurus" RELATED misspelling [] -synonym: "bovine" EXACT common_name [] -synonym: "cattle" EXACT genbank_common_name [] -synonym: "cow" EXACT common_name [] -synonym: "domestic cattle" EXACT common_name [] -synonym: "domestic cow" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:9903 ! Bos -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:9922 -name: Capra -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9963 ! Caprinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:9925 -name: Capra hircus -namespace: ncbi_taxonomy -alt_id: NCBITaxon:57076 -synonym: "Capra aegagrus hircus" RELATED synonym [] -synonym: "Carpa hircus" RELATED misspelling [] -synonym: "domestic goat" EXACT common_name [] -synonym: "goat" EXACT genbank_common_name [] -synonym: "goats" EXACT common_name [] -synonym: "South African angora goat" RELATED misspelling [] -xref: GC_ID:1 -is_a: NCBITaxon:9922 ! Capra -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:9935 -name: Ovis -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9963 ! Caprinae -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:9940 -name: Ovis aries -namespace: ncbi_taxonomy -alt_id: NCBITaxon:9936 -synonym: "domestic sheep" EXACT common_name [] -synonym: "lambs" EXACT common_name [] -synonym: "Ovis ammon aries" RELATED synonym [] -synonym: "Ovis orientalis aries" RELATED synonym [] -synonym: "Ovis ovis" RELATED synonym [] -synonym: "sheep" EXACT genbank_common_name [] -synonym: "wild sheep" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:9935 ! Ovis -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:9963 -name: Caprinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:9895 ! Bovidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: OAE:0000055 -name: contraindication -def: "A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment." [] -is_a: BFO:0000016 -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Contraindication" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/dideo/dev/dideo.owl" xsd:string - -[Term] -id: OBI:0000011 -name: planned process -def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] -is_a: BFO:0000015 -property_value: IAO:0000111 "planned process" xsd:string -property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string -property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \n objectives is a planned process." xsd:string -property_value: IAO:0000117 "Bjoern Peters" xsd:string -property_value: IAO:0000119 "branch derived" xsd:string -property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl - -[Term] -id: OBI:0000047 -name: processed material -def: "Is a material entity that is created or changed during material processing." [] -is_a: BFO:0000040 -property_value: IAO:0000111 "processed material" xsd:string -property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string - -[Term] -id: OBI:0000066 -property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl - -[Term] -id: OBI:0000115 -name: intervention design -def: "An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays." [] -is_a: OBI:0500000 ! study design -property_value: IAO:0000111 "intervention design" xsd:string -property_value: IAO:0000112 "PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Philppe Rocca-Serra" xsd:string -property_value: IAO:0000119 "OBI branch derived" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0000227 -name: data encoding -def: "a documenting process to encode an information entity into a digital document" [] -is_a: IAO:0000572 -property_value: IAO:0000111 "data encoding" xsd:string -property_value: IAO:0000112 "storage of measurement results from an assay into a text file, such as" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string -property_value: IAO:0000119 "OBI branch derived" xsd:string -property_value: IAO:0000232 "We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0000245 -name: organization -def: "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] -property_value: IAO:0000111 "organization" xsd:string -property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000116 "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:\n\n1) there are organization_member_roles (president, treasurer, branch\neditor), with individual persons as bearers\n\n2) there are organization_roles (employer, owner, vendor, patent holder)\n\n3) an organization has a charter / rules / bylaws, which specify what roles\nthere are, how they should be realized, and how to modify the\ncharter/rules/bylaws themselves.\n\nIt is debatable what the organization itself is (some kind of dependent\ncontinuant or an aggregate of people). This also determines who/what the\nbearer of organization_roles' are. My personal favorite is still to define\norganization as a kind of 'legal entity', but thinking it through leads to\nall kinds of questions that are clearly outside the scope of OBI.\n\nInterestingly enough, it does not seem to matter much where we place\norganization itself, as long as we can subclass it (University, Corporation,\nGovernment Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,\nW3C, University of Oklahoma), and have it play roles.\n\nThis leads to my proposal: We define organization through the statements 1 -\n3 above, but without an 'is a' statement for now. We can leave it in its\ncurrent place in the is_a hierarchy (material entity) or move it up to\n'continuant'. We leave further clarifications to BFO, and close this issue\nfor now." xsd:string -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string -property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string -property_value: IAO:0000117 "PERSON: Susanna Sansone" xsd:string -property_value: IAO:0000119 "GROUP: OBI" xsd:string - -[Term] -id: OBI:0000425 -name: averaging objective -def: "An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation." [] -is_a: OBI:0200166 ! data transformation objective -property_value: IAO:0000111 "averaging objective" xsd:string -property_value: IAO:0000112 "A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment." xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string -property_value: IAO:0000117 "James Malone" xsd:string -property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0000471 -property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl - -[Term] -id: OBI:0000576 -name: scattered molecular aggregate -def: "a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates" [] -is_a: BFO:0000027 ! object_aggregate -property_value: IAO:0000111 "scattered molecular aggregate" xsd:string -property_value: IAO:0000112 "the sodium and chloride ions in a glass of salt water" xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000118 "Collective" xsd:string -property_value: IAO:0000119 "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0000658 -name: data representational model -def: "Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax." [] -is_a: IAO:0000033 ! directive information entity -property_value: IAO:0000111 "data representational model" xsd:string -property_value: IAO:0000112 "gene regulatory graph model" xsd:string -property_value: IAO:0000112 "phylogenetic tree" xsd:string -property_value: IAO:0000112 "protein interaction network" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Melanie Courtot" xsd:string -property_value: IAO:0000118 "data structure" xsd:string -property_value: IAO:0000118 "data structure specification" xsd:string -property_value: IAO:0000119 "GROUP: OBI" xsd:string -property_value: IAO:0000232 "2009-02-28: work on this term has been finalized during the OBI workshop winter 2009" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0000674 -name: center value -def: "A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data." [] -is_a: IAO:0000027 ! data item -property_value: APOLLO_SV:0000040 "median" xsd:string -property_value: IAO:0000111 "center value" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "PERSON: James Malone" xsd:string -property_value: IAO:0000117 "PERSON: Monnie McGee" xsd:string -property_value: IAO:0000118 "median" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0000679 -name: average value -def: "A data item that is produced as the output of an averaging data transformation and represents the average value of the input data." [] -is_a: IAO:0000027 ! data item -intersection_of: IAO:0000027 ! data item -intersection_of: OBI:0000312 OBI:0200170 ! averaging data transformation -property_value: APOLLO_SV:0000040 "mean" xsd:string -property_value: IAO:0000111 "average value" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "PERSON: James Malone" xsd:string -property_value: IAO:0000117 "PERSON: Monnie McGee" xsd:string -property_value: IAO:0000118 "arithmetic mean" xsd:string -property_value: IAO:0000118 "false" xsd:boolean -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: IAO:0000600 "A data item that is produced as the output of an averaging data transformation and represents the average value of the input data." xsd:string - -[Term] -id: OBI:0000714 -name: graph of vertices -def: "A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix." [] -is_a: IAO:0000038 -property_value: IAO:0000111 "graph of vertices" xsd:string -property_value: IAO:0000112 "For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities." xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Bjoern Peters" xsd:string -property_value: IAO:0000117 "Chris Stoeckert" xsd:string -property_value: IAO:0000117 "James Malone" xsd:string -property_value: IAO:0000119 "WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0000968 -name: device -def: "A device is a processed material which is designed to perform some function or functions" [] -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:0000114 IAO:0000123 -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 Vancouver workshop 2010" xsd:string - -[Term] -id: OBI:0001092 -name: computer cluster -def: "A group of linked computers, working together closely so that in many respects they form a single computer." [] -is_a: OBI:0400107 ! computer -property_value: IAO:0000111 "computer cluster" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "PERSON: Erik Segerdell" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Cluster_(computing)" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0001173 -name: service -def: "A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer." [] -is_a: OBI:0000011 ! planned process -property_value: IAO:0000111 "service" xsd:string -property_value: IAO:0000112 "providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony " xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Carlo; Matt" xsd:string -property_value: IAO:0000119 "OBI workshop San Diego 2011" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0001226 -name: environmental history design -def: "A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc." [] -is_a: OBI:0500000 ! study design -property_value: IAO:0000111 "environmental history design" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string -property_value: IAO:0000119 "MO_698 environmental_history_design" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0001293 -name: disease state design -def: "A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress." [] -is_a: OBI:0500000 ! study design -property_value: IAO:0000111 "disease state design" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string -property_value: IAO:0000119 "MO_902 disease_state_design" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0001454 -name: pathogenicity design -def: "A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed." [] -is_a: OBI:0500000 ! study design -property_value: IAO:0000111 "pathogenicity design" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string -property_value: IAO:0000119 "MO_807 pathogenicity_design" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0001530 -name: data service -def: "A service that has some information content entity as input and output." [] -comment: Information content entity was used as specified input and output since it was more appropriate then data item or dataset. -is_a: OBI:0001173 ! service -property_value: IAO:0000111 "data service" xsd:string -property_value: IAO:0000112 "Data analysis service such statistical abalysis or storage service such data backup." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "PERSON: Carlo Torniai" xsd:string -property_value: IAO:0000117 "PERSON: Matthew Brush" xsd:string -property_value: IAO:0000119 "PERSON: Carlo Torniai" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0001554 -name: rate measurement datum -def: "A scalar measurement datum that represents the number of events occuring over a time interval" [] -is_a: IAO:0000032 ! scalar measurement datum -property_value: IAO:0000111 "rate measurement datum" xsd:string -property_value: IAO:0000112 "The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time." xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string -property_value: IAO:0000119 "IEDB" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0001615 -name: investigation description -def: "A textual entity that describes an investigation." [] -is_a: IAO:0000300 -property_value: APOLLO_SV:0000040 "investigationDescription" xsd:string -property_value: http://purl.org/dc/elements/1.1/source "NIAID GSCID-BRC" xsd:string -property_value: IAO:0000111 "investigation description" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string -property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: OBI:0001847 "study description" xsd:string -property_value: OBI:0001886 "project description" xsd:string - -[Term] -id: OBI:0001628 -name: investigation identifier -def: "A CRID symbol used to identify an investigation." [] -is_a: IAO:0000577 -property_value: APOLLO_SV:0000040 "investigationLabel" xsd:string -property_value: http://purl.org/dc/elements/1.1/source "NIAID GSCID-BRC" xsd:string -property_value: IAO:0000111 "investigation identifier" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zhneg" xsd:string -property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: OBI:0001886 "project ID" xsd:string - -[Term] -id: OBI:0001629 -name: grant identifier -def: "A CRID symbol used to identify a grant." [] -is_a: IAO:0020000 -property_value: http://purl.org/dc/elements/1.1/source "NIAID GSCID-BRC" xsd:string -property_value: IAO:0000111 "grant identifier" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string -property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: OBI:0001886 "grant ID" xsd:string - -[Term] -id: OBI:0001958 -name: systematic review study design -def: "A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according \\\nto certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were no\\\nt justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed." [] -is_a: OBI:0500000 ! study design -property_value: IAO:0000111 "systematic review study design" xsd:string -property_value: IAO:0000112 "Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/ar\\\nticles/PMC4090399/" xsd:string -property_value: IAO:0000112 "The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic re\\\nview. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string - -[Term] -id: OBI:0002110 -name: digital object identifier -def: "A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles." [] -is_a: IAO:0020000 -property_value: IAO:0000111 "digital object identifier" xsd:string -property_value: IAO:0000112 "The doi symbol: \"10.1109/5.771073\" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "Discussed on Aug 22, 2016 OBI dev call. Details see tracker:\nhttps://sourceforge.net/p/obi/obi-terms/818/" xsd:string -property_value: IAO:0000117 "OBI developers" xsd:string -property_value: IAO:0000118 "DOI" xsd:string -property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Digital_object_identifier\nhttps://www.doi.org/" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -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." [] -property_value: APOLLO_SV:0000040 "Individual" xsd:string -property_value: IAO:0000111 "organism" xsd:string -property_value: IAO:0000114 IAO:0000121 - -[Term] -id: OBI:0200000 -name: data transformation -def: "A data transformation is a process which produces output data from input data" [] -is_a: OBI:0000011 ! planned process -relationship: OBI:0000417 OBI:0200166 ! achieves_planned_objective data transformation objective -property_value: IAO:0000111 "data transformation" xsd:string -property_value: IAO:0000112 "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string -property_value: IAO:0000117 "Helen Parkinson" xsd:string -property_value: IAO:0000117 "James Malone" xsd:string -property_value: IAO:0000117 "Melanie Courtot" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000117 "Richard Scheuermann" xsd:string -property_value: IAO:0000117 "Ryan Brinkman" xsd:string -property_value: IAO:0000117 "Tina Hernandez-Boussard" xsd:string -property_value: IAO:0000118 "data analysis" xsd:string -property_value: IAO:0000118 "data processing" xsd:string -property_value: IAO:0000119 "Branch editors" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0200166 -name: data transformation objective -def: "A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed." [] -is_a: IAO:0000005 ! objective specification -property_value: IAO:0000111 "data transformation objective" xsd:string -property_value: IAO:0000112 "normalize objective" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "James Malone" xsd:string -property_value: IAO:0000119 "PERSON: James Malone" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0200170 -name: averaging data transformation -def: "An averaging data transformation is a data transformation that has objective averaging." [] -is_a: OBI:0200000 ! data transformation -property_value: IAO:0000111 "averaging data transformation" xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "James Malone" xsd:string -property_value: IAO:0000119 "PERSON: James Malone" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0300311 -name: observation design -def: "observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists." [] -is_a: OBI:0500000 ! study design -property_value: IAO:0000111 "observation design" xsd:string -property_value: IAO:0000112 "PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000119 "OBI branch derived" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0302867 -name: calculated datum -name: predicted data item -def: "A data item that was generated on the basis of a calculation or logical reasoning" [] -comment: APOLLO DEVELOPERS: We need to check whether OBI changes the label and the hierarchical place of this class. -is_a: IAO:0000109 ! measurement datum -property_value: IAO:0000111 "predicted data item" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. " xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra; Bjoern Peters" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0302914 -name: digital curation -def: "Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally." [] -is_a: IAO:0000572 -property_value: IAO:0000111 "digital curation" xsd:string -property_value: IAO:0000112 "PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44." xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000119 "wikipedia" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0400107 -name: computer -def: "A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions." [] -is_a: OBI:0000968 ! device -property_value: IAO:0000111 "computer" xsd:string -property_value: IAO:0000112 "Apple PowerBook, Dell OptiPlex" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Melanie Courtot" xsd:string -property_value: IAO:0000117 "Trish Whetzel" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Computer" xsd:string - -[Term] -id: OBI:0500000 -name: study design -def: "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution." [] -is_a: IAO:0000104 ! plan specification -property_value: IAO:0000111 "study design" xsd:string -property_value: IAO:0000112 "a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design." xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000116 "Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available." xsd:string -property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000118 "experimental design" xsd:string -property_value: IAO:0000232 "rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl - -[Term] -id: OBI:0500020 -name: time series design -def: "Groups of assays that are related as part of a time series." [] -is_a: OBI:0500000 ! study design -property_value: IAO:0000111 "time series design" xsd:string -property_value: IAO:0000112 "PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Philippe Rocca-Serra on behalf of MO" xsd:string -property_value: IAO:0000119 "MO_887" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBIws:0000050 -name: software execution -def: "A planned process that realizes the concretization of a software." [] -is_a: OBI:0000011 ! planned process -property_value: IAO:0000117 "ITPPR" xsd:string -property_value: IAO:0000118 "operation" xsd:string -property_value: IAO:0000119 "ITPPR" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/OBIws.owl" xsd:string - -[Term] -id: OBIws:0000104 -name: web service execution -def: "A software execution that is provided by the web service, and involves invoking software execution over network." [] -is_a: OBIws:0000050 ! software execution -property_value: IAO:0000117 "ITPPR" xsd:string -property_value: IAO:0000118 "web service operation" xsd:string -property_value: IAO:0000119 "ITPPR" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/OBIws.owl" xsd:string - -[Term] -id: OGMS:0000014 -name: clinical finding -def: "A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof." [] -is_a: IAO:0000027 ! data item -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: 2010-07-19T10:18:02Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000018 -name: laboratory finding -def: "A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient." [] -is_a: OGMS:0000014 ! clinical finding -property_value: APOLLO_SV:0000040 "result" 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: 2009-06-23T10:21:58Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000023 -name: phenotype -def: "A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species." [] -is_a: BFO:0000019 -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: 2010-07-19T11:13:49Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000027 -name: clinical phenotype -def: "A clinically abnormal phenotype." [] -is_a: OGMS:0000023 ! phenotype -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: 2009-06-23T11:18:05Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000031 -name: disease -def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [] -is_a: BFO:0000016 -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 - -[Term] -id: OGMS:0000032 -name: homeostasis -def: "A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning." [] -is_a: BFO:0000016 -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000117 "Barry Smith" xsd:string -property_value: IAO:0000117 "Richard H. Scheuermann" xsd:string -property_value: IAO:0000117 "Werner Ceusters" xsd:string -property_value: IAO:0000119 "Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. \n\nLink: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/" xsd:string -property_value: IAO:0000232 "creation date: 2009-06-23T11:22:01Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000045 -name: disorder -def: "A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease." [] -is_a: BFO:0000040 -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" xsd:string - -[Term] -id: OGMS:0000063 -name: disease course -def: "The totality of all processes through which a given disease instance is realized." [] -is_a: BFO:0000015 -property_value: IAO:0000111 "disease course" 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: 2009-06-23T11:55:44Z" 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" 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." [] -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 - -[Term] -id: OGMS:0000090 -name: treatment -def: "A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder" [] -comment: Apollo-SV currently defines two subclasses of treatment.\nSee vaccination and antiviral treatment. \n -is_a: OBI:0000011 ! planned process -property_value: APOLLO_SV:0000040 "Treatment" xsd:string -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=35" xsd:string -property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000092 -name: life course -def: "A processual entity which has as parts all the processes in which a given organism is participant." [] -is_a: BFO:0000182 ! history -property_value: APOLLO_SV:0000040 "LifeCycle" xsd:string -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=38" xsd:string -property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string -property_value: IAO:0000600 "A processual entity which has as parts all the processes in which a given organism is participant." xsd:string - -[Term] -id: OGMS:0000096 -name: health care process -def: "A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process" [] -is_a: BFO:0000015 -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string -property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000097 -name: health care encounter -def: "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter" [] -is_a: OGMS:0000096 ! health care process -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string -property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000098 -name: hospitalization -is_a: OGMS:0000097 ! health care encounter -property_value: APOLLO_SV:0000040 "hospitalization" xsd:string -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string -property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000099 -name: outpatient encounter -is_a: OGMS:0000097 ! health care encounter -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string -property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000100 -name: inpatient encounter -is_a: OGMS:0000097 ! health care encounter -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string -property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000101 -name: ED encounter -is_a: OGMS:0000097 ! health care encounter -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string -property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OGMS:0000105 -name: relapse -def: "A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course." [] -is_a: BFO:0000015 -property_value: IAO:0000117 "Albert Goldfain" xsd:string -property_value: IAO:0000119 "http://code.google.com/p/ogms/issues/detail?id=73" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string - -[Term] -id: OMIABIS:0000019 -name: unique resource locator -def: "A CRID that constitutes a reference to an Internet resource." [] -is_a: IAO:0020000 -property_value: APOLLO_SV:0000040 "url" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "uri" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Uniform_resource_locator" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omiabis.owl" xsd:string - -[Term] -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 -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 - -[Term] -id: OMRSE:00000007 -name: gender role -def: "A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture." [] -is_a: BFO:0000023 -property_value: APOLLO_SV:0000040 "sex" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Gender_role" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000008 -name: male gender role -def: "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question." [] -is_a: OMRSE:00000007 ! gender role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "male gender" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000009 -name: female gender role -def: "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question." [] -is_a: OMRSE:00000007 ! gender role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "female gender" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000010 -name: human health care role -def: "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. " [] -comment: Mathias Brochhausen -is_a: OMRSE:00002072 ! role in human social processes -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000118 "health care role" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000011 -name: patient role -def: "A human health care role that inheres in an organism [human?] as the recipient of a health care service." [] -def: "A role borne by an organism being as the recipient of a health care service." [] -is_a: OMRSE:00000010 ! human health care role -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "patient" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Patient" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000015 -name: health care provider organization role -comment: Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). -is_a: OMRSE:00000027 ! organization health care role -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000022 -name: collection of organisms -def: "An object aggregate of organisms." [] -comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class. -is_a: BFO:0000027 ! object_aggregate -intersection_of: BFO:0000027 ! object_aggregate -intersection_of: RO:0002351 OBI:0100026 ! organism -intersection_of: RO:0002351 OBI:0100026 {all_only="true"} ! organism -equivalent_to: PCO:0000000 ! PCO:collection of organisms -property_value: IAO:0000600 "This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species." xsd:string - -[Term] -id: OMRSE:00000023 -name: collection of humans -comment: An object aggregate all of whose components are human beings. -is_a: PCO:0000018 ! collection of organisms of the same species -intersection_of: OMRSE:00000022 ! collection of organisms -intersection_of: RO:0002351 NCBITaxon:9606 -intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000025 -name: organization social role -def: "A role in human social processes that inheres in an organization." [] -comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants. -is_a: OMRSE:00002072 ! role in human social processes -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000026 -name: organism social role -def: "A role in human social processes that inheres in an organism." [] -comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants. -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 -relationship: RO:0000052 OBI:0100026 ! 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 - -[Term] -id: OMRSE:00000027 -name: organization health care role -def: "An organization social role that is realized by a health care process." [] -comment: Previous definition: An organization social role played by an organization in health care processes. -is_a: OMRSE:00000025 ! organization social role -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000033 -name: aggregate of organizations -def: "An aggregate of organizations that have some feature in common, but is not itself an organization." [] -comment: It is often convenient to group organizations together that otherwise might not even interact with one another. -is_a: BFO:0000027 ! object_aggregate -intersection_of: BFO:0000027 ! object_aggregate -intersection_of: RO:0002351 OBI:0000245 ! organization -intersection_of: RO:0002351 OBI:0000245 {all_only="true"} ! organization -property_value: IAO:0000117 "William R. Hogan" xsd:string - -[Term] -id: OMRSE:00000052 -name: hospital function -def: "A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population." [] -is_a: BFO:0000034 -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000053 -name: school function -def: "A function inhering in a facility that manifests by the facility participating in providing formal education to a student population." [] -is_a: BFO:0000034 -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000054 -name: hospital role -def: "A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care." [] -is_a: OMRSE:00000015 ! health care provider organization role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000055 -name: school role -is_a: BFO:0000023 -property_value: IAO:0000117 "An organization social role that inheres in an organization and is realized by providing formal education to students." xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000056 -name: hospital organization -def: "An organization that is the bearer of a hospital role." [] -is_a: OBI:0000245 ! organization -intersection_of: OBI:0000245 ! organization -intersection_of: RO:0000053 OMRSE:00000054 ! is bearer of hospital role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000057 -name: school organization -def: "An organization that is the bearer of a school role." [] -is_a: OBI:0000245 ! organization -intersection_of: OBI:0000245 ! organization -intersection_of: RO:0000053 OMRSE:00000055 ! is bearer of school role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000058 -name: student role -def: "A human social role that is realized by the process of formal education that the bearer undergoes." [] -is_a: OMRSE:00000001 ! human social role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000059 -name: nursery school role -comment: Key motivating use case was Synthia synthetic population data.\n -is_a: OMRSE:00000055 ! school role -property_value: APOLLO_SV:0000040 "preschool" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000060 -name: primary school role -comment: Key motivating use case was Synthia synthetic population data. -is_a: OMRSE:00000055 ! school role -property_value: APOLLO_SV:0000040 "primarySchool" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000061 -name: architectural structure -def: "A material entity that is a human made strcuture with firm connection between its foundation and the ground." [] -comment: "Building" is a subclass of this. -comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". -is_a: BFO:0000040 -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "http://de.wikipedia.org/wiki/Bauwerk" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000062 -name: facility -def: "An architectural structure that bears some function." [] -is_a: OMRSE:00000061 ! architectural structure -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000063 -name: hospital facility -def: "A facility that is run by a hospital organization and is the bearer of a hospital function." [] -is_a: OMRSE:00000102 ! health care facility -property_value: APOLLO_SV:0000040 "HealthcareFacility" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000064 -name: school facility -def: "A facility that is run by a school organization and is the bearer of a school function." [] -is_a: OMRSE:00000062 ! facility -property_value: APOLLO_SV:0000040 "SchoolFacility" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000065 -name: secondary school role -comment: Key motivating use case was Synthia synthetic population data. -is_a: OMRSE:00000055 ! school role -property_value: APOLLO_SV:0000040 "secondarySchool" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000074 -name: housing unit -def: "A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function." [] -comment: Housing units are individuated by their residence functions. -is_a: BFO:0000040 -property_value: APOLLO_SV:0000040 "houses" xsd:string -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000119 "https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000076 -name: household -def: "A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function." [] -is_a: BFO:0000040 -property_value: APOLLO_SV:0000040 "Household" xsd:string -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000078 -name: workplace facility -is_a: OMRSE:00000062 ! facility -property_value: APOLLO_SV:0000040 "workplace" xsd:string -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000079 -name: workplace function -def: "a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out" [] -is_a: BFO:0000034 -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000098 -name: racial identity datum -def: "A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method." [] -is_a: OMRSE:00000132 ! identity datum -property_value: APOLLO_SV:0000040 "race" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000102 -name: health care facility -is_a: OMRSE:00000062 ! facility -property_value: IAO:0000117 "A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000132 -name: identity datum -is_a: IAO:0000030 ! information content entity -property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string -property_value: http://purl.org/dc/elements/1.1/creator "An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00002072 -name: role in human social processes -def: "A role inhering in an entity realized by social interactions in human society." [] -comment: Previous definition: A role played by an entity in human social processes. -is_a: BFO:0000023 -property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl" xsd:string - -[Term] -id: ObsoleteClass -name: Obsolete Class - -[Term] -id: PATO:0000040 -name: distance -namespace: quality -def: "A quality that is the extent of space between two entities." [] -subset: attribute_slim -subset: relational_slim -subset: scalar_slim -is_a: PATO:0001018 ! physical quality -property_value: APOLLO_SV:0000040 "Distance" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0000047 -name: biological sex -def: "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved." [] -is_a: BFO:0000019 -property_value: APOLLO_SV:0000040 "biologicalSex" xsd:string -property_value: IAO:0000111 "biological sex" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: PATO:0000051 -name: morphology -namespace: quality -def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [] -subset: attribute_slim -is_a: PATO:0001241 ! physical object quality -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0000117 -is_a: PATO:0000051 ! morphology - -[Term] -id: PATO:0000122 -is_a: PATO:0001708 ! 1-D extent -property_value: IAO:0000412 http://purl.org/obo/owl/PATO - -[Term] -id: PATO:0000125 -is_a: PATO:0001018 ! physical quality -property_value: IAO:0000412 http://purl.org/obo/owl/PATO - -[Term] -id: PATO:0000141 -name: structure -namespace: quality -alt_id: PATO:0001452 -def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [] -subset: attribute_slim -synonym: "conformation" BROAD [] -synonym: "relational structural quality" EXACT [] -is_a: PATO:0000051 ! morphology -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0000146 -name: temperature -namespace: quality -def: "A physical quality of the thermal energy of a system." [] -subset: attribute_slim -subset: scalar_slim -is_a: PATO:0001018 ! physical quality -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0000383 -name: female -def: "A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes." [] -is_a: PATO:0000047 ! biological sex -property_value: IAO:0000111 "female" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: PATO:0000384 -name: male -def: "A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes." [] -is_a: PATO:0000047 ! biological sex -property_value: IAO:0000111 "male" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: PATO:0001018 -name: physical quality -namespace: quality -alt_id: PATO:0002079 -def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [] -subset: attribute_slim -synonym: "relational physical quality" EXACT [] -xref: Wikipedia:Physical_property -is_a: PATO:0001241 ! physical object quality -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0001241 -name: physical object quality -namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 -def: "A quality which inheres in a continuant." [] -comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. -synonym: "monadic quality of a continuant" EXACT [] -synonym: "monadic quality of an object" NARROW [] -synonym: "monadic quality of continuant" NARROW [] -synonym: "multiply inhering quality of a physical entity " EXACT [] -synonym: "quality of a continuant" EXACT [] -synonym: "quality of a single physical entity" EXACT [] -synonym: "quality of an object" EXACT [] -synonym: "quality of continuant" EXACT [] -xref: snap:Quality -is_a: BFO:0000019 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0001708 -name: 1-D extent -namespace: quality -def: "A size quality inhering in an bearer by virtue of the bearer's extension in one dimension." [] -subset: attribute_slim -synonym: "1-D size" EXACT [] -is_a: PATO:0000117 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0001961 -name: in contact with -namespace: quality -def: "A structural quality inhering in a bearer by virtue of the bearer's touching another entity." [] -subset: relational_slim -subset: value_slim -synonym: "contiguous" RELATED [] -is_a: PATO:0000141 ! structure -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0002390 -name: radius -namespace: quality -def: "A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter." [] -subset: attribute_slim -subset: scalar_slim -is_a: PATO:0000122 -property_value: APOLLO_SV:0000040 "radius" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string -created_by: gkoutos -creation_date: 2012-11-15T05:17:15Z - -[Term] -id: PCO:0000000 -name: PCO:collection of organisms -def: "A material entity that consists of two or more organisms, viruses, or viroids." [] -comment: May be of the same or different species. -is_a: BFO:0000027 ! object_aggregate -property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string -property_value: IAO:0000118 "group of organisms" xsd:string -property_value: IAO:0000118 "organism collection" xsd:string - -[Term] -id: PCO:0000001 -name: population -def: "A collection of organisms, all of the same species, that live in the same place." [] -comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used. -is_a: PCO:0000018 ! collection of organisms of the same species -relationship: BFO:0000177 APOLLO_SV:00000104 ! biotic ecosystem -property_value: APOLLO_SV:0000040 "Population" xsd:string -property_value: IAO:0000116 "Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific." xsd:string -property_value: IAO:0000119 "ISBN:0878932739" xsd:string - -[Term] -id: PCO:0000018 -name: collection of organisms of the same species -def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] -is_a: PCO:0000000 ! PCO:collection of organisms - -[Term] -id: STATO:0000085 -name: effect size estimate -def: "effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval" [] -is_a: IAO:0000109 ! measurement datum -property_value: IAO:0000112 "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string -property_value: IAO:0000117 "Orlaith Burke" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000119 "AGB,PRS" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/stato.owl" xsd:string -property_value: STATO:0000032 "effect size" xsd:string - -[Term] -id: STATO:0000088 -name: study group population size -def: "statistical sample size is a count evaluating the number of individual experimental units" [] -is_a: APOLLO_SV:00000032 ! count -property_value: APOLLO_SV:0000040 "sampleSize" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string -property_value: IAO:0000117 "Orlaith Burke" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000119 "AGB-PRS" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/stato.owl" xsd:string -property_value: STATO:0000032 "" xsd:string -property_value: STATO:0000032 "statistical sample size" xsd:string - -[Term] -id: STATO:0000134 -name: true negative rate -def: "specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1" [] -is_a: IAO:0000109 ! measurement datum -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string -property_value: IAO:0000117 "Orlaith Burke" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000118 "specificity" xsd:string - -[Term] -id: STATO:0000233 -name: true positive rate -def: "sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1" [] -is_a: IAO:0000109 ! measurement datum -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string -property_value: IAO:0000117 "Orlaith Burke" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000118 "recall" xsd:string -property_value: IAO:0000118 "sensitivity" xsd:string -property_value: IAO:0000119 "adapted from:\nhttp://en.wikipedia.org/wiki/Sensitivity_and_specificity\nand\nhttp://mathworld.wolfram.com/Sensitivity.html" xsd:string - -[Term] -id: STATO:0000245 -name: relative risk -def: "Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group." [] -is_a: STATO:0000085 ! effect size estimate -property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string -property_value: IAO:0000117 "Orlaith Burke" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000118 "risk ratio" xsd:string -property_value: IAO:0000119 IAO:0000122 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/stato.owl" xsd:string -property_value: STATO:0000032 "" xsd:string - -[Term] -id: STATO:0000252 -name: categorical variable -def: "a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories" [] -is_a: STATO:0000258 ! variable -property_value: APOLLO_SV:0000040 "categoricalVariable" xsd:string -property_value: http://purl.org/dc/elements/1.1/source "https://onlinecourses.science.psu.edu/stat503/node/7" xsd:string -property_value: IAO:0000112 "" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string -property_value: IAO:0000117 "Orlaith Burke" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000118 "discrete variable" xsd:string -property_value: IAO:0000118 "nominal variable" xsd:string -property_value: IAO:0000118 "qualitative factor" xsd:string -property_value: IAO:0000119 "http://udel.edu/~mcdonald/statvartypes.html" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/stato.owl" xsd:string -property_value: STATO:0000032 "" xsd:string - -[Term] -id: STATO:0000258 -name: variable -def: "a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation." [] -is_a: IAO:0000027 ! data item -property_value: APOLLO_SV:0000040 "variable" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string -property_value: IAO:0000117 "Orlaith Burke" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000119 "adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2.\n\nand from Oxford English Dictionary:\nhttp://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1" xsd:string -property_value: IAO:0000119 "STATO" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/stato.owl" xsd:string -property_value: STATO:0000032 "" xsd:string - -[Term] -id: STATO:0000321 -name: non-parametric distribution -def: "Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution." [] -comment: Initially discussed at https://github.com/incf-nidash/nidm/pull/191 -is_a: APOLLO_SV:00000247 ! unconditional probability distribution -property_value: APOLLO_SV:0000040 "NonparametricProbabilityDistribution" xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Camille Maumet" xsd:string -property_value: IAO:0000117 "Karl Helmer" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000117 "Thomas Nichols" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/stato.owl" xsd:string - -[Term] -id: STATO:0000398 -name: weighted arithmetic mean -def: "The weighted arithmetic mean is a measure of central tendency that is the sum of the products of each observed value and their respective non-negative weights, divided by the sum of the weights, such that the contribution of each observed value to the mean may defer according to its respective weight. It is defined by the formula: A = sum(vi*wi)/sum(wi), where 'i' ranges from 1 to n, 'vi' is the value of each observation, and 'wi' is the value of the respective weight for each observed value.\n\nThe weighted arithmetic mean is a kind of mean similar to an ordinary arithmetic mean (the most common type of average), except that instead of each of the data points contributing equally to the final average, some data points are weighted, meaning they contribute more than others. \n\nThe weighted arithmetic mean is often used if one wants to combine average values from samples of the same population with different sample sizes." [] -is_a: OBI:0000679 ! average value -property_value: bug-database "https://github.com/ISA-tools/stato/issues/59" xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string -property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000117 "Orlaith Burke" xsd:string -property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string -property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Weighted_arithmetic_mean" xsd:string -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: 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." [] -subset: upper_level -synonym: "biological structure" EXACT [] -xref: AAO:0010825 -xref: AEO:0000003 -xref: BILA:0000003 -xref: CARO:0000003 -xref: EHDAA2:0003003 -xref: EMAPA:0 -xref: FBbt:00007001 -xref: FMA:67135 -xref: GAID:781 -xref: HAO:0000003 -xref: http://dbpedia.org/ontology/AnatomicalStructure -xref: MA:0003000 -xref: MESH:A13 -xref: SCTID:362889002 -xref: TAO:0000037 -xref: TGMA:0001823 -xref: VHOG:0001759 -xref: WBbt:0000100 -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 - -[Term] -id: UBERON:0000465 -name: material anatomical entity -namespace: uberon -def: "Anatomical entity that has mass." [] -subset: upper_level -xref: AAO:0010264 -xref: AEO:0000006 -xref: BILA:0000006 -xref: CARO:0000006 -xref: EHDAA2:0003006 -xref: FBbt:00007016 -xref: FMA:67165 -xref: HAO:0000006 -xref: TAO:0001836 -xref: TGMA:0001826 -xref: VHOG:0001721 -is_a: BFO:0000040 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string - -[Term] -id: UBERON:0000467 -name: anatomical system -namespace: uberon -def: "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]." [] -subset: uberon_slim -subset: upper_level -synonym: "body system" EXACT [] -synonym: "organ system" EXACT [] -synonym: "system" BROAD [] -xref: AAO:0000007 -xref: AEO:0000011 -xref: BILA:0000011 -xref: BSA:0000049 -xref: CALOHA:TS-2088 -xref: CARO:0000011 -xref: EHDAA2:0003011 -xref: EHDAA:392 -xref: EMAPA:16103 -xref: EV:0100000 -xref: FBbt:00004856 -xref: FMA:7149 -xref: galen:AnatomicalSystem -xref: HAO:0000011 -xref: MA:0000003 -xref: ncithesaurus:Organ_System -xref: NIF_GrossAnatomy:birnlex_14 -xref: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ -xref: SCTID:278195005 -xref: TAO:0001439 -xref: TGMA:0001831 -xref: UMLS:C0460002 -xref: VHOG:0001725 -xref: WBbt:0005746 -xref: WBbt:0005763 -xref: Wikipedia:Organ_system -xref: XAO:0003002 -xref: ZFA:0001439 -is_a: UBERON:0000480 ! anatomical group -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string -property_value: seeAlso EHDAA2:0001330 -property_value: UBPROP:0000001 "Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]" xsd:string -property_value: UBPROP:0000001 "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]" xsd:string -property_value: UBPROP:0000001 "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]" xsd:string - -[Term] -id: UBERON:0000479 -name: tissue -namespace: uberon -def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [] -comment: Editor note: changed label and definition to reflect CARO2 -subset: upper_level -synonym: "portion of tissue" EXACT [] -synonym: "simple tissue" NARROW [] -synonym: "tissue portion" EXACT [] -xref: AAO:0000607 -xref: AAO:0010054 -xref: AEO:0000043 -xref: BILA:0000043 -xref: CALOHA:TS-2090 -xref: CARO:0000043 -xref: EHDAA2:0003043 -xref: FBbt:00007003 -xref: FMA:9637 -xref: galen:Tissue -xref: HAO:0000043 -xref: MA:0003002 -xref: MESH:A10 -xref: ncithesaurus:Tissue -xref: NIF_GrossAnatomy:birnlex_19 -xref: TAO:0001477 -xref: TGMA:0001844 -xref: UMLS:C0040300 -xref: VHOG:0001757 -xref: WBbt:0005729 -xref: XAO:0003040 -xref: ZFA:0001477 -is_a: UBERON:0010000 ! multicellular anatomical structure -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string - -[Term] -id: UBERON:0000480 -name: anatomical group -namespace: uberon -def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." [] -subset: upper_level -xref: AAO:0010008 -xref: AEO:0000054 -xref: BILA:0000054 -xref: CARO:0000054 -xref: EHDAA2:0003054 -xref: HAO:0000054 -xref: TAO:0001512 -xref: TGMA:0001846 -xref: VHOG:0001724 -xref: XAO:0003001 -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:0002405 -name: immune system -namespace: uberon -def: "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies." [] -comment: This class was created automatically from a combination of ontologies -subset: uberon_slim -subset: vertebrate_core -xref: AAO:0011003 -xref: BILA:0000104 -xref: FMA:9825 -xref: GAID:328 -xref: MA:0002711 -xref: MESH:A15.382 -xref: ncithesaurus:Immune_System -xref: OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA -xref: SCTID:362590003 -xref: TAO:0001159 -xref: UMLS:C0020962 -xref: VHOG:0001247 -xref: Wikipedia:Immune_system -xref: XAO:0003152 -xref: ZFA:0001159 -is_a: UBERON:0000467 ! anatomical system -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string -property_value: UBPROP:0000003 "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" xsd:string - -[Term] -id: UBERON:0010000 -name: multicellular anatomical structure -namespace: uberon -def: "An anatomical structure that has more than one cell as a part." [] -subset: upper_level -synonym: "multicellular structure" EXACT [] -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 - -[Term] -id: UBERON:0035943 -name: life cycle temporal boundary -namespace: uberon -def: "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity." [] -subset: upper_level -is_a: BFO:0000015 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string - -[Term] -id: UBERON:0035944 -name: life-death temporal boundary -namespace: uberon -def: "A life cycle temporal boundary that marks the end of the life cycle of the organism." [] -synonym: "death" RELATED [] -synonym: "end of life" RELATED [] -synonym: "end of life cycle" EXACT [] -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 - -[Term] -id: UO:0000000 -name: unit -namespace: unit.ontology -is_a: IAO:0000030 ! information content entity -property_value: IAO:0000412 "http://purl.org/obo/owl/unit" xsd:string - -[Term] -id: UO:0000003 -is_a: IAO:0000003 ! measurement unit label -property_value: APOLLO_SV:0000040 "unitOfTime" xsd:string -property_value: IAO:0000412 http://purl.org/obo/owl/UO - -[Term] -id: UO:0000186 -name: dimensionless unit -namespace: unit.ontology -def: "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [] -subset: unit_group_slim -is_a: IAO:0000003 ! measurement unit label -property_value: APOLLO_SV:0000040 "DimensionlessUnit" xsd:string -property_value: IAO:0000412 "http://purl.org/obo/owl/unit" xsd:string - -[Term] -id: UO:0000187 -name: percent -namespace: unit.ontology -def: "A dimensionless ratio unit which denotes numbers as fractions of 100." [] -subset: unit_slim -is_a: UO:0000190 ! ratio -property_value: APOLLO_SV:0000040 "Percent" xsd:string -property_value: IAO:0000412 "http://purl.org/obo/owl/unit" xsd:string - -[Term] -id: UO:0000190 -name: ratio -namespace: unit.ontology -def: "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [] -subset: unit_group_slim -is_a: UO:0000186 ! dimensionless unit -property_value: APOLLO_SV:0000040 "Ratio" xsd:string -property_value: IAO:0000412 "http://purl.org/obo/owl/unit" xsd:string - -[Term] -id: UO:0000191 -name: fraction -namespace: unit.ontology -def: "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [] -subset: unit_slim -is_a: UO:0000190 ! ratio -property_value: APOLLO_SV:0000040 "Fraction" xsd:string -property_value: IAO:0000412 "http://purl.org/obo/owl/unit" xsd:string - -[Term] -id: UO:0000280 -name: rate unit -namespace: unit.ontology -def: "A unit which represents a standard measurement occurrence of a process per unit time." [] -subset: unit_group_slim -is_a: IAO:0000003 ! measurement unit label -property_value: APOLLO_SV:0000040 "Rate" xsd:string -property_value: IAO:0000412 "http://purl.org/obo/owl/unit" xsd:string - -[Term] -id: VO:0000001 -name: vaccine -def: "A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine." [] -is_a: OBI:0000047 ! processed material -property_value: APOLLO_SV:0000040 "Vaccine" xsd:string -property_value: IAO:0000116 "Many vaccines are developed to protect against infectious pathogens. Many vaccines are also being developed against some diseases such as cancer and autoimmune diseases. Vaccine is developed against a disease. Allergy." xsd:string -property_value: IAO:0000117 "a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo." xsd:string -property_value: IAO:0000117 "YH, BP, BS, MC, LC, XZ, RS" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/vo.owl" xsd:string -property_value: seeAlso "MeSH: D014612" xsd:string - -[Term] -id: VO:0000207 -name: vaccine contraindication -def: "A vaccine contraindication is a contraindication that increases the risks of a vaccination. " [] -is_a: OAE:0000055 ! contraindication -property_value: APOLLO_SV:0000040 "VaccineContraindications" xsd:string -property_value: IAO:0000117 "YH" xsd:string -property_value: IAO:0000118 "contraindication for vaccination" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/vo.owl" xsd:string - -[Term] -id: VO:0000278 -name: vaccine function -def: "vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host." [] -is_a: BFO:0000034 -property_value: IAO:0000116 "PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term." xsd:string -property_value: IAO:0000117 "YH, MC, XZ, and AR" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/vo.owl" xsd:string - -[Term] -id: VO:0000590 -name: vaccine preparation -def: "vaccine preparation is a manufacturing process to produce a vaccine." [] -is_a: OBI:0000011 ! planned process -property_value: IAO:0000117 "YH, BP" xsd:string -property_value: IAO:0000118 "vaccine generation" xsd:string -property_value: IAO:0000118 "vaccine production" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/vo.owl" xsd:string - -[Typedef] -id: APOLLO_SV:00000004 -name: basis of -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: APOLLO_SV:00000028 -name: obsolete is based on -comment: p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: APOLLO_SV:00000037 -name: commissions -def: "a commissions b, iff a does not participate in the creation or execution of b and participates in a legal agreement that c participates on the creation or execution of b and c getting something in exchange for that participation." [] -property_value: APOLLO_SV:0000040 "commissions" xsd:string -property_value: IAO:0000600 "A relation between two entities where the first entity formally requests a third party to create or execute the second entity." xsd:string -is_asymmetric: true - -[Typedef] -id: APOLLO_SV:00000057 -name: instantiates -def: "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. " [] -comment: Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222. -domain: BFO:0000001 -is_asymmetric: true - -[Typedef] -id: APOLLO_SV:00000067 -name: simulates -def: "a simulates b, iff a is a purely intentional entity that is representing a fictional individual or fact b and a participates in a simulating." [] -domain: APOLLO_SV:00000070 ! simulation -range: BFO:0000001 -is_asymmetric: true - -[Typedef] -id: APOLLO_SV:00000116 -name: causally_precedes -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: APOLLO_SV:00000177 -name: obsoleted_administrated by -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true +[Typedef] +id: APOLLO_SV:00000177 +name: obsoleted_administrated by +is_a: ObsoleteProperty +is_obsolete: true [Typedef] id: APOLLO_SV:00000543 @@ -13342,631 +5938,4 @@ def: "(Q is_a Quality ⋀ D is_a Disposition ⋀ Q base of D) ® ∀q (q instanc comment: The relationship between a disposition and the quality that confers the disposition on the material entity in which they both inhere.\n\nFor example, the disposition of a piece of glass to bend light and the lattice structure of the glass (quality) that results in the bending of the light. property_value: IAO:0000111 "has basis in quality" xsd:string property_value: IAO:0000119 "Representing dispositions\nJohannes Röhl and Ludger Jansen\nJournal of Biomedical Semantics 2011 2(Suppl 4):S4\nDOI: 10.1186/2041-1480-2-S4-S4" xsd:string -domain: BFO:0000016 -range: BFO:0000019 - -[Typedef] -id: BFO:0000050 -is_reflexive: true - -[Typedef] -id: BFO:0000051 -is_reflexive: true -is_transitive: true - -[Typedef] -id: BFO:0000054 -name: is realized by -def: "Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]" [] -property_value: IAO:0000111 "obsolete_is_realized_by" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000116 "replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'" xsd:string -property_value: IAO:0000117 "GROUP:OBI:" xsd:string -property_value: IAO:0000117 "PERSON: Chris Mungall" xsd:string -property_value: IAO:0000118 "executed_during" xsd:string -property_value: IAO:0000118 "has_realization" xsd:string -property_value: IAO:0000118 "is_realized_as" xsd:string -property_value: IAO:0000118 "realized by" xsd:string -property_value: IAO:0000118 "realized_by" xsd:string -property_value: IAO:0000231 IAO:0000228 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -domain: BFO:0000017 -range: BFO:0000015 -inverse_of: BFO:0000055 ! realizes - -[Typedef] -id: BFO:0000055 -name: realizes -property_value: IAO:0000111 "realizes" xsd:string - -[Typedef] -id: BFO:0000062 -name: preceded by -def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string - -[Typedef] -id: BFO:0000063 -name: precedes -def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -subset: ro-eco -property_value: IAO:0000111 "precedes" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string - -[Typedef] -id: BFO:0000066 -name: occurs in -name: unfolds_in -namespace: relationship -comment: Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte -property_value: IAO:0000118 "occurs_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 - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001" [] -property_value: BFO:0000179 "contains-process" xsd:string -property_value: BFO:0000180 "containsProcess" 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 - -[Typedef] -id: BFO:0000075 -name: is aggregate of -property_value: IAO:0000111 "is aggregate of" xsd:string -property_value: IAO:0000118 "aggregate of" xsd:string -property_value: IAO:0000118 "aggregate_of" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Typedef] -id: BFO:0000108 -name: exists at - -[Typedef] -id: BFO:0000113 -name: has material basis at all times -property_value: BFO:0000179 "has-material-basis_at" xsd:string -property_value: BFO:0000180 "hasMaterialBasisAt" xsd:string -property_value: IAO:0000112 "the material basis of John’s disposition to cough is the viral infection in John’s upper respiratory tract" xsd:string -property_value: IAO:0000112 "the material basis of the disposition to wear unevenly of John’s tires is the worn suspension of his car." 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 material basis at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has material basis@en(x,y,t)'." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000600 "b has_material_basis c at t means: b is a disposition & c is a material entity & there is some d bearer_of b at t& c continuant_part_of d at t& d has_disposition b at t because c continuant_part_of d at t. (axiom label in BFO2 Reference: [071-002])" xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (hasMaterialBasisAt x y t) (and (Disposition x) (MaterialEntity y) (exists (z) (and (bearerOfAt z x t) (continuantPartOfAt y z t) (exists (w) (and (Disposition w) (if (hasDisposition z w) (continuantPartOfAt y z t))))))))) // axiom label in BFO2 CLIF: [071-002] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: BFO:0000117 -name: has occurrent part -def: "b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])" [] -property_value: BFO:0000179 "o-has-part" xsd:string -property_value: BFO:0000180 "hasOccurrentPart" xsd:string -property_value: IAO:0000112 "[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life" xsd:string -property_value: IAO:0000112 "[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match." xsd:string -property_value: IAO:0000112 "[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000600 "[copied from inverse property 'part of 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 - -[Typedef] -id: BFO:0000118 -name: has proper occurrent part -def: "[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])" [] -def: "b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" [] -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 -is_a: BFO:0000117 ! has occurrent part - -[Typedef] -id: BFO:0000121 -name: has temporal part -def: "[copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])" [] -def: "[copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" [] -property_value: BFO:0000179 "has-t-part" xsd:string -property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" xsd:string -property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life." xsd:string -property_value: IAO:0000112 "[copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -is_a: BFO:0000117 ! has occurrent part - -[Typedef] -id: BFO:0000132 -name: part of occurrent -def: "[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])" [] -property_value: BFO:0000179 "o-part-of" xsd:string -property_value: BFO:0000180 "occurrentPartOf" xsd:string -property_value: IAO:0000112 "Mary’s 5th birthday occurrent_part_of Mary’s life" xsd:string -property_value: IAO:0000112 "the first set of the tennis match occurrent_part_of the tennis match." xsd:string -property_value: IAO:0000112 "The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." xsd:string -property_value: IAO:0000116 "BFO2 Reference: occurrent" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000600 "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:0000601 "occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])" xsd:string -property_value: IAO:0000601 "occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])" xsd:string -property_value: IAO:0000601 "occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])" xsd:string -property_value: IAO:0000601 "occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])" xsd:string -property_value: IAO:0000601 "occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])" xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] " xsd:string -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 - -[Typedef] -id: BFO:0000136 -name: proper temporal part of -property_value: BFO:0000179 "t-ppart-of" xsd:string -property_value: BFO:0000180 "properTemporalPartOf" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -is_a: BFO:0000138 ! proper part of occurrent -is_a: BFO:0000139 ! temporal part of - -[Typedef] -id: BFO:0000138 -name: proper part of occurrent -def: "[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001" [] -def: "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])" [] -property_value: BFO:0000179 "o-ppart-of" xsd:string -property_value: BFO:0000180 "properOccurrentPartOf" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000602 "(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -is_a: BFO:0000132 ! part of occurrent - -[Typedef] -id: BFO:0000139 -name: temporal part of -def: "b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])" [] -def: "b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])" [] -property_value: BFO:0000179 "t-part-of" xsd:string -property_value: BFO:0000180 "temporalPartOf" xsd:string -property_value: IAO:0000112 "the 4th year of your life is a temporal part of your life\\. The first quarter of a game of football is a temporal part of the whole game\\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\\ The 4th year of your life is a temporal part of your life" xsd:string -property_value: IAO:0000112 "the process boundary which separates the 3rd and 4th years of your life." xsd:string -property_value: IAO:0000112 "your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000601 "if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])" xsd:string -property_value: IAO:0000602 "(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] " xsd:string -property_value: IAO:0000602 "(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] " xsd:string -property_value: IAO:0000602 "(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -is_a: BFO:0000132 ! part of occurrent - -[Typedef] -id: BFO:0000155 -name: occupies temporal region -property_value: BFO:0000179 "spans" xsd:string -property_value: BFO:0000180 "occupiesTemporalRegion" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000600 "p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 -range: BFO:0000008 -is_a: BFO:0000108 ! exists at - -[Typedef] -id: BFO:0000156 -name: has temporal occupant -property_value: BFO:0000179 "span-of" xsd:string -property_value: BFO:0000180 "spanOf" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000600 "[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000008 -range: BFO:0000003 -is_a: BFO:0000157 ! during which exists - -[Typedef] -id: BFO:0000157 -name: during which exists - -[Typedef] -id: BFO:0000169 -name: specifically depends on at some time -property_value: BFO:0000180 "specificallyDependsOn" xsd:string -property_value: IAO:0000112 "a gait s-depends_on the walking object. (All at some specific time.)" xsd:string -property_value: IAO:0000112 "A pain s-depends_on the organism that is experiencing the pain" xsd:string -property_value: IAO:0000112 "a shape s-depends_on the shaped object" xsd:string -property_value: IAO:0000112 "one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head" xsd:string -property_value: IAO:0000112 "one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism" xsd:string -property_value: IAO:0000112 "one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell" xsd:string -property_value: IAO:0000112 "one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant" xsd:string -property_value: IAO:0000112 "one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question" xsd:string -property_value: IAO:0000112 "one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command" xsd:string -property_value: IAO:0000112 "one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat" xsd:string -property_value: IAO:0000112 "one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs" xsd:string -property_value: IAO:0000112 "reciprocal s-dependence between occurrents: a process of buying and the associated process of selling" xsd:string -property_value: IAO:0000112 "reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas" xsd:string -property_value: IAO:0000112 "reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces" xsd:string -property_value: IAO:0000112 "the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball" xsd:string -property_value: IAO:0000112 "the one-sided dependence of an occurrent on an independent continuant: handwave on a hand" xsd:string -property_value: IAO:0000112 "the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45" xsd:string -property_value: IAO:0000112 "the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45" xsd:string -property_value: IAO:0000112 "the two-sided reciprocal s-dependence of the roles of husband and wife [20" 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 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place." xsd:string -property_value: IAO:0000116 "BFO2 Reference: specifically dependent continuant\\; process; process boundary" xsd:string -property_value: IAO:0000600 "To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64" xsd:string -property_value: IAO:0000601 "an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])" xsd:string -property_value: IAO:0000601 "If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])" xsd:string -property_value: IAO:0000601 "if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])" xsd:string -property_value: IAO:0000601 "If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])" xsd:string -property_value: IAO:0000601 "If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])" xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] " xsd:string -property_value: IAO:0000602 "(forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] " xsd:string -property_value: IAO:0000602 "(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: BFO:0000181 -name: has proper temporal part -property_value: BFO:0000179 "has-t-ppart" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -is_a: BFO:0000118 ! has proper occurrent part -is_a: BFO:0000121 ! has temporal part - -[Typedef] -id: BFO:0000184 -name: history of -domain: BFO:0000015 -range: BFO:0000040 -is_a: BFO:0000066 ! unfolds_in - -[Typedef] -id: BFO:0000185 -name: has history -domain: BFO:0000040 -range: BFO:0000015 - -[Typedef] -id: IAO:0000039 -name: has measurement unit label -range: IAO:0000003 ! measurement unit label -is_functional: true -is_a: BFO:0000051 - -[Typedef] -id: IAO:0000136 -name: is about -property_value: IAO:0000114 IAO:0000125 - -[Typedef] -id: IAO:0000413 -name: is duration of -def: "relates a process to a time-measurement-datum that represents the duration of the process" [] -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string - -[Typedef] -id: IAO:0000581 -name: has time stamp -def: "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken" [] -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Alan Ruttenberg" xsd:string -domain: IAO:0000582 ! time stamped measurement datum -range: IAO:0000416 ! time measurement datum -is_functional: true -is_a: BFO:0000051 - -[Typedef] -id: IAO:0000583 -name: has measurement datum -def: "relates a time stamped measurement datum to the measurement datum that was measured" [] -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Alan Ruttenberg" xsd:string -domain: IAO:0000582 ! time stamped measurement datum -is_a: BFO:0000051 - -[Typedef] -id: IAO:0020012 -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: IAO:0020018 -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: OBI:0000308 -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: OBI:0000417 -name: achieves_planned_objective -def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] -property_value: IAO:0000111 "achieves_planned_objective" xsd:string -property_value: IAO:0000112 "A cell sorting process achieves the objective specification 'material separation objective'" xsd:string -property_value: IAO:0000117 "BP, AR, PPPB branch" xsd:string -property_value: IAO:0000119 "PPPB branch derived" xsd:string -property_value: IAO:0000232 "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Typedef] -id: OMIABIS:0000008 -name: owns -property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string -property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. " xsd:string - -[Typedef] -id: OMIABIS:0000048 -name: is owned by -def: "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." [] -property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Typedef] -id: OMRSE:00000070 -name: is enrolled in school -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Typedef] -id: OMRSE:00000071 -name: is admitted to hospital -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Typedef] -id: ObsoleteProperty -name: ObsoleteProperty - -[Typedef] -id: RO:0000053 -name: is bearer of -property_value: IAO:0000118 "bearer of" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Typedef] -id: RO:0000057 -name: has_participant -property_value: IAO:0000111 "has_participant" xsd:string - -[Typedef] -id: RO:0000059 -property_value: IAO:0000111 "is_concretization_of" xsd:string - -[Typedef] -id: RO:0002090 -name: immediately_precedes -is_a: BFO:0000063 ! precedes - -[Typedef] -id: RO:0002093 -name: ends during -comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "o" xsd:string -property_value: IAO:0000118 "overlaps" xsd:string -is_a: RO:0002222 ! temporal relation - -[Typedef] -id: RO:0002163 -name: spatially disjoint from -def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] -subset: ro-eco -property_value: http://xmlns.com/foaf/0.1/page "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl" xsd:string -property_value: RO:0001900 RO:0001901 -expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] - -[Typedef] -id: RO:0002212 -name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string - -[Typedef] -id: RO:0002218 -name: has active participant -def: "x has participant y if and only if x realizes some active role that inheres in y" [] -subset: ro-eco -property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "has agent" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string -is_a: RO:0000057 ! has_participant - -[Typedef] -id: RO:0002220 -name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary." [] -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 -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso issuecomment-218584934 -is_a: RO:0002163 ! spatially disjoint from - -[Typedef] -id: RO:0002222 -name: temporal relation -name: temporally related to -comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "move to BFO?" xsd:string -property_value: IAO:0000119 "Allen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -domain: BFO:0000003 -range: BFO:0000003 - -[Typedef] -id: RO:0002224 -name: starts with -def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -is_a: RO:0002222 ! temporal relation - -[Typedef] -id: RO:0002229 -name: ends -def: "inverse of ends with" [] -property_value: http://purl.org/dc/elements/1.1/source "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl" xsd:string -property_value: IAO:0000114 IAO:0000125 -is_a: RO:0002222 ! temporal relation - -[Typedef] -id: RO:0002230 -name: ends with -def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -property_value: http://purl.org/dc/elements/1.1/source "http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "finished with" xsd:string -is_transitive: true -is_a: RO:0002222 ! temporal relation - -[Typedef] -id: RO:0002325 -name: colocalizes with -def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] -property_value: http://purl.org/dc/elements/1.1/creator "Gene Ontology Consortium" xsd:string -property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 "http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with" xsd:string -property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl" xsd:string - -[Typedef] -id: RO:0002404 -name: causally downstream of -def: "inverse of upstream of" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string -is_a: RO:0002501 ! causal relation between processes - -[Typedef] -id: RO:0002411 -name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string -is_a: RO:0002501 ! causal relation between processes - -[Typedef] -id: RO:0002501 -name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string - -[Typedef] -id: bearer_of -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: has_disposition -name: obsolete has_disposition -namespace: relationship -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: has_proper_part -name: obsolete has proper part -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: immediately_preceded_by -name: immediately_preceded_by -namespace: uberon -def: "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" [] -synonym: "directly preceded by" EXACT [] -synonym: "is directly preceded by" EXACT [] -synonym: "is immediately preceded by" EXACT [] -synonym: "starts_at_end_of" EXACT [] -xref: http://semanticscience.org/resource/SIO_000251 -xref: RO:0002087 -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uberon.owl" xsd:string -property_value: UBPROP:0000001 "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." xsd:string -is_a: BFO:0000062 ! preceded by - -[Typedef] -id: inheres_in -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: location_of -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: negatively_regulates -name: negatively_regulates -namespace: relationship -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: proper_part_of -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: realized_by -name: obsolete_realized_by -namespace: relationship -alt_id: OBO_REL:0000035 -alt_id: OBO_REL:realized_as -comment: NOTE: there appears to be some consistency in usage as to whether processes or continuants realize -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true - -[Typedef] -id: regulates -name: regulates -namespace: relationship -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ido.owl" xsd:string -is_a: ObsoleteProperty ! ObsoleteProperty -is_obsolete: true diff --git a/apollo_sv-base.owl b/apollo_sv-base.owl index d5acd97..8e8aed0 100644 --- a/apollo_sv-base.owl +++ b/apollo_sv-base.owl @@ -24,7 +24,7 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -41,7 +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 - 2024-02-23 + 2024-04-19 @@ -144,305 +144,67 @@ For the 1982-10-17 date, we suggest the dc:created annotation. A comment that summarizes the most relevant or salient features and history of the entity for human readers. William R. Hogan human readable synopsis - - - - - - - - - BFO OWL specification label - - - - - - - - BFO CLIF specification label - - - - - - - - VIVO-ISF - There are several URL and hasURL annotation properties out there in the ontology world. This one had the most sensible source ontology and OBO ID URI combination out there. - hasURL - - - editor preferred label - editor preferred label - editor preferred term - editor preferred term - editor preferred term~editor preferred label - + - - - example of usage - example of usage - - - - - - - - has curation status - has curation status - + - - - definition - definition - textual definition - - - - - - - - - editor note - editor note - + - - - definition editor - definition editor - term editor - term editor - + - - - alternative term - alternative term - + - - - definition source - definition source - - - - - - - - has obsolescence reason - + - - - curator note - curator note - - - - - - - - - imported from - - - - - - - - expand expression to - - - - - - - - - OBO foundry unique label - + - - elucidation - - - - - - - - has associated axiom(nl) - - - - - - - - has associated axiom(fol) - + - - - - - - - - - - ISA alternative term - - - - - - - - NIAID GSCID-BRC alternative term - - - - - - - - temporal interpretation - - - - - - - - an alternative term used for STATO statistical ontology and ISA team - Alejandra Gonzalez-Beltran - Orlaith Burke - Philippe Rocca-Serra - STATO alternative term - - - - - - - - - - - - - - - - - - - - - external_definition - - - - - - - - homology_notes - - - - - - - - - - - - - - - - - - - - - - - - - + - - This annotation property gives the unique label of all Apollo_SV entities that are refered to in the schema. The UAL is the denotator for the Apollo_SV class in the schema. There can at all times only be ONE value of UAL for each class. - UAL - Unique Apollo Label - - - - - - - - A metadata relation between a class and its taxonomic rank (eg species, family) - ncbi_taxonomy - This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored - has_rank - + @@ -454,10 +216,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - - Creator - + @@ -469,11 +228,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - - Source - Source - + @@ -485,10 +240,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - - dc:type - + @@ -504,152 +256,15 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - - - - - - - - - - - - - - - - - - - - - has_alternative_id - - - - - - - - has_broad_synonym - - - - - - - - database_cross_reference - - - - - - - - - - - - - - has_exact_synonym - - - - - - - - has_narrow_synonym - - - - - - - - has_obo_namespace - - - - - - - - has_related_synonym - - - - - - - - - - - - - - id - - - - - - - - in_subset - - - - - - - - shorthand - - - - - - ontology instance unique identifier - ontology IUI - + - - ontology version instance unique identifier - ontology version IUI - - - - - - - - - - - - - - label - label - - - - - - - + @@ -688,25 +303,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - - - - - - - - - - - - - - - - - - a commissions b, iff a does not participate in the creation or execution of b and participates in a legal agreement that c participates on the creation or execution of b and c getting something in exchange for that participation. A relation between two entities where the first entity formally requests a third party to create or execute the second entity. commissions @@ -718,9 +314,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - - A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222. instantiates @@ -731,10 +324,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - - - a simulates b, iff a is a purely intentional entity that is representing a fictional individual or fact b and a participates in a simulating. simulates @@ -765,8 +354,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - has basis in quality (Q is_a Quality ⋀ D is_a Disposition ⋀ Q base of D) ® ∀q (q instance_of Q ® b (q inheres_in b ⋀ d (d instance_of D ⋀ d inheres_in b))) Representing dispositions @@ -783,131 +370,43 @@ For example, the disposition of a piece of glass to bend light and the lattice s - - - + - - - - + - - - - - - obsolete_is_realized_by - - Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] - replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' - GROUP:OBI:<http://obi.sourceforge.net> - PERSON: Chris Mungall - executed_during - has_realization - is_realized_as - realized by - realized_by - - http://purl.obolibrary.org/obo/obi.owl - is realized by - + - - realizes - realizes - - - - - - - - - preceded by - 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. - 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. - is preceded by - preceded_by - http://purl.obolibrary.org/obo/ro.owl - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - http://purl.obolibrary.org/obo/ro.owl - - precedes - + - - occurs_in - http://purl.obolibrary.org/obo/ido.owl - http://purl.obolibrary.org/obo/obi.owl - relationship - Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte - occurs in - unfolds_in - + - - - contains-process - containsProcess - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001 - http://purl.obolibrary.org/obo/bfo.owl - - contains process - - - - - - - - - is aggregate of - aggregate of - aggregate_of - http://purl.obolibrary.org/obo/obi.owl - is aggregate of - + - - exists at - + @@ -919,330 +418,43 @@ For example, the disposition of a piece of glass to bend light and the lattice s - - - has-material-basis_at - hasMaterialBasisAt - the material basis of John’s disposition to cough is the viral infection in John’s upper respiratory tract - the material basis of the disposition to wear unevenly of John’s tires is the worn suspension of his car. - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has material basis at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has material basis@en(x,y,t)'. - http://purl.obolibrary.org/obo/bfo.owl - b has_material_basis c at t means: b is a disposition & c is a material entity & there is some d bearer_of b at t& c continuant_part_of d at t& d has_disposition b at t because c continuant_part_of d at t. (axiom label in BFO2 Reference: [071-002]) - (forall (x y t) (if (hasMaterialBasisAt x y t) (and (Disposition x) (MaterialEntity y) (exists (z) (and (bearerOfAt z x t) (continuantPartOfAt y z t) (exists (w) (and (Disposition w) (if (hasDisposition z w) (continuantPartOfAt y z t))))))))) // axiom label in BFO2 CLIF: [071-002] - - has material basis at all times - + - - - o-has-part - hasOccurrentPart - [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life - [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. - [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. - b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) - [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. - [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent - http://purl.obolibrary.org/obo/bfo.owl - [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]) - (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] - - has occurrent part - + - - - 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]) - b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 - http://purl.obolibrary.org/obo/bfo.owl - - has proper occurrent part - + - + - - - has-t-part - [copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life - [copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life. - [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating - [copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) - [copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) - http://purl.obolibrary.org/obo/bfo.owl - - has temporal part - + - - - - - o-part-of - occurrentPartOf - Mary’s 5th birthday occurrent_part_of Mary’s life - The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. - the first set of the tennis match occurrent_part_of the tennis match. - [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]) - BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. - BFO2 Reference: occurrent - http://purl.obolibrary.org/obo/bfo.owl - b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) - occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001]) - occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002]) - occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001]) - occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001]) - occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001]) - (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] - (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] - (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] - (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] - (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] - - part of occurrent - + + + - + - - - - t-ppart-of - properTemporalPartOf - http://purl.obolibrary.org/obo/bfo.owl - - proper temporal part of - - - - - - - - - - - - - - - o-ppart-of - properOccurrentPartOf - [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 - 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]) - http://purl.obolibrary.org/obo/bfo.owl - (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] - - proper part of occurrent - - - - - - - - - t-part-of - temporalPartOf - the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life - the process boundary which separates the 3rd and 4th years of your life. - your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating - b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) - b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) - http://purl.obolibrary.org/obo/bfo.owl - if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) - (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] - (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] - (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] - - temporal part of - - - - - - - - - - - spans - occupiesTemporalRegion - http://purl.obolibrary.org/obo/bfo.owl - p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) - - occupies temporal region - - - - - - - - - - - - span-of - spanOf - http://purl.obolibrary.org/obo/bfo.owl - [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) - - has temporal occupant - - - - - - - - during which exists - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - specificallyDependsOn - A pain s-depends_on the organism that is experiencing the pain - a gait s-depends_on the walking object. (All at some specific time.) - a shape s-depends_on the shaped object - one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head - one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism - one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell - one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant - one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question - one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command - one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat - one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs - reciprocal s-dependence between occurrents: a process of buying and the associated process of selling - reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas - reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces - the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball - the one-sided dependence of an occurrent on an independent continuant: handwave on a hand - the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 - the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 - the two-sided reciprocal s-dependence of the roles of husband and wife [20 - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) - BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 - BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 - BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. - BFO2 Reference: specifically dependent continuant\; process; process boundary - To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 - If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) - If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) - If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) - an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) - if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) - (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] - (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] - (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] - (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] - (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] - - specifically depends on at some time - - - - - - - - - - - - - - - - has-t-ppart - http://purl.obolibrary.org/obo/bfo.owl - - has proper temporal part - - - - - - - - - - - history of - - - - - - - - - - has history - - - - - - - - - - - has measurement unit label - + - - - is about - + @@ -1252,73 +464,6 @@ For example, the disposition of a piece of glass to bend light and the lattice s - - - - - relates a process to a time-measurement-datum that represents the duration of the process - Person:Alan Ruttenberg - is duration of - - - - - - - - - - - - - relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken - Alan Ruttenberg - has time stamp - - - - - - - - - - - - - - - - - - - - - relates a time stamped measurement datum to the measurement datum that was measured - Alan Ruttenberg - has measurement datum - - - - - - - - - true - - - - - - - - - true - - - - @@ -1331,84 +476,27 @@ For example, the disposition of a piece of glass to bend light and the lattice s - - - - - true - - - - - - - - - achieves_planned_objective - A cell sorting process achieves the objective specification 'material separation objective' - This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. - BP, AR, PPPB branch - PPPB branch derived - modified according to email thread from 1/23/09 in accordince with DT and PPPB branch - http://purl.obolibrary.org/obo/obi.owl - achieves_planned_objective - - - - - - - - - Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. - http://purl.obolibrary.org/obo/omrse.owl - This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. - owns - - - - - - - - - a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. - Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. - http://purl.obolibrary.org/obo/omrse.owl - is owned by - - - - - - - http://purl.obolibrary.org/obo/omrse.owl - is enrolled in school - + - - - http://purl.obolibrary.org/obo/omrse.owl - is admitted to hospital - + @@ -1420,13 +508,7 @@ For example, the disposition of a piece of glass to bend light and the lattice s - - - bearer of - bearer_of - http://purl.obolibrary.org/obo/omrse.owl - is bearer of - + @@ -1438,18 +520,13 @@ For example, the disposition of a piece of glass to bend light and the lattice s - - has_participant - has_participant - + - - is_concretization_of - + @@ -1473,189 +550,31 @@ For example, the disposition of a piece of glass to bend light and the lattice s - - - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - http://purl.obolibrary.org/obo/uberon.owl - A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. - RO:0002087 - http://semanticscience.org/resource/SIO_000251 - directly preceded by - is directly preceded by - is immediately preceded by - starts_at_end_of - uberon - immediately_preceded_by - immediately_preceded_by - immediately_preceded_by - + - - - immediately_precedes - - - - - - - - - David Osumi-Sutherland - o - overlaps - X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). - ends during - + - - - - A is spatially_disjoint_from B if and only if they have no parts in common - There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy - http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl - BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - - - spatially disjoint from - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - + - - - - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y - Chris Mungall - - http://purl.obolibrary.org/obo/ro.owl - negatively regulates (process to process) - negatively regulates - + - - - 'heart development' has active participant some Shh protein - - x has participant y if and only if x realizes some active role that inheres in y - This may be obsoleted and replaced by the original 'has agent' relation - Chris Mungall - has agent - http://purl.obolibrary.org/obo/ro.owl - - has active participant - - - - - - - - - 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. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - 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. - - x adjacent to y if and only if x and y share a boundary. - This relation acts as a join point with BSPO - Chris Mungall - http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl - - adjacent to - - - - - - - - - - - - - move to BFO? - Allen - http://purl.obolibrary.org/obo/obi.owl - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporal relation - temporally related to - - - - - - - - - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - started by - http://purl.obolibrary.org/obo/obi.owl - starts with - - - - - - - - - - inverse of ends with - http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl - ends - - - - - - - - - - - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - finished with - http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl - ends with - - - - - - - - - Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) - a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall - http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with - In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl - Gene Ontology Consortium - colocalizes with - + @@ -1673,242 +592,84 @@ For example, the disposition of a piece of glass to bend light and the lattice s - - - - inverse of upstream of - Chris Mungall - http://purl.obolibrary.org/obo/ro.owl - causally downstream of - + - - - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain - Chris Mungall - http://purl.obolibrary.org/obo/ro.owl - causally upstream of - - - - - - - - - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - http://purl.obolibrary.org/obo/ro.owl - causal relation between processes - - - - - - - - - http://purl.obolibrary.org/obo/ido.owl - relationship - obsolete has_disposition - true - + - + - - - http://purl.obolibrary.org/obo/ido.owl - relationship - negatively_regulates - true - + - + - - - http://purl.obolibrary.org/obo/ido.owl - OBO_REL:0000035 - OBO_REL:realized_as - relationship - NOTE: there appears to be some consistency in usage as to whether processes or continuants realize - obsolete_realized_by - true - - + - - - http://purl.obolibrary.org/obo/ido.owl - relationship - regulates - true - + + is expressed as + - + - - ObsoleteProperty - - + - - - true - + + + A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content. + A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content. + Ingarden, R. (1964) Der Streit um die Existenz der Welt I. Existentalontologie. Max Niemeyer, Tübingen. + Ingarden, R. (1965a) Das literarische Kunstwerk. 3. Auflage. Max Niemeyer, Tübingen. + Ingarden, R. (1965b) Der Streit um die Existenz der Welt II/1. Formalontologie 1. Teil. Max Niemeyer, Tübingen. + Johansson I. (2009) Proof of the existence of universals – and Roman Ingarden's Ontology. Metaphysica. International Journal for Ontology & Metaphysics. 10, 65-87 + Thomasson AL. "Ingarden and the Ontology of Cultural Objects." In: Chrudziminski A (ed.): Existence, Culture, and Person. The Ontology of Roman Ingarden. Frankfurt: ontos, 2005, 115-136. + MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'. + purely intentional entity + - + - - - obsolete has proper part - true - + + + A disease transmission model whose concretization is realized as a simulation of infectious disease epidemic or infectious disease pandemic. + William Hogan and Michael Wagner + An algorithm the concretizations of which models the transmission of transmissible disease. + epidemic model + - - - - - true - - - - - - - - - true - - - - - - - - - true - - - - - - - - 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 - - - - - - - - - - - - - - is expressed as - - - - - - - - - has measurement value - - - - - - - - - - - - - - Stegomyia albopicta - forest day mosquito - Aedes albopictus - - - - - - - - - A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content. - A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content. - Ingarden, R. (1964) Der Streit um die Existenz der Welt I. Existentalontologie. Max Niemeyer, Tübingen. - Ingarden, R. (1965a) Das literarische Kunstwerk. 3. Auflage. Max Niemeyer, Tübingen. - Ingarden, R. (1965b) Der Streit um die Existenz der Welt II/1. Formalontologie 1. Teil. Max Niemeyer, Tübingen. - Johansson I. (2009) Proof of the existence of universals – and Roman Ingarden's Ontology. Metaphysica. International Journal for Ontology & Metaphysics. 10, 65-87 - Thomasson AL. "Ingarden and the Ontology of Cultural Objects." In: Chrudziminski A (ed.): Existence, Culture, and Person. The Ontology of Roman Ingarden. Frankfurt: ontos, 2005, 115-136. - MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'. - purely intentional entity - - - - - - - - - A disease transmission model whose concretization is realized as a simulation of infectious disease epidemic or infectious disease pandemic. - William Hogan and Michael Wagner - An algorithm the concretizations of which models the transmission of transmissible disease. - epidemic model - - - - - + - @@ -2009,6 +770,27 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire + + + + + + + + + + + + + + + + + + + + + An identifier that refers to the legal person that commissions a simulation process. An identifier that refers to the person or organization who is requesting one or more executions of the simulator software. Class was originally created to correspond with a complex type from Apollo XSD v3.1.0. @@ -2032,7 +814,46 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A planned process that has specified output a software product and that involves the creation of source code. + Mathias Brochhausen + William R. Hogan + http://en.wikipedia.org/wiki/Software_development + A planned process resulting in a software product involving the creation of source code. + software development + @@ -2076,6 +897,37 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An identifier that refers to the legal person that creates and maintains a simulator. An identifier that refers to the person or organization who is responsible for the simulator. It is intended to uniquely identify a person or organization. That said, we do not plan to control the namespace for simulator developer at this point in development. We will add our ideas about alternatives at a future date. simulator developer identifier @@ -2097,13 +949,19 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire - + + + + + + + An identifier that refers to all version of a specific simulator. An identifier that refers to all versions of a specific simulator, such as “FRED”. We intend that it uniquely identify a simulator when combined with simulator developer. For example, the combination www.psc.edu/FRED would differentiate the FRED simulator created by a Pittsburgh organization from another “FRED” simulator maintained elsewhere. The implementation of namespace control for simulator name (i.e., making sure that they don’t use “FRED” twice) is the responsibility of simulator developer. simulator identifier @@ -2298,7 +1156,6 @@ Note that the susceptible and infected organisms can be of different species. - @@ -2405,6 +1262,18 @@ can't recall whether we should use process or processual_entity for future + + + + + + + + + + + + Mathias Brochhausen Motivating use case is Synthia synthetic population data. school facility census @@ -2442,6 +1311,27 @@ can't recall whether we should use process or processual_entity for future + + + + + + + + + + + + + + + + + + + + + A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. infectious disease control strategy execution @@ -2504,6 +1394,18 @@ can't recall whether we should use process or processual_entity for future + + + + + + + + + + + + A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval. Mathias Brochhausen A simulated population is a set of simulated organisms. The set can be null (e.g., the set of 200 year-old H. sapiens). A simulated population can include more than one species, in which case it may be convenient to define each species as a simulated population and form the overall simulated population by set union. Similarly, it may be convenient to define sociodemographic or geographic strata within a simulated population as simulated populations and obtain the overall simulated population by set union. See examples in “Programmer’s Guide, page x) @@ -2528,6 +1430,12 @@ can't recall whether we should use process or processual_entity for future + + + + + + A measurement datum that is the output of counting. Mathias Brochhausen A measurement datum that is the output of counting. @@ -2540,6 +1448,24 @@ can't recall whether we should use process or processual_entity for future + + + + + + + + + + + + + + + + + + The planned process of finding the number of elements in a finite set of objects. Mathias Brochhausen http://en.wikipedia.org/wiki/Counting @@ -2571,6 +1497,19 @@ can't recall whether we should use process or processual_entity for future + + + + + + + + + + + + + a simulation that is about an organism simulation of organism @@ -2655,27 +1594,47 @@ can't recall whether we should use process or processual_entity for future - A simulated organism in a simulated population that is not susceptible. - A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. -Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’ However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’ The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage. - - simulation of recovered organism - - - - - - - - - + - - + + + + + + + + + + + + + + + A simulated organism in a simulated population that is not susceptible. + A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. +Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’ However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’ The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage. + + simulation of recovered organism + + + + + + + + + + + + + + + + @@ -2696,7 +1655,6 @@ Note that the name for this concept, were it to be named based on its intent, wo - @@ -2914,6 +1872,12 @@ MB: This issue will need to be taken care of in the axiomatization of simulated + + + + + + An identifier that refers to a specific simulator. Mathias Brochhausen The combination of simulator developer, simulator name, and simulator version, for example “www.psc.edu/FRED/2.0” The combination is intended to uniquely identify the simulation algorithm that produced output X, given input Y to support scientific audit, error analysis, and reproducibility of results. @@ -2926,7 +1890,6 @@ MB: This issue will need to be taken care of in the axiomatization of simulated - @@ -2962,6 +1925,12 @@ MB: This issue will need to be taken care of in the axiomatization of simulated + + + + + + Mathias Brochhausen Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast). hospital patient population census @@ -3109,6 +2078,22 @@ Maybe we need to discuss this. + + + + + + + + + + + + + + + + A simulation of an organism in a simulated population that has participated in an epidemic control measure. A simulated organism in a simulated population has participated in a particular simulated control measure. (e.g. an organism received antiviral treatment) simulation of control measure participant @@ -3152,6 +2137,12 @@ While in many pieces of fiction the order in which the purely intentional entiti + + + + + + A numeral that indexes a specific simulation. The run id indexes a run of a specific simulator version on a specific simulated population, disease(s), and optionally control measures. The simulator is responsible for generating a run id and ensuring its uniqueness. Class was originally created to correspond with an element from Apollo XSD v3.1.0. @@ -3245,6 +2236,12 @@ The time step value and unit are specified using a scalar value specification. + + + + + + A numeral that indexes a specific time step of a simulation. The time step number of a simulation. simulatorTime @@ -3268,6 +2265,12 @@ The time step value and unit are specified using a scalar value specification. + + + + + + A purely intentional entity that simulates an entity and its properties. @@ -3321,6 +2324,22 @@ The time step value and unit are specified using a scalar value specification. + + + + + + + + + + + + + + + + A simulation of a susceptible organism in a simulated population. A simulated organism in a simulated population that is capable of acquiring a particular simulated disease. simulation of susceptible organism @@ -3357,6 +2376,12 @@ The time step value and unit are specified using a scalar value specification. + + + + + + A simulation of an asymptomatic infectious agent host. A simulated organism in a simulated population that has no symptoms caused by a particular simulated disease. simulation of asymptomatic organism @@ -3542,6 +2567,12 @@ The time step value and unit are specified using a scalar value specification. + + + + + + A plan specification whose objective specification is an infectious disease control objective specification. A plan with the goal of preventing or mitigating the effects of infections in a population due to one or more pathogens. InfectiousDiseaseControlMeasure @@ -3643,6 +2674,18 @@ The time step value and unit are specified using a scalar value specification. + + + + + + + + + + + + a study design execution that has as its specified output one or more measured vaccination efficacy data items an experiment that measures vaccination efficacy from a sample of vaccinated and possibly unvaccinated individuals VaccinationEfficacyStudy @@ -3858,6 +2901,27 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic + + + + + + + + + + + + + + + + + + + + + An identifier that refers to the legal person that creates and maintains software. An identifier that refers to the legal person that creates and maintains software. softwareDeveloper @@ -3882,6 +2946,12 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic + + + + + + An identifier that refers to a specific piece of software. An identifier that refers to a specific piece of software. SoftwareIdentification @@ -3943,6 +3013,12 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic + + + + + + An identifier that refers to all version of a specific software. An identifier that refers to all version of a specific software. softwareName @@ -4042,6 +3118,22 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic + + + + + + + + + + + + + + + + @@ -4108,6 +3200,49 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources Mathias Brochhausen A process where a susceptible organism from a particular species becomes infected by a particular pathogen. The infection is acquired from an infected organism of a particular species or from a contaminated thing. @@ -4176,6 +3311,32 @@ An infection is acquired from an infectious organism or a contaminated thing. + + + + + + + + + + + + + + + + + + + + + + + + + + Mathias Brochhausen latent period @@ -4525,6 +3686,34 @@ For example, once a vaccination control strategy starts, individual vaccinations + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mathias Brochhausen infectious period @@ -4598,32 +3787,85 @@ For example, once a vaccination control strategy starts, individual vaccinations - A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Vaccination - A treatment of an individual with antigenic material from a pathogen that has the goal of inducing resistance of the individual to infection with the pathogen. - Vaccination - vaccination - - - - - - - - Mathias Brochhausen - replaced with VO 'vaccine function' - vaccine disposition - true - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen. + Mathias Brochhausen + http://en.wikipedia.org/wiki/Vaccination + A treatment of an individual with antigenic material from a pathogen that has the goal of inducing resistance of the individual to infection with the pathogen. + Vaccination + vaccination + + + + + + + + Mathias Brochhausen + replaced with VO 'vaccine function' + vaccine disposition + true + + + + + + + + + @@ -4642,6 +3884,12 @@ For example, once a vaccination control strategy starts, individual vaccinations + + + + + + Mathias Brochhausen disposition to become contaminated with a pathogen @@ -4800,6 +4048,32 @@ Somehow, it's not innate and it's temporary, ie, the body will eventua + + + + + + + + + + + + + + + + + + + + + + + + + + A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria, and that realizes some concretization of a census objective specification. Mathias Brochhausen A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria. @@ -4831,6 +4105,18 @@ Somehow, it's not innate and it's temporary, ie, the body will eventua + + + + + + + + + + + + A census that is the outcome of a population survey. A census that is the outcome of a population survey. population census @@ -4924,6 +4210,46 @@ Somehow, it's not innate and it's temporary, ie, the body will eventua + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A population survey that counts the number of individuals in the population who are infected with a particular pathogen. Mathias Brochhausen A population survey that counts the number of individuals in the population who are infected with a particular pathogen. @@ -4988,6 +4314,18 @@ I checked because an infection and immunity census would involve two different c + + + + + + + + + + + + A census that is the result of a population infection survey and a population immunity survey. Mathias Brochhausen PII Census @@ -5026,6 +4364,12 @@ I checked because an infection and immunity census would involve two different c + + + + + + A census that is the specific outcome of a population demographic survey. Mathias Brochhausen A census that is the specific outcome of a population demographic survey. @@ -5104,6 +4448,44 @@ I checked because an infection and immunity census would involve two different c + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An information content entity that is about a MIDAS scenario and contains population disease census data. Mathias Brochhausen An information content entity that is about a MIDAS scenario and contains population disease census data. @@ -5166,6 +4548,22 @@ I checked because an infection and immunity census would involve two different c + + + + + + + + + + + + + + + + A census that is the specified output of a agent-level ecosystem data generation that had census data as an input. Mathias Brochhausen A census that is the specified output of a agent-level ecosystem data generation that had census data as an input. @@ -5203,6 +4601,26 @@ I checked because an infection and immunity census would involve two different c + + + + + + + + + + + + + + + + + + + + An independent continuant that is the localization of a pathogen, but is not undergoing an infection. Mathias Brochhausen An independent continuant that is the localization of a pathogen, but is not undergoing an infection. @@ -5246,7 +4664,38 @@ I checked because an infection and immunity census would involve two different c + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A biological process whereby an entity that is not in contact with a pathogen of a particular biological taxon begins to undergo contamination with that pathogen. Mathias Brochhausen William R. Hogan @@ -5272,6 +4721,12 @@ I checked because an infection and immunity census would involve two different c + + + + + + Motivating use case is Synthia synthetic population data. nursery school student population census @@ -5293,6 +4748,12 @@ I checked because an infection and immunity census would involve two different c + + + + + + Motivating use case is Synthia synthetic population data. primary school student population census @@ -5314,6 +4775,12 @@ I checked because an infection and immunity census would involve two different c + + + + + + Motivating use case is Synthia synthetic population data. secondary school student population census @@ -5335,10 +4802,16 @@ I checked because an infection and immunity census would involve two different c - A treatment with an antiviral drug. - A treatment of a particular host with a particular antiviral drug with activity against a particular viral pathogen. - AntiviralTreatment - antiviral treatment + + + + + + + A treatment with an antiviral drug. + A treatment of a particular host with a particular antiviral drug with activity against a particular viral pathogen. + AntiviralTreatment + antiviral treatment @@ -5382,7 +4855,6 @@ I checked because an infection and immunity census would involve two different c - @@ -5467,6 +4939,12 @@ I checked because an infection and immunity census would involve two different c + + + + + + Mathias Brochhausen Motivating use case is Synthia synthetic population data. school student population census @@ -5737,6 +5215,12 @@ The infectious disease scenario typically also includes a lot of additional data + + + + + + A host who is able to transmit some infection to another organism. An infected organism of a particular species who is able to transmit the infection to a susceptible organism of a particular species. @@ -5962,6 +5446,12 @@ So I am comfortable with disease outcome as a process. It is also consistent wi + + + + + + An organism that is the bearer of a susceptibility disposition. William R. Hogan An organism of a particular species that can undergo infection with a particular pathogen. @@ -5985,7 +5475,13 @@ So I am comfortable with disease outcome as a process. It is also consistent wi - + + + + + + + An organism that is the bearer of an immune resistance disposition. William R. Hogan An organism of a particular species that has developed immune resistance to infection with a pathogen of a particular species. @@ -6010,6 +5506,12 @@ So I am comfortable with disease outcome as a process. It is also consistent wi + + + + + + an organism that is the bearer of resistance to infection William R. Hogan An organism of a particular species that is unable to undergo infection with a particular pathogen. @@ -6212,6 +5714,12 @@ The clade name is a string in XSD version 2.0.1. + + + + + + A material entity that is part of an abiotic ecosystem. Mathias Brochhausen A material entity that is part of an abiotic ecosystem. @@ -6483,6 +5991,12 @@ can't recall whether we should use process or processual_entity for future + + + + + + An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon. An organism, virus, or prion that can infect another organism. pathogen @@ -6506,10 +6020,16 @@ can't recall whether we should use process or processual_entity for future + + + + + + An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. host - host + host organism @@ -6912,7 +6432,13 @@ For example, it may take time to communicate to workers to stop vaccinating and - + + + + + + + An infection acquisition whereby a susceptible host acquires an infection from a contaminated thing. William R. Hogan An infection acquisition from a contaminated thing. @@ -6964,7 +6490,23 @@ For example, it may take time to communicate to workers to stop vaccinating and - + + + + + + + + + + + + + + + + + An infection acquisition whereby a susceptible host acquires an infection from an infectious host. William R. Hogan An infection acquisition from an individual who is infectious. @@ -7407,20 +6949,6 @@ The abnormal state could be having a disease, carrier status, a syndrome, a stru - - - - - - - - - - - - - - A process whose beginning is demarcated by accelerating infection acquisition by one or more host species of a particular pathogen in a particular location and whose end is demarcated by the time when the rate of infection acquisition becomes constant. William R. Hogan epidemic of infection @@ -7486,7 +7014,13 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + + + + + + + An organism that is the bearer of a naturally-acquired, active immune resistance to infection. William R. Hogan An organism that has recovered from infection with a particular pathogen, is no longer infectious to other organisms of any species, and is not able to be infected again with that pathogen. @@ -7581,6 +7115,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + An infectious disease control strategy that has a vector control action specification as part. William R. Hogan An infectious disease control strategy that attempts to reduce infections in a population of a particular host species by limiting infection acquisitions from a second host species, called the 'vector'. @@ -7634,6 +7174,40 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A census of entities of a certain type or types in the abiotic ecosystem. William R. Hogan A census of things in the abiotic ecosystem. @@ -7683,6 +7257,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157) William R. Hogan Reproduction of a single mosquito @@ -7712,6 +7292,22 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + The duration of the temporal interval occupied by a gonotropic period. Matthew Diller William R. Hogan @@ -7803,6 +7399,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + A treatment with a drug product. William R. Hogan Treatment with a drug. @@ -7903,6 +7505,24 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + biological colonization a reproduction of a pathogen of a particular biological taxon inside a host organism of another taxon, without invasion of the tissues of the host. William R. Hogan @@ -8002,6 +7622,41 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + establishment of infection from self colonization An infection acquisition by which a pathogen organism from a particular biological taxon, which previously was participating in a colonization process in a host organism from another taxon, begins to invade the tissues of the same host organism and reproduce there. William R. Hogan @@ -8014,7 +7669,6 @@ The constant rate may be zero. The period of an epidemic may be defined using s - @@ -8080,6 +7734,22 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + A symbiosis where the organisms that are interacting remain physically external to one another. Matthew Diller William R. Hogan @@ -8147,6 +7817,22 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + An ectosymbiosis that results in harm to one of the participating organisms but neither harms nor benefits the other participating organisms. Matthew Diller William R. Hogan @@ -8196,6 +7882,38 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An ectosymbiosis that results in harm to one of the participating organisms and benefit to another participating organism. Matthew Diller William R. Hogan @@ -8247,20 +7965,40 @@ The constant rate may be zero. The period of an epidemic may be defined using s - An intimate agonism in which the harm is not fatal to the host. - Matthew Diller - William R. Hogan - ectoparasitism - An intimate agonism in which the harm is not fatal to the host. - Example: Temnocephala chilensis and various marine wildlife - ectosymbiotic parasitism - - - - - - - + + + + + + + + + + + + + + + + + + + + + An intimate agonism in which the harm is not fatal to the host. + Matthew Diller + William R. Hogan + ectoparasitism + An intimate agonism in which the harm is not fatal to the host. + Example: Temnocephala chilensis and various marine wildlife + ectosymbiotic parasitism + + + + + + + @@ -8287,6 +8025,26 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + An ectosymbiotic parasitism that realizes some facultative parasite role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan @@ -8331,6 +8089,30 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + An ectosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite. Matthew Diller William R. Hogan @@ -8404,6 +8186,30 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + An ectosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid. Matthew Diller William R. Hogan @@ -8448,6 +8254,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + An ectosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms. Matthew Diller William R. Hogan @@ -8487,6 +8299,26 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + An ectosymbiotic commensalism that realizes some facultative commensal role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan @@ -8531,6 +8363,30 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + An ectosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits. Matthew Diller William R. Hogan @@ -8561,6 +8417,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + An ectosymbiosis that results in benefit to all participating organisms. Matthew Diller William R. Hogan @@ -8600,6 +8462,26 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + An ectosymbiotic mutualism that realizes some facultative mutualist role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan @@ -8644,6 +8526,30 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + An ectosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating. Matthew Diller William R. Hogan @@ -8680,6 +8586,22 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + A symbiosis where one organism is physically contained within another organism (called the 'host'). Matthew Diller William R. Hogan @@ -8718,6 +8640,26 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + An endosymbiosis that results in benefit to the parasite and harm to the host. Matthew Diller William R. Hogan @@ -8786,6 +8728,42 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A non-intimate agonism in which the harm is fatal. Matthew Diller William R. Hogan @@ -8825,6 +8803,26 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + A non-intimate agonism in which the harm is not fatal. Matthew Diller William R. Hogan @@ -8864,14 +8862,34 @@ The constant rate may be zero. The period of an epidemic may be defined using s - An endosymbiotic parasitism that realizes some facultative parasite role inhering in an organism that is also realized by a bodily benefit to that organism. - Matthew Diller - William R. Hogan - facultative endoparasitism - An endosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions. - Example: Strongyloides stercoralis (roundworm) and humans - facultative endosymbiotic parasitism - + + + + + + + + + + + + + + + + + + + + + An endosymbiotic parasitism that realizes some facultative parasite role inhering in an organism that is also realized by a bodily benefit to that organism. + Matthew Diller + William R. Hogan + facultative endoparasitism + An endosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions. + Example: Strongyloides stercoralis (roundworm) and humans + facultative endosymbiotic parasitism + @@ -8908,6 +8926,30 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + An endosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite. Matthew Diller William R. Hogan @@ -8944,6 +8986,22 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + An endosymbiosis that results in benefit to the parasitoid and is fatal to the host. Matthew Diller William R. Hogan @@ -8983,6 +9041,26 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + An endosymbiotic parasitoidism that realizes some facultative parasitoid role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan @@ -9027,6 +9105,30 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + An endosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid. Matthew Diller William R. Hogan @@ -9071,6 +9173,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + An endosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms. Matthew Diller William R. Hogan @@ -9110,6 +9218,26 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + An endosymbiotic commensalism that realizes some facultative commensal role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan @@ -9154,6 +9282,30 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + An endosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits. Matthew Diller William R. Hogan @@ -9184,6 +9336,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + An endosymbiosis that results in benefit to all participating organisms. Matthew Diller William R. Hogan @@ -9223,6 +9381,26 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + An endosymbiotic mutualism that realizes some facultative mutualist role inhering in an organism that is also realized by a bodily benefit to that organism. Matthew Diller William R. Hogan @@ -9267,6 +9445,30 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + An endosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating. Matthew Diller William R. Hogan @@ -9666,6 +9868,22 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + A data set whose data items are about a host and its participation in an infection and potentially other activities occuring in the same time interval as the infection. Matthew Diller William R. Hogan @@ -9766,6 +9984,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + infectious disposition 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. William R. Hogan @@ -9805,6 +10029,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + potentially infectous contact role A role borne by an organism that is realized in a potentially infectious contact process. William R. Hogan @@ -9832,6 +10062,12 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + potentially infectious contact organism An organism that is the bearer of a potentially infectious contact role during a potentially infectious contact process. William R. Hogan @@ -11406,6 +11642,33 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + software source code version control repository + A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. + William R. Hogan + Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based source code repository @@ -11414,7 +11677,28 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + + + + + + + + + + + + + + + + + + + + + + process of compiling software A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. William R. Hogan @@ -11900,6 +12184,33 @@ The constant rate may be zero. The period of an epidemic may be defined using s + + + + + + + + + + + + + + + + + + + + + + + + + + + An investigation that realizes the concretization of some disease state design and that has as an occurrent part some population survey that has specified input some case definition. Matthew Diller @@ -11940,6 +12251,12 @@ has specified input some case definition. + + + + + + A data set about an instance of an epidemic. Matthew Diller William R. Hogan @@ -12087,6 +12404,28 @@ has specified input some case definition. + + + + + + + + + + + + + + + + + + + + + + A count of the total number of diseased indivduals in a population during a particular time interval. Matthew Diller William R. Hogan @@ -12364,6 +12703,12 @@ has specified input some case definition. + + + + + + website that has data as a part William R. Hogan This class was created for use case for MIDAS Digital Repository to index websites that have useful data in them, albeit rarely as machine-interpretable, downloadable datasets. Much of the data are locked in PDF or other text-based formats. @@ -12449,6 +12794,19 @@ has specified input some case definition. + + + + + + + + + + + + + abiotic ecosystem data set A data set that is about some abiotic ecosystem or abiotic ecosystem element. William R. Hogan @@ -12480,6 +12838,17 @@ has specified input some case definition. + + + + + + + + + + + data set about Earth's atmosphere or some part of it A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere. William R. Hogan @@ -12492,7 +12861,6 @@ has specified input some case definition. - @@ -12569,6 +12937,12 @@ has specified input some case definition. + + + + + + disease identifier an identifier that denotes a disease. William R. Hogan @@ -12595,6 +12969,12 @@ has specified input some case definition. + + + + + + dataset about infectious disease acquisitions The dataset at this link is rdf:type this class: https://figshare.com/articles/dataset/COVID19_settings_of_transmission_-_collected_reports_database/12173343 a dataset that is about infectious disease acquisitions at particular times and particular places. @@ -12654,6 +13034,12 @@ has specified input some case definition. + + + + + + human daily movement behavior data set https://www.google.com/covid19/mobility/ a data set that is about the human daily movement behavior of the individual huamns in a given population. @@ -12680,6 +13066,12 @@ has specified input some case definition. + + + + + + potentially infectious contact process data set in a population a data set that is about one or more potentially infectious contact processes in a population of host organisms. William R. Hogan @@ -12705,7 +13097,13 @@ has specified input some case definition. - + + + + + + + infectious disease control strategy census a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem. William R. Hogan @@ -12731,6 +13129,12 @@ has specified input some case definition. + + + + + + school closure infectious disease control strategy census an infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region. William R. Hogan @@ -12757,6 +13161,12 @@ has specified input some case definition. + + + + + + vaccination infectious disease control strategy census William R. Hogan @@ -12782,6 +13192,12 @@ has specified input some case definition. + + + + + + population vaccination census vaccine / immunization registry data, vaccination / immunization records extracted from an EHR a population treatment census that is about one or more vaccinations of organisms in a population. @@ -12948,6 +13364,22 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + + + + + + + + + + + data set about Earth's atmospheric weather A data set about the Earth's atmospheric weather William R. Hogan @@ -12972,6 +13404,12 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + monkeypox disease inhering in a human being A monkeypox disease inhering in a human being. William R. Hogan @@ -13061,6 +13499,7 @@ 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. @@ -13074,6 +13513,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si + 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. @@ -13188,14584 +13628,1099 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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 - - - - - - - - - epidemic simulator action specification - William R. Hogan - epidemic simulator action specification - - - - - - - - - infectious disease control strategy action specification - William R. Hogan - infectious disease control strategy action specification - - - - - - - - - individual treatment control strategy action specification - William R. Hogan - individual treatment control strategy action specification - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - - - - - - - - - - - - - - - - - creating a copyright license - A planned process that has a copyright license as its specified output. - William R. Hogan - copyright license creation - Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time. - creating a copyright license - - - - - - - - - copyright license for a creative work - A document that is about the legal rights, claims, and obligations of a legal person (person or organization) under copyright law, and how that legal person intends for those rights, claims, and obligations to be handled/managed by users of the creative work to which this document is attached. - William R. Hogan - Can be for any creative work including fiction. But the license itself is an ICE, and refers to real claims and obligations. - copyright license - - - - - - - - - data service software application - A software application that implements a data service. - William R. Hogan - data service software - - - - - - - - - TODO - - - - - - - - - facultative role - A role borne by an organism in virtue of the fact that it is in intimate association with one or more organisms of different species, and is realized by bodily benefit to that organism as an occurrent part of a symbiosis with the other organisms. This bodily benefit takes the place of the organism or some relatively isolated part of the organism realizing some normal homeostasis disposition itself. - facultative role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries. - Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital - Synonyms: substance aggregate - object_aggregate - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Interval - - - - - - - - - - - - - - - - - - - - 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. - history - - - - - - - - - The usage or intended usage of a drug product to act against a viral infection of a host. - antiviral drug - - - - - - - - - A viral infectious disease that has_material_basis in Zika virus, which is transmitted_by Aedes aegypti mosquitoes and targets neural progenitor cells and neuronal cells in all stages of maturity and has_symptom fever, has_symptom rash, has_symptom headaches and has_symptom joint pain. - http://purl.obolibrary.org/obo/doid.owl - ICD10:U06 - ICD10CM:A92.8 - MESH:D000071243 - Zika virus disease - Zika fever - - - - - - - - - A viral infectious disease that results_in infection, has_material_basis_in Dengue virus [NCBITaxon:12637] with four serotypes (Dengue virus 1, 2, 3 and 4), which are transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom severe headache, has_symptom severe pain behind the eyes, has_symptom joint pain, has_symptom muscle and bone pain, has_symptom rash, and has_symptom mild bleeding. - http://purl.obolibrary.org/obo/doid.owl - DOID:0050142 - ICD10CM:A90 - ICD9CM:061 - MESH:D003715 - NCI:C34528 - SNOMEDCT_US_2016_03_01:154345006 - SNOMEDCT_US_2016_03_01:266194002 - SNOMEDCT_US_2016_03_01:38362002 - UMLS_CUI:C0011311 - Dengue Fever - breakbone fever - classic dengue - disease_ontology - classical dengue - DOID:12205 - - dengue disease - - - - - - - - - A dengue disease that occurs when a person experiences a second infection with a heterologous Dengue virus serotype, which is transmitted_by Aedes mosquito bite. The infection has_symptom hemorrhagic lesions of the skin, has_symptom thrombocytopenia, has_symptom reduction in the fluid part of the blood, and has_symptom high fever. - http://purl.obolibrary.org/obo/doid.owl - ICD10CM:A91 - MESH:D019595 - NCI:C34683 - SNOMEDCT_US_2016_03_01:186598001 - SNOMEDCT_US_2016_03_01:186599009 - SNOMEDCT_US_2016_03_01:20927009 - UMLS_CUI:C0019100 - DHF - disease_ontology - Dengue haemorrhagic fever - DOID:12206 - - dengue hemorrhagic fever - - - - - - - - - A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus, which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy. - http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl - - GARD:10722 - ICD10CM:B04 - ICD9CM:059.01 - MESH:D045908 - NCI:C128421 - SNOMEDCT_US_2021_09_01:240466002 - UMLS_CUI:C0276180 - url:http://www.cdc.gov/ncidod/monkeypox/factsheet2.htm - disease_ontology - DOID:3292 - - - monkeypox - - - - - - - - - A viral infectious disease that results_in infection, located_in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness. - http://purl.obolibrary.org/obo/doid.owl - DOID:8468 - ICD10CM:J11.1 - ICD9CM:487 - MESH:D007251 - NCI:C53482 - SNOMEDCT_US_2016_03_01:155559006 - SNOMEDCT_US_2016_03_01:155562009 - SNOMEDCT_US_2016_03_01:195931008 - SNOMEDCT_US_2016_03_01:266353003 - SNOMEDCT_US_2016_03_01:266393000 - SNOMEDCT_US_2016_03_01:6142004 - UMLS_CUI:C0021400 - Influenza with non-respiratory manifestation (disorder) - Influenza with other manifestations - Influenza with other manifestations (disorder) - Influenza with other manifestations NOS (disorder) - flu - influenza with non-respiratory manifestation - disease_ontology - DOID:8469 - influenza - - - - - - - - - a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role - William Hogan - http://purl.obolibrary.org/obo/dron.owl - William Hogan - drug product - - - - - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - http://purl.obolibrary.org/obo/envo.owl - portion of environmental material - ENVO - ENVO:00010483 - Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. - environmental material - - - - - - - - - - An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. - http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl - ORCID:0000-0002-4366-3088 - 2013-04-07T14:35:18Z - DOI:10.1186/2041-1480-4-43 - envoPolar - A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional. - environmental condition - - - - - - - - - Water vapour is a vapour which is the gas phase of water. - http://purl.obolibrary.org/obo/envo.owl - ORCID:0000-0002-4366-3088 - 2013-10-10T07:58:18Z - aqueous vapor - aqueous vapour - water vapor - ENVO - ENVO:01000266 - Perhaps a better relation between water vapour and water can be found in or added to RO? - water vapour - - - - - - - - - Atmospheric water vapour is water vapour that is part of an atmosphere. - http://purl.obolibrary.org/obo/envo.owl - ORCID:0000-0002-4366-3088 - 2013-10-10T08:22:07Z - atmospheric water vapor - ENVO - ENVO:01000268 - atmospheric water vapour - - - - - - - - - Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. - http://purl.obolibrary.org/obo/envo.owl - precipitation - "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) - hydrological precipitation process - - - - - - - - - A temperature that inheres in some portion of air. - Draft class. In discussion in Issue #278. - http://purl.obolibrary.org/obo/envo.owl - air temperature - - - - - - - - - A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. - This class is to be populated by inference. - http://purl.obolibrary.org/obo/envo.owl - gas - gaseous environmental material - - - - - - - - - Environmental variability which inheres in an astronomical body part or in outer space. - http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl - https://en.wikipedia.org/wiki/Space_weather - https://en.wikipedia.org/wiki/Weather - This class refers to all weather, including atmospheric and space weather. Please use a subclass for more specificity. - weather - - - - - - - - - Weather which inheres in an atmosphere. - http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl - https://en.wikipedia.org/wiki/Weather - This class refers to the common usage of "weather", referencing the state of a (part of) an astronomical body's atmosphere. - atmospheric weather - - - - - - - - - A condition which inheres in an environmental system by virtue of that system undergoing variation in its composition, the distribution of the qualities its components bear, and/or in the processes which occur within it and which it participates in. - http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl - This class is very general, but the nature of environmental variability is indeed quite variable. This class may be refined once we have more subclasses to consider. - environmental variability - - - - - - - - - http://purl.obolibrary.org/obo/envo.owl - Should environmental feature become something more towards a disposition, the assert would be updated to something like "has participant (environmental system or (material entity and has disposition some environmental feature))". There are several issues surrounding the reconcilliation of environmental feature and environmental system, both theoretical and practical. - environmental system process - - - - - - - - - The temperature of a environmental material. - http://purl.obolibrary.org/obo/envo.owl - environmental material temperature - temperature of environmental material - - - - - - - - - The temperature of a air. - http://purl.obolibrary.org/obo/envo.owl - air temperature - temperature of air - - - - - - - - - - A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research. - PERSON: Nicole Vasilevsky - community genomic analysis - ecogenomic analysis - environmental genomic analysis - http://en.wikipedia.org/wiki/Metagenomics - http://purl.obolibrary.org/obo/ero.owl - metagenomics analysis - - - - - - - - - A set of related web pages containing content such as text, images, video, audio, etc., prepared and maintained as a collection of information on a particular subject. - http://purl.obolibrary.org/obo/fbcv.owl - pub_type - FBcv:0000667 - website - - - - - - - - - A publication issued on a regular, ongoing basis containing separate research articles and other writings such as reviews, comments and conference reports. - http://purl.obolibrary.org/obo/fbcv.owl - djs93 - 2012-07-10T04:08:06Z - MeSH:D020492 - pub_type - Periodicals - FBcv:0000787 - journal - - - - - - - - - - - - - - A site designated by some relative spatial orientation. - Matthew Diller - William R. Hogan - An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers. - Location - - - - - - - - - - - - - - - The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. - 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 - GO:0019952 - GO:0050876 - biological_process - - - - - reproduction - - - - - - - - - Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). - http://purl.obolibrary.org/obo/go.owl - biological_process - response to abiotic stress - response to biotic stress - GO:0006950 - - - - - - - - - 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. - response to stress - - - - - - - - - Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. - http://purl.obolibrary.org/obo/go.owl - GO:0002217 - GO:0042829 - defence response - physiological defense response - biological_process - antimicrobial peptide activity - defense/immunity protein activity - GO:0006952 - - defense response - - - - - - - - - The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. - http://purl.obolibrary.org/obo/go.owl - Inflammation - Wikipedia:Inflammation - biological_process - GO:0006954 - This term was improved by GO_REF:0000022. It was moved. - inflammatory response - - - - - - - - - The emergence of an adult insect from a pupa case. - http://purl.org/obo/owl/gene_ontology - - - - - - - biological_process - eclose - eclosion - - - - - - - - - The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. - http://purl.obolibrary.org/obo/go.owl - Wikipedia:Gestation - gestation - biological_process - carrying of young - GO:0007565 - - female pregnancy - - - - - - - - - The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs. - http://purl.obolibrary.org/obo/go.owl - giving birth - egg laying - biological_process - GO:0007567 - parturition - - - - - - - - - http://purl.org/obo/owl/gene_ontology - GO:0016280 - - - - - - - - - - - - - biological_process - - aging - - - - - - - - - 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 - behavioral response to stimulus - behaviour - behavioural response to stimulus - biological_process - GO:0007610 - - - - 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. - behavior - - - - - - - - - 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 - biological_process - GO:0007617 - mating behavior - - - - - - - - - biological_process - 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 - biological process - - - - - - - - - An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700). - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0010259 - multicellular organismal aging - - - - - - - - - Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0010941 - regulation of cell death - - - - - - - - - http://purl.org/obo/owl/gene_ontology - - - - - - - - - - - - - - - - - - - biological_process - oviposition - - - - - - - - - The process in which a virus effects a change in the structure or processes of its host organism. - http://purl.obolibrary.org/obo/go.owl - GO:0044792 - virus-host interaction - Reactome:REACT_6323 - VZ:886 - host-virus interaction - modulation by virus of host anatomical structure or process - modulation by virus of host anatomy or process - viral interaction with host - viral-host process - virus-host process - biological_process - GO:0019048 - - - modulation by virus of host morphology or physiology - - - - - - - - - The set of viral processes that induce an apoptotic process in infected host cells, facilitating release and spread of progeny virions. - http://purl.obolibrary.org/obo/go.owl - activation by virus of host apoptosis - activation by virus of host apoptotic programmed cell death - activation of apoptosis in host by virus - induction by virus of host apoptotic programmed cell death - induction of apoptosis in host by virus - induction by virus of host apoptosis - biological_process - GO:0019051 - induction by virus of host apoptotic process - - - - - - - - - The process in which a virus effects a change in the processes and activities of its host organism. - http://purl.obolibrary.org/obo/go.owl - Reactome:REACT_6222 - modification by virus of host cellular process - regulation by virus of host cellular process - regulation of cellular process in host by virus - regulation of host cellular process by virus - viral host cell process manipulation - biological_process - modulation of cellular process in host by virus - GO:0019054 - - modulation by virus of host process - - - - - - - - - - http://purl.org/obo/owl/gene_ontology - - - - - - - biological_process - reproductive behavior - - - - - - - - - A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0022414 - - reproductive process - - - - - - - - - http://purl.org/obo/owl/gene_ontology - - - - - - - biological_process - - - - developmental process - - - - - - - - - The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0032504 - multicellular organism reproduction - - - - - - - - - http://purl.org/obo/owl/gene_ontology - - - - - - - biological_process - multicellular organismal reproductive behavior - - - - - - - - - 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 - biological_process - cooperative behavior - GO:0035176 - Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. - social behavior - - - - - - - - - The process in which an organism effects a change in the structure or processes of a second organism. - http://purl.obolibrary.org/obo/go.owl - rfoulger - 2011-04-21T01:31:51Z - regulation of morphology of other organism - regulation of physiological process of other organism - regulation of physiology of other organism - biological_process - regulation of morphology or physiology of other organism - GO:0035821 - modification of morphology or physiology of other organism - - - - - - - - - Any process in which a virus increases the frequency, rate or extent of host cysteine-type endopeptidase activity (also called caspase activity) which contributes to the apoptotic process. - http://purl.obolibrary.org/obo/go.owl - rfoulger - 2012-10-09T15:44:29Z - activation of host caspases by virus - induction by virus of host caspase activity - biological_process - GO:0039651 - induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process - - - - - - - - - Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. - http://purl.obolibrary.org/obo/go.owl - GO:0043070 - regulation of non-apoptotic programmed cell death - biological_process - GO:0043067 - regulation of programmed cell death - - - - - - - - - The process in which a symbiont organism effects a change in the structure or processes of its host organism. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0044003 - - modification by symbiont of host morphology or physiology - - - - - - - - - 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 - - - - - - - - - Any process in which an organism has an effect on an organism of a different species. - interspecies interaction between organisms - - - - - - - - - A process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism. - http://purl.obolibrary.org/obo/go.owl - janelomax - 2012-03-20T04:48:41Z - biological_process - GO:0044531 - modulation of programmed cell death in other organism - - - - - - - - - A biological process that directly contributes to the process of producing new individuals, involving another organism. - http://purl.obolibrary.org/obo/go.owl - janelomax - 2012-09-19T15:56:30Z - biological_process - GO:0044703 - multi-organism reproductive process - - - - - - - - - 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 - biological_process - GO:0044705 - multi-organism reproductive behavior - - - - - - - - - The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. - http://purl.obolibrary.org/obo/go.owl - organismal reproductive process - reproductive process in a multicellular organism - biological_process - GO:0048609 - multicellular organismal reproductive process - - - - - - - - - Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - http://purl.obolibrary.org/obo/go.owl - GO:0050791 - regulation of physiological process - biological_process - GO:0050789 - - - - regulation of biological process - - - - - - - - - Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - http://purl.obolibrary.org/obo/go.owl - GO:0051244 - regulation of cellular physiological process - biological_process - GO:0050794 - - regulation of cellular process - - - - - - - - - Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - http://purl.obolibrary.org/obo/go.owl - GO:0051869 - physiological response to stimulus - biological_process - GO:0050896 - - - - 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. - response to stimulus - - - - - - - - - establishment of localization - The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. - http://purl.obolibrary.org/obo/ido.owl - establishment of localization - establishment of localization - - - - - - - - - An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0051701 - - interaction with host - - - - - - - - - A biological process which involves another organism of the same or different species. - multi-organism process - - - - - - - - - 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 - GOC:ai - GOC:mah - behavioral interaction between organisms - behavioral interaction with other organism - behavioural interaction between organisms - behavioural interaction with other organism - behavioral signaling - behavioral signalling - biological_process - GO:0051705 - - multi-organism behavior - - - - - - - - - The process in which an organism effects a change in the structure or processes of a second organism, where the two organisms are in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - regulation of morphology of other organism during symbiotic interaction - regulation of physiological process in other organism during symbiotic interaction - regulation of physiology of other organism during symbiotic interaction - biological_process - modification of morphology or physiology of other organism during symbiotic interaction - modulation of morphology or physiology of other organism during symbiotic interaction - regulation of morphology or physiology of other organism during symbiotic interaction - GO:0051817 - - modification of morphology or physiology of other organism involved in symbiotic interaction - - - - - - - - - Any process in which an organism modulates the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0052152 - modulation of host PCD - modulation by symbiont of host non-apoptotic programmed cell death - biological_process - GO:0052040 - - modulation by symbiont of host programmed cell death - - - - - - - - - Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0012504 - GO:0052044 - GO:0052045 - GO:0052153 - GO:0052397 - GO:0052400 - activation by organism of host programmed cell death - activation by organism of programmed cell death in other organism during symbiotic interaction - enhancement of host programmed cell death - enhancement of host programmed cell death by organism - induction by organism of programmed cell death in other organism involved in symbiotic interaction - induction by symbiont of host programmed cell death - upregulation by symbiont of host programmed cell death - activation by organism of non-apoptotic programmed cell death in other organism - activation by symbiont of host programmed cell death - induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction - positive regulation by symbiont of host non-apoptotic programmed cell death - stimulation by symbiont of host programmed cell death - biological_process - induction by organism of programmed cell death in other organism during symbiotic interaction - induction of non-apoptotic programmed cell death by other organism - GO:0052042 - - positive regulation by symbiont of host programmed cell death - - - - - - - - - Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0033669 - GO:0052030 - activation by organism of host apoptosis - activation by organism of host apoptotic programmed cell death - induction by organism of host apoptotic programmed cell death - induction by symbiont of host apoptosis - positive regulation by organism of host apoptotic programmed cell death - up regulation by organism of host apoptotic programmed cell death - up regulation by symbiont of host apoptosis - up-regulation by organism of host apoptotic programmed cell death - up-regulation by symbiont of host apoptosis - upregulation by organism of host apoptotic programmed cell death - upregulation by symbiont of host apoptosis - activation by symbiont of host apoptosis - positive regulation by symbiont of host apoptosis - stimulation by symbiont of host apoptosis - biological_process - GO:0052151 - - Note that term is to be used to annotate gene products in the symbiont. To annotate host gene products, consider the biological process term 'positive regulation of apoptosis ; GO:0043065'. - positive regulation by symbiont of host apoptotic process - - - - - - - - - Any process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism, where the two organisms are in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0052459 - modulation by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction - biological_process - modulation of programmed cell death in other organism during symbiotic interaction - GO:0052248 - - modulation of programmed cell death in other organism involved in symbiotic interaction - - - - - - - - - Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism, where the two organisms are in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0052388 - induction by organism of apoptosis in other organism involved in symbiotic interaction - activation by organism of apoptosis in other organism during symbiotic interaction - positive regulation by organism of apoptosis in other organism involved in symbiotic interaction - positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction - stimulation by organism of apoptosis in other organism during symbiotic interaction - biological_process - activation by organism of apoptotic programmed cell death in other organism during symbiotic interaction - induction by organism of apoptosis in other organism during symbiotic interaction - induction by organism of apoptotic programmed cell death in other organism during symbiotic interaction - positive regulation by organism of apoptosis in other organism during symbiotic interaction - positive regulation by organism of apoptotic programmed cell death in other organism during symbiotic interaction - up regulation by organism of apoptosis in other organism during symbiotic interaction - up-regulation by organism of apoptosis in other organism during symbiotic interaction - upregulation by organism of apoptosis in other organism during symbiotic interaction - GO:0052501 - - positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction - - - - - - - - - Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process. - http://purl.obolibrary.org/obo/go.owl - positive regulation of apoptosis by virus - biological_process - GO:0060139 - positive regulation of apoptotic process by virus - - - - - - - - - Any viral process that modulates the rate or extent of progression through the cell cycle. - http://purl.obolibrary.org/obo/go.owl - VZ:1636 - modulation of host cell cycle by virus - regulation by virus of host cell cycle - regulation of host cell cycle by virus - viral process regulating host cell cycle - biological_process - GO:0060153 - - modulation by virus of host cell cycle - - - - - - - - - http://purl.org/obo/owl/gene_ontology - biological_process - post-mating oviposition - - - - - - - - - Any process that modulates a measurable attribute of any biological process, quality or function. - http://purl.obolibrary.org/obo/go.owl - regulation - biological_process - GO:0065007 - - - biological regulation - - - - - - - - - Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. - http://purl.obolibrary.org/obo/go.owl - regulation of biological attribute - regulation of biological characteristic - biological_process - GO:0065008 - - regulation of biological quality - - - - - - - - - http://purl.org/obo/owl/gene_ontology - biological_process - organism emergence from protective structure - - - - - - - - - - - - - - - - - measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - unitId - measurement unit label - - - - - - - - - objective specification - purpose of a study; support of hypothesis, discovery of new information - - - a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an -non realizable information entity which can serve as that proper part -of a plan towards which the realization of the plan is directed." - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - OBI Plan and Planned Process/Roles Branch - OBI_0000217 - objective specification - - - - - - - - - Pour the contents of flask 1 into flask 2 - - - a directive information entity that describes an action the bearer will take - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - - - - - label - - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - label - - - - - - - - - software - - Software is a plan specification composed of a series of instructions that can be -interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI - software - - - - - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - - a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data - data item - - - - - - - - symbol - - a smallish, word-like datum... - 20091104, MC: this needs work and will most probably change - PERSON: Jonathan Rees - symbol - - - - - - - - - - - - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - - - an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 - information content entity - - - - - - - - - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - - a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - scalar measurement datum - - - - - - - - - - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be -concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - directive information entity - - - - - - - - - - - - - - - - - - - - - - - - - - algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - - A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - algorithm - - - - - - - - data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - - - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI - dataSets - data set - - - - - - - - - - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - - a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - - Action specification not well enough specified. - Conditional specification not well enough specified. - Question whether all plan specifications have objective specifications. - - Request that IAO either clarify these or change definitions not to use them - plan specification - - - - - - - - - measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - - - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI - measurement datum - - - - - - - - - version number - - - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. - Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version - GROUP: IAO - version number - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measuring a temporal interval - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - time measurement datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - time stamped measurement datum - - - - - - - - - - - - - - - pmid:20604925 - time-lapse live cell microscopy - - A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. - Alan Ruttenberg - experimental time series - time sampled measurement data set - - - - - - - - - - - - - - - - name - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/MF.owl - George Gkoutos - 2011-04-14T01:03:39Z - "Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG] - behavior_ontology - sexual activity - - - - - - - - - Mus musculus - William R. Hogan - House mouse - Mus musculus - - - - - - - - - Virus - - - - - - - - - Poxviridae - - - - - - - - - Chordopoxvirinae - - - - - - - - - Orthopoxvirus - - - - - - - - - Mirela L Vasconcelos - monkey pox virus - Monkeypox virus - - - - - - - - - Variola virus - - - - - - - - - H5N1 subtype of Influenza A virus - H5N1 subtype - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Herpesviridae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Alphaherpesvirinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Simplexvirus - - - - - - - - - - HSV-1 - HSV1 - GC_ID:1 - Herpes simplex virus type 1 - ncbi_taxonomy - Herpes simplex virus 1 - Human Herpesvirus-1 - Human herpesvirus 1 - Human herpesvirus type 1 - herpes simplex virus 1 HSV-1 - herpes simplex virus HSV-1 - herpes simplex virus type 1 HSV-1 - herpes simplex virus type 1 HSV1 - herpes simplex virus type-1 HSV-1 - Human alphaherpesvirus 1 - - - - - HSV-1 - - - - - - HSV1 - - - - - - Herpes simplex virus type 1 - - - - - - Herpes simplex virus 1 - - - - - - Human Herpesvirus-1 - - - - - - Human herpesvirus 1 - - - - - - Human herpesvirus type 1 - - - - - - herpes simplex virus 1 HSV-1 - - - - - - herpes simplex virus HSV-1 - - - - - - herpes simplex virus type 1 HSV-1 - - - - - - herpes simplex virus type 1 HSV1 - - - - - - herpes simplex virus type-1 HSV-1 - - - - - - - - - - - HSV2 - GC_ID:1 - Herpes simplex virus type 2 (HSV-2) - ncbi_taxonomy - Herpes simplex virus (type 2) - Herpes simplex virus 2 - Herpes simplex virus II - Herpes simplex virus type 2 - Human herpesvirus 2 - herpes simplex virus type 2 HSV-2 - Human alphaherpesvirus 2 - - - - - HSV2 - - - - - - Herpes simplex virus type 2 (HSV-2) - - - - - - Herpes simplex virus (type 2) - - - - - - Herpes simplex virus 2 - - - - - - Herpes simplex virus II - - - - - - Herpes simplex virus type 2 - - - - - - Human herpesvirus 2 - - - - - - herpes simplex virus type 2 HSV-2 - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Varicellovirus - - - - - - - - - - HHV-3 - VZV - GC_ID:1 - Varicella-zoster virus - ncbi_taxonomy - Human alphaherpesvirus 3 - Human herpes virus 3 - Varicella Zoster Virus - varicella zoster virus VZV - varicella-zoster virus VZV - Human herpesvirus 3 - - - - - HHV-3 - - - - - - VZV - - - - - - Varicella-zoster virus - - - - - - Human alphaherpesvirus 3 - - - - - - Human herpes virus 3 - - - - - - Varicella Zoster Virus - - - - - - varicella zoster virus VZV - - - - - - varicella-zoster virus VZV - - - - - - - - - - - NCBITaxon:44156 - PRV - GC_ID:1 - Pseudorabies virus - ncbi_taxonomy - Alphaherpesvirus pseudorabies virus PRV - Aujeszky's disease virus - Pseudorabies Virus PRV - Suid herpesvirus type 1 - Suid herpesvirus 1 - - - - - PRV - - - - - - Pseudorabies virus - - - - - - Alphaherpesvirus pseudorabies virus PRV - - - - - - Aujeszky's disease virus - - - - - - Pseudorabies Virus PRV - - - - - - Suid herpesvirus type 1 - - - - - - - - - - - GC_ID:1 - hepatitis B-type viruses - ncbi_taxonomy - Hepadnaviridae - - - - - hepatitis B-type viruses - - - - - - - - - - - GC_ID:1 - mammalian hepatitis B-type viruses - ncbi_taxonomy - Orthohepadnavirus - - - - - mammalian hepatitis B-type viruses - - - - - - - - - - - HBV - GC_ID:1 - ncbi_taxonomy - Human hepatitis B virus - hepatitis B virus (HBV) - hepatitis B virus HBV - hepatitis B virus, HBV - human hepatitis B virus HBV - Hepatitis B virus - - - - - HBV - - - - - - Human hepatitis B virus - - - - - - hepatitis B virus (HBV) - - - - - - hepatitis B virus HBV - - - - - - hepatitis B virus, HBV - - - - - - human hepatitis B virus HBV - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Escherichia coli O157 - - - - - - - - - Aedini - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - canis group - - - - - - - - - - GC_ID:11 - phagocytophila group - ncbi_taxonomy - phagocytophilum group - - - - - phagocytophila group - - - - - - - - - - Mirela L Vasconcelos - Reoviridae - - - - - - - - - Mirela L Vasconcelos - Rotaviruses - Rotavirus - - - - - - - - - Togaviridae - - - - - - - - - - GC_ID:1 - arboviruses group A - ncbi_taxonomy - Alphaviridae - Alphavirus - Alphavirus - - - - - arboviruses group A - - - - - - Alphaviridae - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Barmah Forest virus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Eastern equine encephalomyelitis virus - eastern equine encephalomyelitis EEE - eastern equine encephalomyelitis virus EEEV - Eastern equine encephalitis virus - - - - - Eastern equine encephalomyelitis virus - - - - - - eastern equine encephalomyelitis EEE - - - - - - eastern equine encephalomyelitis virus EEEV - - - - - - - - - - - RRV - GC_ID:1 - ncbi_taxonomy - Ross River virus - - - - - RRV - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Western equine encephaliomyelitis virus - Western equine encephalomyelitis virus - Western equine encephalitis virus - - - - - Western equine encephaliomyelitis virus - - - - - - Western equine encephalomyelitis virus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Rubivirus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Rubella virus - - - - - - - - - Flaviviridae - - - - - - - - - - GC_ID:1 - arboviruses group B - ncbi_taxonomy - Flavivirus - Flavivirus - - - - - arboviruses group B - - - - - - - - - - Dengue virus group - - - - - - - - - Dengue virus 1 - - - - - - - - - Dengue virus 2 - - - - - - - - - Dengue virus 3 - - - - - - - - - Dengue virus 4 - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Japanese encephalitis viruses - Japanese encephalitis virus group - - - - - Japanese encephalitis viruses - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Japanese encephalitis - Japanese encephalitis (JE) virus - Japanese encephalitis virus JE - Japanese encephalitis virus JEV - Japanese encephalitis virus - - - - - Japanese encephalitis - - - - - - Japanese encephalitis (JE) virus - - - - - - Japanese encephalitis virus JE - - - - - - Japanese encephalitis virus JEV - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Murray Valley encephalitis virus - - - - - - - - - - NCBITaxon:64321 - GC_ID:1 - ncbi_taxonomy - Saint Louis encephalitis virus - St. Louis encephalitis virus SLEV - St. Louis encephalitis virus - - - - - Saint Louis encephalitis virus - - - - - - St. Louis encephalitis virus SLEV - - - - - - - - - - - WNV - GC_ID:1 - ncbi_taxonomy - West Nile virus - - - - - WNV - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Flavivirus powassan - Powassan virus - - - - - Flavivirus powassan - - - - - - - - - - - YFV - GC_ID:1 - ncbi_taxonomy - Flavivirus febricis - yellow fever virus YFV - Yellow fever virus - - - - - YFV - - - - - - Flavivirus febricis - - - - - - yellow fever virus YFV - - - - - - - - - - Mirela L Vasconcelos - Hepatitis C virus group - Hepatitis C viruses - Hepatitis C-like viruses - Hepacivirus - - - - - - - - - Mirela L Vasconcelos - hepatitis C virus HCV - human hepatitis C virus - human hepatitis C virus HCV - human hepatitis virus C HCV - post-transfusion hepatitis non A non B virus - Hepatitis C virus - - - - - - - - - Coronaviridae - http://purl.obolibrary.org/obo/obi.owl - Coronaviridae - - - - - - - - - Mirela L Vasconcelos - Chlamydia/Chlamydophila group - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - pseudomallei group - - - - - - - - - Mononegavirales - - - - - - - - - Paramyxoviridae - - - - - - - - - Paramyxovirinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Mumps virus - - - - - - - - - Mirela L Vasconcelos - Morbilliviruses - Morbillivirus - - - - - - - - - Measles virus - - - - - - - - - Mirela L Vasconcelos - Pneumovirinae - Pneumoviridae - - - - - - - - - Mirela L Vasconcelos - Pneumovirus - - - - - - - - - Filoviridae - - - - - - - - - - MBG - GC_ID:1 - ncbi_taxonomy - Lake Victoria marburgvirus - Marburg virus MBG - Marburg marburgvirus - - - - - MBG - - - - - - Lake Victoria marburgvirus - - - - - - Marburg virus MBG - - - - - - - - - - Mirela L Vasconcelos - Rhabdoviridae - - - - - - - - - Mirela L Vasconcelos - Lyssavirus - - - - - - - - - Mirela L Vasconcelos - Rabies virus - Rabies lyssavirus - - - - - - - - - Orthomyxoviridae - - - - - - - - - Influenza A virus - - - - - - - - - - GC_ID:11 - PMID:9734038 - ncbi_taxonomy - spotted fever group - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - typhus group - - - - - - - - - H1N1 subtype of Influenza A virus - H1N1 subtype - - - - - - - - - H2N2 subtype of Influenza A virus - H2N2 subtype - - - - - - - - - Mirela L Vasconcelos - Influenza virus type B - Influenza B virus - - - - - - - - - Mirela L Vasconcelos - - GC_ID:1 - ncbi_taxonomy - Bunyaviridae - Bunyaviridae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Bunyavirus - Bunyaviruses - Orthobunyavirus - - - - - Bunyavirus - - - - - - Bunyaviruses - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Bunyavirus la crosse - La Crosse virus - - - - - Bunyavirus la crosse - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Bunyavirus snowshoe hare - Snowshoe hare bunyavirus - Snowshoe hare virus - - - - - Bunyavirus snowshoe hare - - - - - - Snowshoe hare bunyavirus - - - - - - - - - - Mirela L Vasconcelos - Phleboviruses - Phlebovirus - - - - - - - - - Mirela L Vasconcelos - Rift Valley fever virus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Hantaviurs - Hantavirus - - - - - Hantaviurs - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Arenaviridae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Junin arenavirus - Junin virus - Junn mammarenavirus - Junin mammarenavirus - - - - - Junin arenavirus - - - - - - Junin virus - - - - - - Junn mammarenavirus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lassa virus - Lassa mammarenavirus - - - - - Lassa virus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Machupo virus - Machupo mammarenavirus - - - - - Machupo virus - - - - - - - - - - Retroviridae - - - - - - - - - Lentivirinae - Lentivirus - - - - - - - - - Primate immunodeficiency viruses - Primate lentivirus group - - - - - - - - - HIV-1 - Human immunodeficiency virus type 1 - human immunodeficiency virus 1 HIV-1 - human immunodeficiency virus HIV-1 - human immunodeficiency virus type 1 HIV 1 - human immunodeficiency virus type 1 HIV-1 - human immunodeficiency virus type 1 HIV1 - human immunodeficiency virus type 1, HIV-1 - human immunodeficiency virus type I HIV-1 - human immunodeficiency virus type-1 HIV-1 - human immunodeficiency virus-1 HIV-1 - Human immunodeficiency virus 1 - - - - - - - - - HIV type 2 - HIV-2 - Human immunodeficiency virus type 2 - Human immunodeficiency virus-2 - human immunodeficiency virus type 2 HIV-2 - human immunodeficiency virus type 2, HIV-2 - Human immunodeficiency virus 2 - - - - - - - - - Teleostomi - - - - - - - - - bony vertebrates - Euteleostomi - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Brucellaceae Breed et al. 1957 - Brucellaceae - - - - - Brucellaceae Breed et al. 1957 - - - - - - - - - - - GC_ID:11 - PMID:16280474 - ncbi_taxonomy - Coxiella group - Coxiellaceae - - - - - Coxiella group - - - - - - - - - - - GC_ID:11 - PMID:16280474 - ncbi_taxonomy - Legionellaceae group - Legionellales Garrity et al. 2005 - Legionellales - - - - - Legionellaceae group - - - - - - Legionellales Garrity et al. 2005 - - - - - - - - - - - NCBITaxon:119063 - GC_ID:11 - PMID:16403855 - ncbi_taxonomy - Burkholderia group - Burkholderiaceae - - - - - Burkholderia group - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Enoplea - - - - - - - - - - NCBITaxon:27837 - GC_ID:1 - ncbi_taxonomy - Adenophorea - Chromadorea - - - - - Adenophorea - - - - - - - - - - H3N2 subtype of Influenza A virus - H3N2 subtype - - - - - - - - - H7N2 subtype of Influenza A virus - H7N2 subtype - - - - - - - - - H7N7 subtype of Influenza A virus - H7N7 subtype - - - - - - - - - H5N2 subtype of Influenza A virus - H5N2 subtype - - - - - - - - - Mirela L Vasconcelos - Caliciviridae - - - - - - - - - Picornaviridae - - - - - - - - - Enterovirus - - - - - - - - - Ecdysozoa - - - - - - - - - Human poliovirus type 1 - Poliovirus type 1 - poliovirus type 1 PV1 - Human poliovirus 1 - - - - - - - - - Human poliovirus type 3 - Poliovirus type 3 - Human poliovirus 3 - - - - - - - - - Mirela L Vasconcelos - Hepatovirus - - - - - - - - - Mirela L Vasconcelos - Hepatitis A virus - Hepatovirus A - - - - - - - - - Mirela L Vasconcelos - Aphthovirus - - - - - - - - - Mirela L Vasconcelos - Foot and mouth disease virus - foot and mouth disease virus FMDV - foot-and-mouth disease virus FMDV - Foot-and-mouth disease virus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Nipah virus - Nipah henipavirus - - - - - Nipah virus - - - - - - - - - - Mirela L Vasconcelos - Alphaproteobacteraeota - purple bacteria - purple bacteria and relatives - purple non-sulfur bacteria - purple photosynthetic bacteria - purple photosynthetic bacteria and relatives - Proteobacteria - - - - - - - - - Mirela L Vasconcelos - Proteobacteria gamma subdivision - Purple bacteria, gamma subdivision - gamma proteobacteria - gamma subdivision - gamma subgroup - Gammaproteobacteria - - - - - - - - - Gram-postive bacterium - Firmicutes - - - - - - - - - HEV - GC_ID:1 - ncbi_taxonomy - Hepatitis E virus HEV - Hepatitis E virus - - - - - HEV - - - - - - Hepatitis E virus HEV - - - - - - - - - - Mirela L Vasconcelos - Hepatitis D virus - hepatitis delta virus HDV - Hepatitis delta virus - - - - - - - - - Dengue virus - - - - - - - - - Staphylococcus - Aurococcus - Staphylococcus - - - - - - - - - Mirela L Vasconcelos - Vibrio cholerae serogroup O1 - Vibrio cholerae O1 - - - - - - - - - Staphylococcus aureus - Micrococcus aureus - Micrococcus pyogenes - Staphlococcus pyogenes citreus - Staphylococcus pyogenes aureus - Streptococcus aureus - Staphylococcus aureus - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Conoidasida - - - - - - - - - Mirela L Vasconcelos - respiratory syncytial virus RS - respiratory syncytial virus RS virus - respiratory syncytial virus RSV - Respiratory syncytial virus - - - - - - - - - Mirela L Vasconcelos - Streptococcaceae - - - - - - - - - Mirela L Vasconcelos - Streptococcus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Charophyta/Embryophyta group - charophyte/embryophyte group - Streptophytina - - - - - Charophyta/Embryophyta group - - - - - - charophyte/embryophyte group - - - - - - - - - - Mirela L Vasconcelos - Diplococcus pneumoniae - Micrococcus pneumoniae - Streptococcus pneumoniae - - - - - - - - - GC_ID:1 - PMID:22839753 - PMID:25450099 - ncbi_taxonomy - Archosauria-Testudines - Testudines + Archosauria group - Archelosauria - - - - - Archosauria-Testudines - - - - - - Testudines + Archosauria group - - - - - - - - - - Middle East respiratory syndrome coronavirus - - - - - - - - - Dipnotetrapodomorpha - - - - - - - - - Mirela L Vasconcelos - Vibrionaceae group - Vibrionales - - - - - - - - - Mirela L Vasconcelos - Pasteruellaceae group - Pasteurellales - - - - - - - - - - GC_ID:11 - PMID:11075904 - PMID:11542017 - PMID:16558735 - PMID:1917844 - PMID:23908650 - ncbi_taxonomy - spirochetes - Spirochaetales - - - - - spirochetes - - - - - - - - - - - GC_ID:11 - PMID:23908650 - ncbi_taxonomy - Treponemataceae - Spirochaetaceae - - - - - Treponemataceae - - - - - - - - - - - GC_ID:11 - PMID:24744012 - PMID:8863409 - PMID:8863416 - ncbi_taxonomy - Relapsing Fever Borrelia - Borrelia - - - - - Relapsing Fever Borrelia - - - - - - - - - - Bacillales - - - - - - - - - Bacillus - - - - - - - - - Mirela L Vasconcelos - Coxsackievirus A - Enterovirus EV-A - Human coxsackievirus A - Human enterovirus A - Enterovirus A - - - - - - - - - Enterovirus EV-C - Human enterovirus C - Poliovirus - Enterovirus C - - - - - - - - - Enterovirus D - - - - - - - - - Mirela L Vasconcelos - Bacillus cereus var. anthracis - Bacteridium anthracis - anthrax - anthrax bacterium - Bacillus anthracis - - - - - - - - - Mirela L Vasconcelos - Norwalk-like viruses - Norovirus - - - - - - - - - GC_ID:1 - PMID:11743200 - PMID:11791233 - ncbi_taxonomy - Boreotheria - Boreoeutheria - Boreoeutheria - - - - - Boreotheria - - - - - - - - - - - NCBITaxon:92178 - GC_ID:1 - PMID:10701576 - Trichinella T5 - Trichinella sp. T5 - ncbi_taxonomy - Trichinella murrelli - - - - - Trichinella T5 - - - - - - Trichinella sp. T5 - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Dorylaimia - - - - - - - - - - GC_ID:1 - true yeasts - ncbi_taxonomy - Saccharomycotina - - - - - true yeasts - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Euascomycota - Pezizomycotina - - - - - Euascomycota - - - - - - - - - - - NCBITaxon:147540 - GC_ID:1 - ncbi_taxonomy - Loculoascomycetes - Plectomycetes - bitunicate ascomycetes - Eurotiomycetes - - - - - Loculoascomycetes - - - - - - Plectomycetes - - - - - - bitunicate ascomycetes - - - - - - - - - - Rhinovirus A - Rhinovirus A - - - - - - - - - - NCBITaxon:69207 - GC_ID:11 - PMID:26643615 - ncbi_taxonomy - Anaerobacter - Clostridium - - - - - Anaerobacter - - - - - - - - - - - NCBITaxon:29368 - GC_ID:11 - PMID:10028279 - PMID:15244052 - ncbi_taxonomy - Bacillus botulinus - Bacillus putrificus - Botulobacillus botulinus - Clostridium putrificum - Ermengemillus botulinus - Pacinia putrifica - Clostridium botulinum - - - - - Bacillus botulinus - - - - - - Bacillus putrificus - - - - - - Botulobacillus botulinus - - - - - - Clostridium putrificum - - - - - - Ermengemillus botulinus - - - - - - Pacinia putrifica - - - - - - - - - - Mirela L Vasconcelos - Bacillus difficilis - Clostridium difficile - Peptoclostridium difficile - Clostridioides difficile - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Bacillus tetani - Clostridium tetani - - - - - Bacillus tetani - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Clavispora/Candida clade - - - - - - - - - GC_ID:1 - ducks, geese, chickens, fowl, quail, currasows and allies - ncbi_taxonomy - Galloanseri - Galloanserae - - - - - ducks, geese, chickens, fowl, quail, currasows and allies - - - - - - Galloanseri - - - - - - - - - - - GC_ID:11 - PMID:23961314 - PMID:9019153 - PMID:9734025 - ncbi_taxonomy - Microspironema - Treponema - - - - - Microspironema - - - - - - - - - - NCBITaxon:34383 - GC_ID:1 - ncbi_taxonomy - Onygenales incertae sedis - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Microspironema pallidum - Spirillum pallidum - Spirochaeta pallida - Spironema pallidum - Treponema pallidum - - - - - Microspironema pallidum - - - - - - Spirillum pallidum - - - - - - Spirochaeta pallida - - - - - - Spironema pallidum - - - - - - - - - - - GC_ID:11 - Treponema pallidum pallidum - syphilis treponeme - ncbi_taxonomy - Treponema pallidum subsp. pallidum - - - - - Treponema pallidum pallidum - - - - - - syphilis treponeme - - - - - - - - - - - GC_ID:11 - PMID:10408878 - PMID:15709360 - PMID:1713054 - PMID:1899799 - PMID:8427807 - PMID:8782674 - PMID:9226919 - PMID:9542083 - ncbi_taxonomy - Listerella - Listeria - - - - - Listerella - - - - - - - - - - - GC_ID:11 - PMID:8782698 - ncbi_taxonomy - Listeria bulgarica - Listeria monocytogenes subsp. perhaemolytica - Listeria perhaemolytica - Listeria ivanovii - - - - - Listeria bulgarica - - - - - - Listeria monocytogenes subsp. perhaemolytica - - - - - - Listeria perhaemolytica - - - - - - - - - - - NCBITaxon:1634566 - GC_ID:11 - PMID:17773427 - PMID:1906732 - PMID:8782698 - ncbi_taxonomy - Bacterium monocytogenes - Bacterium monocytogenes hominis - Corynebacterium infantisepticum - Corynebacterium parvulum - Erysipelothrix monocytogenes - Listerella hepatolytica - Listeria momocytogenes - Lysteria monocytogenes - Listeria monocytogenes - - - - - Bacterium monocytogenes - - - - - - Bacterium monocytogenes hominis - - - - - - Corynebacterium infantisepticum - - - - - - Corynebacterium parvulum - - - - - - Erysipelothrix monocytogenes - - - - - - Listerella hepatolytica - - - - - - Listeria momocytogenes - - - - - - Lysteria monocytogenes - - - - - - - - - - Mirela L Vasconcelos - Plasmodiidae - - - - - - - - - - NCBITaxon:1644 - NCBITaxon:47986 - GC_ID:11 - PMID:1736964 - Listeria grayi grayi - ncbi_taxonomy - Listeria grayi murrayi - Listeria grayi subsp. grayi - Listeria murrayi - Murraya grayi - Murraya grayi subsp. grayi - Listeria grayi - - - - - Listeria grayi grayi - - - - - - Listeria grayi murrayi - - - - - - Listeria grayi subsp. grayi - - - - - - Listeria murrayi - - - - - - Murraya grayi - - - - - - Murraya grayi subsp. grayi - - - - - - - - - - - GC_ID:11 - PMID:23908650 - ncbi_taxonomy - Borreliaceae - - - - - - - - - GC_ID:11 - PMID:23908650 - ncbi_taxonomy - Leptospiriales - Leptospirales - - - - - Leptospiriales - - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Yersinia pseudotuberculosis complex - - - - - - - - - - GC_ID:11 - PMID:19244447 - Coryneform bacteria - ncbi_taxonomy - Corynebacteriaceae - - - - - Coryneform bacteria - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Mammarenavirus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Orthohepevirus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Orthohepevirus A - - - - - - - - - - GC_ID:11 - PMID:16014471 - ncbi_taxonomy - Treponemataceae - Leptospiraceae - - - - - Treponemataceae - - - - - - - - - - - NCBITaxon:29512 - NCBITaxon:29514 - NCBITaxon:29516 - GC_ID:11 - PMID:10425768 - PMID:1581182 - PMID:19868121 - PMID:9103653 - ncbi_taxonomy - Ancona - Canela - Jequitaia - Leptospira - - - - - Ancona - - - - - - Canela - - - - - - Jequitaia - - - - - - - - - - - GC_ID:11 - PMID:10425754 - PMID:19661509 - PMID:7547284 - PMID:7547291 - PMID:7547293 - ncbi_taxonomy - Corynebacterium - - - - - - - - - - GC_ID:11 - PMID:7729671 - ncbi_taxonomy - Bacillus diphtheriae - Bacterium diphtheriae - Microsporon diphthericum - Microsporon diphtheriticum - Mycobacterium diphtheriae - Pacinia loeffleri - Corynebacterium diphtheriae - - - - - Bacillus diphtheriae - - - - - - Bacterium diphtheriae - - - - - - Microsporon diphthericum - - - - - - Microsporon diphtheriticum - - - - - - Mycobacterium diphtheriae - - - - - - Pacinia loeffleri - - - - - - - - - - Actinomycetes - High GC gram-positive bacteria - Actinobacteria <class> - - - - - - - - - Mycobacteriaceae - - - - - - - - - Mycobacterium Lehmann and Neumann 1896 - Mycobacterium - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Bacillus leprae - Mycoplasma leprae - Mycobacterium leprae - - - - - Bacillus leprae - - - - - - Mycoplasma leprae - - - - - - - - - - Bacillus tuberculosis - Bacterium tuberculosis - Mycobacterium tuberculosis typus humanus - Mycobacterium tuberculosis var. hominis - Mycobacterium tuberculosis - - - - - - - - - GC_ID:1 - ncbi_taxonomy - EEEV complex - - - - - - - - - GC_ID:1 - ncbi_taxonomy - WEEV complex - - - - - - - - - SFV complex - - - - - - - - - Mirela L Vasconcelos - PVC group - - - - - - - - - Mirela L Vasconcelos - Terrabacteria group - - - - - - - - - Ebola-like virus - Ebolavirus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Marburg-like viruses - Marburgvirus - - - - - Marburg-like viruses - - - - - - - - - - Zaire ebolavirus - - - - - - - - - Ebola virus Reston - REBOV - Reston Ebola virus - Reston ebolavirus - - - - - - - - - Ebolavirus Sudan - SEBOV - Sudan Ebola virus - Sudan ebolavirus - - - - - - - - - CIEBOV - Côte d'Ivoire Ebola virus - Côte d'Ivoire ebolavirus - Ivory Coast ebolavirus - Tai Forest ebolavirus - - - - - - - - - Mirela L Vasconcelos - Clostridia - - - - - - - - - Mirela L Vasconcelos - Clostridiales - - - - - - - - - Mirela L Vasconcelos - Clostridium cluster XI - Peptostreptococcaceae - - - - - - - - - Bacillaceae - - - - - - - - - - GC_ID:11 - PMID:20212322 - ncbi_taxonomy - Listeriaceae - - - - - - - - - Mirela L Vasconcelos - Lactobacillales - - - - - - - - - Mirela L Vasconcelos - Clostridioides - - - - - - - - - - GC_ID:11 - PMID:27620848 - ncbi_taxonomy - Yersiniaceae - - - - - - - - - Mirela L Vasconcelos - Rift Valley fever phlebovirus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - California encephalitis orthobunyavirus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Guaroa orthobunyavirus - - - - - - - - - - GC_ID:11 - PMID:11542086 - PMID:12361288 - PMID:16627635 - PMID:1704793 - PMID:19801389 - ncbi_taxonomy - Ampylobacter - Campylobacter - - - - - Ampylobacter - - - - - - - - - - Pancrustacea - - - - - - - - - Mandibulata - - - - - - - - - Influenzavirus A - - - - - - - - - Mirela L Vasconcelos - Influenzavirus B - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Bunyavirales - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Nairoviridae - - - - - - - - - - NCBITaxon:11571 - GC_ID:1 - ncbi_taxonomy - Bunyaviridae - Peribunyaviridae - - - - - Bunyaviridae - - - - - - - - - - - NCBITaxon:11592 - GC_ID:1 - ncbi_taxonomy - Nairovirus - Nairoviruses - Orthonairovirus - - - - - Nairovirus - - - - - - Nairoviruses - - - - - - - - - - - NCBITaxon:11593 - CCHFV - GC_ID:1 - ncbi_taxonomy - Crimean Congo Hemorrhagic Fever virus - Crimean-Congo haemorrhagic fever virus - Crimean-Congo hemorrhagic fever nairovirus - Crimean-Congo hemorrhagic fever virus - Crimean-Congo hemorrhagic virus - Crimean-Congo hemorrhagic fever orthonairovirus - - - - - CCHFV - - - - - - Crimean Congo Hemorrhagic Fever virus - - - - - - Crimean-Congo haemorrhagic fever virus - - - - - - Crimean-Congo hemorrhagic fever nairovirus - - - - - - Crimean-Congo hemorrhagic fever virus - - - - - - Crimean-Congo hemorrhagic virus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Coccidioides posadasii - - - - - - - - - Bacteria - - - - - - - - - 'Actinobacteria' - not Actinobacteria Cavalier-Smith 2002 - Actinobacteria <phylum> - - - - - - - - - - GC_ID:11 - PMID:11837318 - PMID:26654112 - ncbi_taxonomy - Spirochaetae - Spirochaetaeota - Spirochaetes - - - - - Spirochaetae - - - - - - Spirochaetaeota - - - - - - - - - - - GC_ID:11 - PMID:11837318 - PMID:25288668 - PMID:26654112 - ncbi_taxonomy - Spirochaetes - Spirochaetia - - - - - Spirochaetes - - - - - - - - - - Mirela L Vasconcelos - Chlamydaeota - Chlamydiae - - - - - - - - - Mirela L Vasconcelos - Chlamydiae - Chlamydiia - - - - - - - - - Mirela L Vasconcelos - Neisseriales - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Diplomonadida group - Fornicata - - - - - Diplomonadida group - - - - - - - - - - Mirela L Vasconcelos - Helicobacter - - - - - - - - - Mirela L Vasconcelos - Campylobacter pylori - Campylobacter pylori subsp. pylori - Campylobacter pyloridis - Helicobacter nemestrinae - Helicobacter pylori - - - - - - - - - Mirela L Vasconcelos - Campylobacterales - - - - - - - - - NCBITaxon:261182 - GC_ID:1 - ncbi_taxonomy - Sarcoptidia - Psoroptidia - - - - - Sarcoptidia - - - - - - - - - - SARS coronavirus - - - - - - - - - H5N8 subtype of Influenza A virus - H5N8 subtype - - - - - - - - - - GC_ID:11 - PMID:8573514 - ncbi_taxonomy - Brucella Meyer and Shaw 1920 - Brucella - - - - - Brucella Meyer and Shaw 1920 - - - - - - - - - - - GC_ID:11 - Brucella melitensis bv. Abortus - ncbi_taxonomy - Bacterium abortus - Brucella melitensis biovar Abortus - Brucella abortus - - - - - Brucella melitensis bv. Abortus - - - - - - Bacterium abortus - - - - - - Brucella melitensis biovar Abortus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cryptosporidium hominis - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Henipavirus - - - - - - - - - - GC_ID:11 - PMID:19783615 - PMID:8123561 - ncbi_taxonomy - Francisella - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Bacterium tularense - Brucella tularensis - Francisella tularense - Pasteurella tularensis - Francisella tularensis - - - - - Bacterium tularense - - - - - - Brucella tularensis - - - - - - Francisella tularense - - - - - - Pasteurella tularensis - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Metschnikowiaceae - - - - - - - - - Eukaryota - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Bovinae - - - - - - - - - - GC_ID:11 - PMID:11541974 - PMID:11837318 - PMID:16166687 - PMID:16403855 - PMID:19060069 - ncbi_taxonomy - Alphabacteria - Proteobacteria alpha subdivision - Purple bacteria, alpha subdivision - a-proteobacteria - alpha proteobacteria - alpha subdivision - alpha subgroup - Alphaproteobacteria - - - - - Alphabacteria - - - - - - Proteobacteria alpha subdivision - - - - - - Purple bacteria, alpha subdivision - - - - - - a-proteobacteria - - - - - - alpha proteobacteria - - - - - - alpha subdivision - - - - - - alpha subgroup - - - - - - - - - - Mirela L Vasconcelos - Proteobacteria beta subdivision - Purple bacteria, beta subdivision - beta proteobacteria - beta subdivision - beta subgroup - Betaproteobacteria - - - - - - - - - PEDV - Porcine epidemic diarrhea virus - - - - - - - - - - NCBITaxon:1435366 - NCBITaxon:1435368 - NCBITaxon:1435988 - NCBITaxon:1439853 - NCBITaxon:1487954 - NCBITaxon:1487955 - GC_ID:11 - PMID:12734250 - PMID:1283774 - ncbi_taxonomy - Bacillus pseudomallei - Bacterium whitmori - Burkholderia pseudomallai - Burkholderia pseudomallei MSHR4009 - Burkholderia pseudomallei MSHR4018 - Burkholderia pseudomallei MSHR44 - Burkholderia pseudomallei MSHR7839 - Burkholderia sp. MSHR7839 - Loefflerella pseudomallei - Malleomyces pseudomallei - Pseudomonas pseudomallei - Burkholderia pseudomallei - - - - - Bacillus pseudomallei - - - - - - Bacterium whitmori - - - - - - Burkholderia pseudomallai - - - - - - Burkholderia pseudomallei MSHR4009 - - - - - - Burkholderia pseudomallei MSHR4018 - - - - - - Burkholderia pseudomallei MSHR44 - - - - - - Burkholderia pseudomallei MSHR7839 - - - - - - Burkholderia sp. MSHR7839 - - - - - - Loefflerella pseudomallei - - - - - - Malleomyces pseudomallei - - - - - - Pseudomonas pseudomallei - - - - - - - - - - Mirela L Vasconcelos - Bacillus cholerae-suis - Salmonella cholerae-suis - Salmonella choleraesuis - Salmonella enterica ser. choleraesuis - Salmonella enterica - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Hepeviridae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ancylostoma - - - - - - - - - - GC_ID:1 - dog hookworm - ncbi_taxonomy - Ancylostoma caninum - - - - - dog hookworm - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Tick-borne encephalitis viruses - tick-borne encephalitis virus group - - - - - Tick-borne encephalitis viruses - - - - - - - - - - - GC_ID:11 - PMID:8573514 - ncbi_taxonomy - Micrococcus melitensis - Streptococcus Miletensis - Brucella melitensis - - - - - Micrococcus melitensis - - - - - - Streptococcus Miletensis - - - - - - - - - - - GC_ID:11 - Brucella melitensis bv. Suis - ncbi_taxonomy - Brucella melitensis biovar Suis - Brucella suis - - - - - Brucella melitensis bv. Suis - - - - - - Brucella melitensis biovar Suis - - - - - - - - - - Mirela L Vasconcelos - Proteobacteria epsilon subdivision - Purple bacteria, epsilon subdivision - epsilon proteobacteria - epsilon subdivision - epsilon subgroup - not Epsilobacteria - Epsilonproteobacteria - - - - - - - - - Spondweni virus group - Spondweni virus group - - - - - - - - - Mirela L Vasconcelos - Schistosomatoidea - - - - - - - - - Mirela L Vasconcelos - blood flukes - Schistosomatidae - - - - - - - - - - GC_ID:1 - PMID:11214318 - PMID:11214319 - PMID:12878460 - ncbi_taxonomy - Laurasiatheria - - - - - - - - - Euarchontoglires - - - - - - - - - Anthropoidea - Simiiformes - - - - - - - - - Cercopithecoidea - - - - - - - - - CV-A16 - CVA-16 - CVA16 - GC_ID:1 - ncbi_taxonomy - Coxsackie A virus type 16 - Human coxsackievirus A16 - Human enterovirus CVA16 - Coxsackievirus A16 - - - - - CV-A16 - - - - - - CVA-16 - - - - - - CVA16 - - - - - - Coxsackie A virus type 16 - - - - - - Human coxsackievirus A16 - - - - - - Human enterovirus CVA16 - - - - - - - - - - GC_ID:1 - higher plants - land plants - plants - ncbi_taxonomy - land plants - Embryophyta - - - - - higher plants - - - - - - land plants - - - - - - plants - - - - - - land plants - - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Clostridiaceae - - - - - - - - - - GC_ID:11 - PMID:10555347 - PMID:1283774 - PMID:25566316 - ncbi_taxonomy - Pseudomonas RNA homology group II - Burkholderia - - - - - Pseudomonas RNA homology group II - - - - - - - - - - tetrapods - Tetrapoda - - - - - - - - - amniotes - GC_ID:1 - amniotes - ncbi_taxonomy - Amniota - Amniota - - - - - amniotes - - - - - - - - - - authority: Theria Parker & Haswell, 1897 - Theria - - - - - - - - - GC_ID:1 - diapsids - ncbi_taxonomy - Diapsida - Sauria - - - - - diapsids - - - - - - Diapsida - - - - - - - - - - Orthoretrovirinae - - - - - - - - - H5N6 subtype of Influenza A virus - H5N6 subtype - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Entamoebida - Entamoebidae - - - - - Entamoebida - - - - - - - - - - - GC_ID:1 - green plants - ncbi_taxonomy - Chlorobionta - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group - green plants - Viridiplantae - - - - - green plants - - - - - - Chlorobionta - - - - - - Chlorophyta/Embryophyta group - - - - - - chlorophyte/embryophyte group - - - - - - green plants - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Fungi/Metazoa group - opisthokonts - Opisthokonta - Opisthokonta - - - - - Fungi/Metazoa group - - - - - - opisthokonts - - - - - - - - - - - NCBITaxon:259362 - NCBITaxon:36053 - NCBITaxon:5102 - GC_ID:1 - PMID:17486980 - ncbi_taxonomy - Gymnoascales - Onygenales - - - - - Gymnoascales - - - - - - - - - - Metazoa - - - - - - - - - Bilateria - - - - - - - - - - GC_ID:1 - hookworms - ncbi_taxonomy - Ancylostomatoidea - - - - - hookworms - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ancylostomatidae - - - - - - - - - Protostomia - - - - - - - - - H7N9 subtype of Influenza A virus - H7N9 subtype - - - - - - - - - Neoptera - - - - - - - - - Endopterygota - - - - - - - - - deuterostomes - Deuterostomia - - - - - - - - - - GC_ID:1 - carnivores - ncbi_taxonomy - carnivores - Carnivora - - - - - carnivores - - - - - - carnivores - - - - - - - - - - Matthew Diller - William R. Hogan - alveolates - Alveolata - - - - - - - - - Mirela L Vasconcelos - Euglenozoans - Euglenozoa - - - - - - - - - - GC_ID:11 - PMID:11760958 - PMID:8240958 - ncbi_taxonomy - Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993 - Rickettsieae - - - - - Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993 - - - - - - - - - - - GC_ID:11 - PMID:16280474 - PMID:22939414 - PMID:26747442 - ncbi_taxonomy - Francisella group - Francisellaceae - - - - - Francisella group - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cryptosporidae - Cryptosporiidae - Cryptosporidiidae - - - - - Cryptosporidae - - - - - - Cryptosporiidae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - dsDNA virus, no RNA stage - dsDNA viruses, no RNA stage - - - - - - - - - Retroid viruses - Retro-transcribing viruses - - - - - - - - - ssRNA positive-strand viruses, no DNA stage - http://purl.obolibrary.org/obo/obi.owl - ssRNA positive-strand viruses, no DNA stage - - - - - - - - - ssRNA negative-strand virus - - - - - - - - - NCBITaxon:35512 - GC_ID:1 - ncbi_taxonomy - California bunyavirus group - California encephalitis virus group - California serogroup - California virus - California encephalitis virus - - - - - California bunyavirus group - - - - - - California encephalitis virus group - - - - - - California serogroup - - - - - - California virus - - - - - - - - - - Mirela L Vasconcelos - dsRNA nonenveloped viruses - dsRNA viruses - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Streptophyta - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Artiodactyla - Suiformes - Suina - - - - - Artiodactyla - - - - - - Suiformes - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Pecora - - - - - - - - - - GC_ID:1 - Equus - ncbi_taxonomy - Equus subg. Equus - Equus <subgenus> - - - - - Equus - - - - - - Equus subg. Equus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Jamestown Canyon virus - - - - - - - - - - GC_ID:11 - PMID:16403855 - PMID:1854635 - rhizobacteria - ncbi_taxonomy - Rhizobiaceae group - alpha-2 proteobacteria - Rhizobiales - - - - - rhizobacteria - - - - - - Rhizobiaceae group - - - - - - alpha-2 proteobacteria - - - - - - - - - - Matthew Diller - malaria parasite p. ovale - Plasmodium ovale - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Streptococcus sp. (group A) - group A streptococci - group A streptococcus - Streptococcus sp. 'group A' - - - - - Streptococcus sp. (group A) - - - - - - group A streptococci - - - - - - group A streptococcus - - - - - - - - - - - GC_ID:11 - Brucella melitensis bv. Canis - ncbi_taxonomy - Brucella melitensis biovar Canis - Brucella canis - - - - - Brucella melitensis bv. Canis - - - - - - Brucella melitensis biovar Canis - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Clavispora - - - - - - - - - Chikungunya virus - - - - - - - - - Haplorrhini - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Caniformia - - - - - - - - - EV-71 - EV-A71 - EV71 - GC_ID:1 - ncbi_taxonomy - Enterovirus 71 - Enterovirus EV-A71 - Human enterovirus 71 - Human enterovirus A71 - Human enterovirus type 71 - enterovirus type 71 - Enterovirus A71 - - - - - EV-71 - - - - - - EV-A71 - - - - - - EV71 - - - - - - Enterovirus 71 - - - - - - Enterovirus EV-A71 - - - - - - Human enterovirus 71 - - - - - - Human enterovirus A71 - - - - - - Human enterovirus type 71 - - - - - - enterovirus type 71 - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Rubulavirus - - - - - - - - - Mirela L Vasconcelos - Deltavirus - - - - - - - - - - GC_ID:11 - PMID:10555350 - ncbi_taxonomy - Calymmatobacterium granulomatis - Donovania granulomatis - Encapsulatus inguinalis - Klebsiella granulomatis - - - - - Calymmatobacterium granulomatis - - - - - - Donovania granulomatis - - - - - - Encapsulatus inguinalis - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Yellow fever viruses - Yellow fever virus group - - - - - Yellow fever viruses - - - - - - - - - - mammals - Mammalia - - - - - - - - - Matthew Diller - plasmodium - Plasmodium (Plasmodium) - - - - - - - - - Matthew Diller - laverania - Plasmodium (Laverania) - - - - - - - - - Culicoidea - - - - - - - - - Matthew Diller - William R. Hogan - hematozoa - Aconoidasida - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Eimeriorina - - - - - - - - - Enterovirus D68 - - - - - - - - - GC_ID:1 - dinosaur - dinosaurs - ncbi_taxonomy - Dinosauria - - - - - dinosaur - - - - - - dinosaurs - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Saurischia - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Theropoda - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Coelurosauria - - - - - - - - - Culicomorpha - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Anophelinae - - - - - - - - - Culicinae - - - - - - - - - ssRNA virus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Koutango virus - - - - - - - - - - GC_ID:11 - PMID:434652 - ncbi_taxonomy - Legionellaceae Brenner et al. 1979 - Legionellaceae - - - - - Legionellaceae Brenner et al. 1979 - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cyclospora - - - - - - - - - - GC_ID:1 - Anopheles - ncbi_taxonomy - Anopheles <subgenus> - - - - - Anopheles - - - - - - - - - - - NCBITaxon:29550 - GC_ID:11 - PMID:16166707 - PMID:434652 - PMID:8573522 - PMID:9734026 - ncbi_taxonomy - Legionella - - - - - - - - - - GC_ID:1 - PMID:15689432 - PMID:16151185 - PMID:17010206 - PMID:17051209 - PMID:17572334 - ncbi_taxonomy - Dikarya - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Eurotiomycetidae - - - - - - - - - - GTOV - GC_ID:1 - ncbi_taxonomy - Guanarito arenavirus - Guanarito virus - Guanarito mammarenavirus - - - - - GTOV - - - - - - Guanarito arenavirus - - - - - - Guanarito virus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Inkoo virus - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Tahyna virus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Sabi mammarenavirus - Sabia arenavirus - Sabia virus - Sabio virus - Sabia mammarenavirus - - - - - Sabi mammarenavirus - - - - - - Sabia arenavirus - - - - - - Sabia virus - - - - - - Sabio virus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Trichinella britovi - - - - - - - - - Picornavirales - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Perdicinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Meleagridinae - - - - - - - - - Mirela L Vasconcelos - Acinetobacteraceae - Branhamaceae - Moraxellaceae - - - - - - - - - Mirela L Vasconcelos - Acinetobacter - - - - - - - - - Mirela L Vasconcelos - Acinetobacter genomosp. 2 - Acinetobacter genomospecies 2 - Bacterium anitratum - Acinetobacter baumannii - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Sarcoptinae - - - - - - - - - - GC_ID:1 - PMID:11062127 - PMID:12684019 - fungi - ncbi_taxonomy - fungi - Fungi - - - - - fungi - - - - - - fungi - - - - - - - - - - Mirela L Vasconcelos - Schizotrypanum - - - - - - - - - - GC_ID:11 - PMID:19019760 - PMID:25831531 - ncbi_taxonomy - Mycobacterium lepromatosis - - - - - - - - - Mirela L Vasconcelos - Neisseriaceae - - - - - - - - - Mirela L Vasconcelos - "Gonococcus" Lindau 1898 - "Merismopedia" Zopf 1885 - Gonococcus - Neisseria - - - - - - - - - Mirela L Vasconcelos - Diplococcus gonorrhoeae - Gonococcus neisseri - Merismopedia gonorrhoeae - Micrococcus der gonorrhoe - Micrococcus gonococcus - Micrococcus gonorrhoeae - Neisseria gonorrhoeae - - - - - - - - - Mirela L Vasconcelos - Diplokokkus intracellularis meningitidis - Micrococcus intracellularis - Micrococcus meningitidis - Micrococcus meningitidis cerebrospinalis - Neisseria weichselbaumii - Neisseria meningitidis - - - - - - - - - - GC_ID:1 - PMID:17572334 - ascomycetes - sac fungi - ncbi_taxonomy - ascomycetes - Ascomycota - - - - - ascomycetes - - - - - - sac fungi - - - - - - ascomycetes - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Hemiascomycetes - Saccharomycetes - - - - - Hemiascomycetes - - - - - - - - - - - GC_ID:1 - budding yeasts - ncbi_taxonomy - Endomycetales - Saccharomycetales - - - - - budding yeasts - - - - - - Endomycetales - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Candida auris - - - - - - - - - Insecta - - - - - - - - - Mirela L Vasconcelos - Alcaligenaceae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ancylostoma duodenale - - - - - - - - - Mirela L Vasconcelos - Chlamydiales - - - - - - - - - Mirela L Vasconcelos - Bordetella - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Culex pipiens complex - - - - - - - - - Mirela L Vasconcelos - Bacterium tussis-convulsivae - Hemophilus pertussis - Microbe de la coqueluche - Bordetella pertussis - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Sarcoptidae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Sarcoptes - - - - - - - - - - NCBITaxon:197185 - NCBITaxon:198574 - NCBITaxon:268761 - NCBITaxon:268762 - NCBITaxon:268763 - NCBITaxon:337908 - GC_ID:1 - ncbi_taxonomy - Sarcoptes scabiei type canis - Sarcoptes scabiei type chimp - Sarcoptes scabiei type hominis - Sarcoptes scabiei type suis - Sarcoptes scabiei type wallaby - Sarcoptes scabiei type wombati - Sarcoptes scabiei var. canis - Sarcoptes scabiei var. chimp - Sarcoptes scabiei var. hominis - Sarcoptes scabiei var. nyctereutis - Sarcoptes scabiei var. suis - Sarcoptes scabiei var. wallaby - Sarcoptes scabiei var. wombati - Sarcoptes scabiei - - - - - Sarcoptes scabiei type canis - - - - - - Sarcoptes scabiei type chimp - - - - - - Sarcoptes scabiei type hominis - - - - - - Sarcoptes scabiei type suis - - - - - - Sarcoptes scabiei type wallaby - - - - - - Sarcoptes scabiei type wombati - - - - - - Sarcoptes scabiei var. canis - - - - - - Sarcoptes scabiei var. chimp - - - - - - Sarcoptes scabiei var. hominis - - - - - - Sarcoptes scabiei var. nyctereutis - - - - - - Sarcoptes scabiei var. suis - - - - - - Sarcoptes scabiei var. wallaby - - - - - - Sarcoptes scabiei var. wombati - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ancylostomatinae - - - - - - - - - - GC_ID:1 - Culex - ncbi_taxonomy - Culex <subgenus> - - - - - Culex - - - - - - - - - - Stegomyia - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Culicini - - - - - - - - - Mirela L Vasconcelos - Enterobacteraceae - Enterobacteriaceae - - - - - - - - - Mirela L Vasconcelos - Bacterium paratyphi - Bacterium paratyphi typhus A - Salmonella choleraesuis choleraesuis (serotype paratyphi A) - Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A - Salmonella paratyphi - Salmonella paratyphi A - Salmonella paratyphi-a - Salmonella enterica subsp. enterica serovar Paratyphi A - - - - - - - - - - NCBITaxon:59206 - GC_ID:11 - PMID:15653929 - PMID:15653930 - PMID:2915026 - PMID:4011990 - PMID:7149525 - ncbi_taxonomy - Salmonella cholerae-suis subsp. bongori - Salmonella choleraesuis subsp. bongori - Salmonella enterica V - Salmonella enterica subsp. V - Salmonella enterica subsp. bongori - Salmonella bongori - - - - - Salmonella cholerae-suis subsp. bongori - - - - - - Salmonella choleraesuis subsp. bongori - - - - - - Salmonella enterica V - - - - - - Salmonella enterica subsp. V - - - - - - Salmonella enterica subsp. bongori - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Herpesvirales - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Coccidioides - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Coccidioides immitis - - - - - - - - - GC_ID:1 - PMID:23020233 - ncbi_taxonomy - Amoebozoa - - - - - - - - - GC_ID:1 - PMID:23020233 - ncbi_taxonomy - Archamoebae - - - - - - - - - Mirela L Vasconcelos - Escherichia - - - - - - - - - Mirela L Vasconcelos - Bacillus coli - Bacterium coli - Bacterium coli commune - E. coli - Enterococcus coli - Escherichia coli - - - - - - - - - Mirela L Vasconcelos - Kinetoplastea - Protomonadida - kinetoplasts - Kinetoplastida - - - - - - - - - Mirela L Vasconcelos - Trypanosomatidae - - - - - - - - - Ebolavirus bundibugyo - Bundibugyo ebolavirus - - - - - - - - - Mirela L Vasconcelos - Trypanosoma - - - - - - - - - Mirela L Vasconcelos - Trypanosoma cruzi - - - - - - - - - - NCBITaxon:39823 - GC_ID:11 - PMID:10555350 - PMID:11411716 - PMID:12635932 - ncbi_taxonomy - Hyalococcus - Klebsiella - - - - - Hyalococcus - - - - - - - - - - GC_ID:1 - diplomonads - ncbi_taxonomy - diplomonads - Diplomonadida - - - - - diplomonads - - - - - - diplomonads - - - - - - - - - - - GC_ID:6 - ncbi_taxonomy - Hexamitidae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Giardia - - - - - - - - - - GC_ID:1 - PMID:11432808 - PMID:19135417 - ncbi_taxonomy - Giardia duodenalis - Giardia lamblia - Lamblia intestinalis - Giardia intestinalis - - - - - Giardia duodenalis - - - - - - Giardia lamblia - - - - - - Lamblia intestinalis - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Entamoeba - - - - - - - - - Matthew Diller - William R. Hogan - apicomplexans - Apicomplexa - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - coccidians - Coccidia - - - - - coccidians - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Eimeriids - Eimeriidae - - - - - Eimeriids - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cryptosporidium - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cryptosporidium parvum - - - - - - - - - Matthew Diller - William R. Hogan - haemosporidians - haemosporina - Haemosporida - - - - - - - - - Matthew Diller - Plasmodium - - - - - - - - - Matthew Diller - Mirela L Vasconcelos - malaria parasite P. falciparum - plasmodium (laverania) falciparum - Plasmodium falciparum - - - - - - - - - Matthew Diller - malaria parasite p. vivax - Plasmodium vivax - - - - - - - - - Matthew Diller - Plasmodium malariae - - - - - - - - - Mirela L Vasconcelos - Salmonella - - - - - - - - - Mirela L Vasconcelos - Salmonella cholerae-suis subsp. cholerae-suis - Salmonella choleraesuis subsp. choleraesuis - Salmonella enterica I - Salmonella enterica subsp. I - Salmonella enterica subsp. enterica - - - - - - - - - Eumetazoa - - - - - - - - - Mirela L Vasconcelos - flatworms - Platyhelminthes - - - - - - - - - Mirela L Vasconcelos - Trematoda - - - - - - - - - Mirela L Vasconcelos - flukes - Digenea - - - - - - - - - Mirela L Vasconcelos - Strigeidida - - - - - - - - - Mirela L Vasconcelos - Schistosoma - - - - - - - - - Mirela L Vasconcelos - Schistosoma mansoni - - - - - - - - - Mirela L Vasconcelos - Schistosoma haematobium - - - - - - - - - - GC_ID:11 - PMID:26834722 - ncbi_taxonomy - Shigella - - - - - - - - - - GC_ID:11 - PMID:12054222 - Escherichia/Shigella dysenteriae - ncbi_taxonomy - Bacillus dysenteriae - Bacillus dysentericus - Bacillus shigae - Eberthella dysenteriae - Shigella shigae - Shigella dysenteriae - - - - - Escherichia/Shigella dysenteriae - - - - - - Bacillus dysenteriae - - - - - - Bacillus dysentericus - - - - - - Bacillus shigae - - - - - - Eberthella dysenteriae - - - - - - Shigella shigae - - - - - - - - - - - GC_ID:11 - Escherichia/Shigella flexneri - ncbi_taxonomy - Shigella paradysenteriae - Shigella flexneri - - - - - Escherichia/Shigella flexneri - - - - - - Shigella paradysenteriae - - - - - - - - - - - GC_ID:1 - nematode - nematodes - roundworm - roundworms - ncbi_taxonomy - Nemata - nematodes - Nematoda - - - - - nematode - - - - - - nematodes - - - - - - roundworm - - - - - - roundworms - - - - - - Nemata - - - - - - nematodes - - - - - - - - - - - NCBITaxon:33251 - GC_ID:1 - ncbi_taxonomy - Rhabditida - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Bacterium sonnei - Shigella sonnei - - - - - Bacterium sonnei - - - - - - - - - - - GC_ID:11 - Yersinia - ncbi_taxonomy - Yersinia <bacteria> - - - - - Yersinia - - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Bacterium enterocoliticum - Yersinia enterocolitica - - - - - Bacterium enterocoliticum - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Strongylida - - - - - - - - - - GC_ID:11 - PMID:15084509 - ncbi_taxonomy - Bacillus pestis - Bacterium pestis - Pasteurella pestis - Pestisella pestis - Yersinia pseudotuberculosis subsp. pestis - Yersinia pestis - - - - - Bacillus pestis - - - - - - Bacterium pestis - - - - - - Pasteurella pestis - - - - - - Pestisella pestis - - - - - - Yersinia pseudotuberculosis subsp. pestis - - - - - - - - - - - NCBITaxon:36085 - NCBITaxon:6331 - GC_ID:1 - ncbi_taxonomy - Trichocephalida - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Trichinellidae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Trichinella - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Trichinella spiralis - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Trichinella nativa - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Trichinella nelsoni - - - - - - - - - Mirela L Vasconcelos - Vibrionaceae - - - - - - - - - Zika virus - Zika virus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Lujo virus - Lujo mammarenavirus - - - - - Lujo virus - - - - - - - - - - Mirela L Vasconcelos - Beneckea - Listonella - Microspira - Pacinia - Vibrio - - - - - - - - - Arthropoda - - - - - - - - - Mirela L Vasconcelos - Bacillo virgola del Koch - Bacillus cholerae - Bacillus cholerae-asiaticae - Kommabacillus - Liquidivibrio cholerae - Microspira comma - Pacinia cholerae-asiaticae - Spirillum cholerae - Spirillum cholerae-asiaticae - Vibrio cholera - Vibrio cholerae Pacini 1854 - Vibrio cholerae-asiaticae - Vibrio comma - Vibrio cholerae - - - - - - - - - - GC_ID:11 - PMID:14071901 - PMID:4935323 - ncbi_taxonomy - Beneckea parahaemolytica - Oceanomonas parahaemolytica - Pasteurella parahaemolytica - Vibrio parahemolyticus - Vibrio parahaemolyticus - - - - - Beneckea parahaemolytica - - - - - - Oceanomonas parahaemolytica - - - - - - Pasteurella parahaemolytica - - - - - - Vibrio parahemolyticus - - - - - - - - - - - GC_ID:11 - PMID:1015934 - PMID:8186099 - ncbi_taxonomy - Beneckea vulnifica - Vibrio vulnificus - - - - - Beneckea vulnifica - - - - - - - - - - - GC_ID:1 - chelicerates - ncbi_taxonomy - Chelicerata - - - - - chelicerates - - - - - - - - - - - GC_ID:6 - ncbi_taxonomy - Giardiinae - - - - - - - - - Mirela L Vasconcelos - not Thiobacteria - delta/epsilon subdivisions - - - - - - - - - - GC_ID:1 - arachnids - ncbi_taxonomy - arachnids - Arachnida - - - - - arachnids - - - - - - arachnids - - - - - - - - - - Mirela L Vasconcelos - Sedoreovirinae - - - - - - - - - - GC_ID:1 - mites and ticks - ncbi_taxonomy - Acarina - mites & ticks - Acari - - - - - mites and ticks - - - - - - Acarina - - - - - - mites & ticks - - - - - - - - - - Coronavirinae - - - - - - - - - Coronavirus group 1 - Group 1 species - Alphacoronavirus - - - - - - - - - Betacoronavirus - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Acariformes - - - - - - - - - - NCBITaxon:41437 - NCBITaxon:41440 - NCBITaxon:41441 - GC_ID:1 - ncbi_taxonomy - Astigmata - - - - - - - - - Hexapoda - - - - - - - - - Mirela L Vasconcelos - Pasteurellaceae - - - - - - - - - Diptera - - - - - - - - - Nematocera - - - - - - - - - mosquitos - Culicidae - - - - - - - - - Aedes - - - - - - - - - Stegomyia aegypti - Aedes aegypti - - - - - - - - - - GC_ID:1 - Anopheles - ncbi_taxonomy - Anopheles <genus> - - - - - Anopheles - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - saccharomyceta - - - - - - - - - GC_ID:1 - ncbi_taxonomy - leotiomyceta - - - - - - - - - - NCBITaxon:44555 - GC_ID:1 - Culex - ncbi_taxonomy - Culex <genus> - - - - - Culex - - - - - - - - - - - GC_ID:1 - PMID:12597651 - southern house mosquito - ncbi_taxonomy - Culex fatigan - Culex fatigans - Culex pipiens fatigans - Culex pipiens quinquefasciatus - Culex pipiens quiquefasciatus - Culex quinquifasciatus - Culex quinquifasiatus - Culex quiquefasciatus - Culex quinquefasciatus - - - - - southern house mosquito - - - - - - Culex fatigan - - - - - - Culex fatigans - - - - - - Culex pipiens fatigans - - - - - - Culex pipiens quinquefasciatus - - - - - - Culex pipiens quiquefasciatus - - - - - - Culex quinquifasciatus - - - - - - Culex quinquifasiatus - - - - - - Culex quiquefasciatus - - - - - - - - - - - GC_ID:11 - PMID:17704223 - ncbi_taxonomy - Vibrio harveyi clade - Vibrio harveyi group - - - - - Vibrio harveyi clade - - - - - - - - - - - GC_ID:11 - PMID:16280474 - ncbi_taxonomy - Thiomicrospira group - Thiothrix/Francisella group - Thiotrichales - - - - - Thiomicrospira group - - - - - - Thiothrix/Francisella group - - - - - - - - - - Mirela L Vasconcelos - Pseudomonaceae/Moraxellaceae group - Pseudomonadales - - - - - - - - - Mirela L Vasconcelos - Helicobacter group - Helicobacteraceae - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Campylobacter group - Campylobacteraceae Vandamme and De Ley 1991 - Campylobacteraceae - - - - - Campylobacter group - - - - - - Campylobacteraceae Vandamme and De Ley 1991 - - - - - - - - - - Mirela L Vasconcelos - Haemophilus - - - - - - - - - Mirela L Vasconcelos - Bacterium influenzae - Coccobacillus pfeifferi - Haemophilus meningitidis - Influenza-bacillus - Mycobacterium influenzae - Haemophilus influenzae - - - - - - - - - - GC_ID:11 - Haemophilus ducreyi - ncbi_taxonomy - Bacillus ulceris cancrosi - Coccobacillus ducreyi - [Haemophilus] ducreyi - - - - - Haemophilus ducreyi - - - - - - Bacillus ulceris cancrosi - - - - - - Coccobacillus ducreyi - - - - - - - - - - Pterygota - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Eucoccidiida - Eucoccidiorida - - - - - Eucoccidiida - - - - - - - - - - - GC_ID:11 - PMID:11760958 - PMID:8240958 - rickettsias - ncbi_taxonomy - Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993 - Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001 - alpha-1 proteobacteria - Rickettsiales - - - - - rickettsias - - - - - - Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993 - - - - - - Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001 - - - - - - alpha-1 proteobacteria - - - - - - - - - - - GC_ID:11 - PMID:11760958 - ncbi_taxonomy - Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001 - Anaplasma - - - - - Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001 - - - - - - - - - - Nidovirales - http://purl.obolibrary.org/obo/obi.owl - Nidovirales - - - - - - - - - chordates - Chordata - - - - - - - - - vertebrates - authority: Vertebrata Cuvier, 1812 - Vertebrata - - - - - - - - - - GC_ID:11 - PMID:11760958 - PMID:2592342 - PMID:8240958 - ncbi_taxonomy - Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Brenner et al. 1993 - Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Dumler et al. 2001 - Rickettsiaceae - - - - - Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Brenner et al. 1993 - - - - - - Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Dumler et al. 2001 - - - - - - - - - - - GC_ID:11 - Coxiella - ncbi_taxonomy - Burnetia - Coxiella <Bacteria> - - - - - Coxiella - - - - - - Burnetia - - - - - - - - - - Mycobacterium tuberculosis complex - - - - - - - - - - GC_ID:11 - PMID:9226923 - ncbi_taxonomy - Coxiella burnetii8 - Rickettsia burneti - Rickettsia diaporica - Coxiella burnetii - - - - - Coxiella burnetii8 - - - - - - Rickettsia burneti - - - - - - Rickettsia diaporica - - - - - - - - - - jawed vertebrates - Gnathostomata - - - - - - - - - - GC_ID:11 - PMID:10939649 - PMID:11491333 - PMID:9103608 - ncbi_taxonomy - Rickettsia da Rocha-Lima 1916 - Rickettsia - - - - - Rickettsia da Rocha-Lima 1916 - - - - - - - - - - - GC_ID:11 - PMID:15879256 - ncbi_taxonomy - Rickettsia prowazekii - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - "Dermacentroxenus rickettsii" Wolbach 1919 - Dermacentroxenus rickettsii - Rickettsia rickettsii (Wolbach 1919) Brumpt 1922 - Rickettsia rickettsii - - - - - "Dermacentroxenus rickettsii" Wolbach 1919 - - - - - - Dermacentroxenus rickettsii - - - - - - Rickettsia rickettsii (Wolbach 1919) Brumpt 1922 - - - - - - - - - - - GC_ID:11 - ncbi_taxonomy - Dermacentroxenus typhi - Rickettsia mooseri - Rickettsia typhi - - - - - Dermacentroxenus typhi - - - - - - Rickettsia mooseri - - - - - - - - - - Mirela L Vasconcelos - Burkholderia/Oxalobacter/Ralstonia group - Burkholderiales - - - - - - - - - Mirela L Vasconcelos - Chlamydiaceae - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Guaroa virus - - - - - - - - - Mirela L Vasconcelos - Bedsonia - Chlamydophila - Miyagawanella - Rakeia - Rickettsiaformis - Chlamydia - - - - - - - - - Mirela L Vasconcelos - Chlamydozoon trachomatis - Rickettsia trachomae - Rickettsia trachomatis - Chlamydia trachomatis - - - - - - - - - Sarcopterygii - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Sarcoptiformes - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Listrophoroidea - Psoroptoidea - Sarcoptoidea - - - - - Listrophoroidea - - - - - - Psoroptoidea - - - - - - - - - - - NCBITaxon:812 - GC_ID:11 - PMID:10319462 - PMID:12807198 - PMID:8102247 - PMID:8347519 - ncbi_taxonomy - Chlamydia psitacci - Chlamydophila psittaci - Chlamydozoon psittaci - Ehrlichia psittaci - Rickettsia psittaci - Rickettsiaformis psittacosis - Chlamydia psittaci - - - - - Chlamydia psitacci - - - - - - Chlamydophila psittaci - - - - - - Chlamydozoon psittaci - - - - - - Ehrlichia psittaci - - - - - - Rickettsia psittaci - - - - - - Rickettsiaformis psittacosis - - - - - - - - - - GC_ID:1 - sauropsids - ncbi_taxonomy - Sauropsida - - - - - sauropsids - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Archosauria - - - - - - - - - Corynebacterineae - Corynebacteriales - - - - - - - - - Dicondylia - - - - - - - - - Bacillus cereus group - - - - - - - - - - GC_ID:1 - birds - ncbi_taxonomy - birds - Aves - - - - - birds - - - - - - birds - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Neognathae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Anseriformes - - - - - - - - - - GC_ID:1 - waterfowl - ncbi_taxonomy - Anatidae - - - - - waterfowl - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cyclospora cayetanensis - - - - - - - - - Panarthropoda - - - - - - - - - Craniata - - - - - - - - - - GC_ID:1 - fowls - ncbi_taxonomy - Galliformes - - - - - fowls - - - - - - - - - - - NCBITaxon:9099 - GC_ID:1 - turkeys - ncbi_taxonomy - Phasianidae - - - - - turkeys - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Gallus - - - - - - - - - - GC_ID:1 - bantam - chicken - chickens - ncbi_taxonomy - Gallus domesticus - Gallus gallus domesticus - Gallus gallus - - - - - bantam - - - - - - chicken - - - - - - chickens - - - - - - Gallus domesticus - - - - - - Gallus gallus domesticus - - - - - - - - - - Mirela L Vasconcelos - Bacillus typhi - Bacterium (subgen. Eberthella) typhi - Salmonella choleraesuis serovar Typhi - Salmonella choleraesuis typhi - Salmonella enterica ser. typhi - Salmonella enterica serotype Typhi - Salmonella enterica serovar Typhi - Salmonella typhi - Salmonella enterica subsp. enterica serovar Typhi - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Phasianinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Coturnix - - - - - - - - - Staphylococcaceae - Staphylococcus group - Staphylococcaceae - - - - - - - - - Mirela L Vasconcelos - Acinetobacter calcoaceticus/baumannii complex - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Meleagris - - - - - - - - - - GC_ID:1 - common turkey - turkey - wild turkey - ncbi_taxonomy - Meleagris gallopavo - - - - - common turkey - - - - - - turkey - - - - - - wild turkey - - - - - - - - - - Mirela L Vasconcelos - Bacillus/Lactobacillus/Strptococcus group - Firmibacteria - Bacilli - - - - - - - - - Mirela L Vasconcelos - Enterobacteriaceae and related endosymbionts - Enterobacteriaceae group - Enterobacteriales - Enterobacterales - - - - - - - - - GC_ID:1 - whales, hippos, ruminants, pigs, camels etc. - ncbi_taxonomy - even-toed ungulates - Cetartiodactyla - - - - - whales, hippos, ruminants, pigs, camels etc. - - - - - - even-toed ungulates - - - - - - - - - - Placentalia - eutherian mammals - placental mammals - placentals - Eutheria - - - - - - - - - - GC_ID:1 - Japanese quail - ncbi_taxonomy - Coturnix coturnix Japonicus - Coturnix coturnix japanica - Coturnix coturnix japonica - Coturnix japonica japonica - Coturnix japonica - - - - - Japanese quail - - - - - - Coturnix coturnix Japonicus - - - - - - Coturnix coturnix japanica - - - - - - Coturnix coturnix japonica - - - - - - Coturnix japonica japonica - - - - - - - - - - - GC_ID:11 - PMID:11760958 - ncbi_taxonomy - Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001 - Ehrlichiae - Anaplasmataceae - - - - - Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001 - - - - - - Ehrlichiae - - - - - - - - - - - NCBITaxon:778 - GC_ID:11 - PMID:11414267 - PMID:11760958 - ncbi_taxonomy - "Ehrlichia (subgen. Cowdria)" Moshkovski 1945 - "Kurlovia" Zhdanov 1953 - "Nicollea" (in part) Macchiavello 1947 - "Nicollea" Macchiavello 1947 - "Rickettsia (subgen. Ehrlichia)" Moshkovski 1937 - Cowdria - Cowdria Moshkovski 1947 - Ehrlichia (subgen. Cowdria) - Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001 - Kurlovia - Nicollea - Rickettsia (subgen. Ehrlichia) - possibly "Donatienella" Rousselot 1948 - Ehrlichia - - - - - "Ehrlichia (subgen. Cowdria)" Moshkovski 1945 - - - - - - "Kurlovia" Zhdanov 1953 - - - - - - "Nicollea" (in part) Macchiavello 1947 - - - - - - "Nicollea" Macchiavello 1947 - - - - - - "Rickettsia (subgen. Ehrlichia)" Moshkovski 1937 - - - - - - Cowdria - - - - - - Cowdria Moshkovski 1947 - - - - - - Ehrlichia (subgen. Cowdria) - - - - - - Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001 - - - - - - Kurlovia - - - - - - Nicollea - - - - - - Rickettsia (subgen. Ehrlichia) - - - - - - possibly "Donatienella" Rousselot 1948 - - - - - - - - - - Primata - primate - primates - Primates - - - - - - - - - - GC_ID:11 - PMID:11760958 - PMID:1757557 - ncbi_taxonomy - Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001 - Ehrlichia chaffensis - Ehrlichia chaffeensis - - - - - Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001 - - - - - - Ehrlichia chaffensis - - - - - - - - - - - NCBITaxon:59888 - NCBITaxon:75053 - NCBITaxon:75115 - NCBITaxon:946 - GC_ID:11 - PMID:1115421 - PMID:11760958 - PMID:8195363 - agent of human granulocytic ehrlichiosis - ncbi_taxonomy - Anaplasma phagocytophila - Cytoecetes bovis - Cytoecetes phagocytophila - Ehrlichia equi - Ehrlichia phagocytophila - Ehrlichia sp. 'HGE agent' - HGE agent - Rickettsia phagocytophila - Rickettsia phagocytophila ovis - human granulocytic Ehrlichia - Anaplasma phagocytophilum - - - - - agent of human granulocytic ehrlichiosis - - - - - - Anaplasma phagocytophila - - - - - - Cytoecetes bovis - - - - - - Cytoecetes phagocytophila - - - - - - Ehrlichia equi - - - - - - Ehrlichia phagocytophila - - - - - - Ehrlichia sp. 'HGE agent' - - - - - - HGE agent - - - - - - Rickettsia phagocytophila - - - - - - Rickettsia phagocytophila ovis - - - - - - human granulocytic Ehrlichia - - - - - - - - - - Catarrhini - - - - - - - - - Old World monkeys - monkey - monkeys - Cercopithecidae - - - - - - - - - Cercopithecinae - - - - - - - - - macaque - macaques - Macaca - - - - - - - - - - NCBITaxon:36519 - GC_ID:1 - crab eating macaque - crab-eating macaque - cynomolgus monkey - cynomolgus monkeys - long-tailed macaque - ncbi_taxonomy - Macaca cynomolgus - Macaca irus - cynomolgus macaque - Macaca fascicularis - - - - - crab eating macaque - - - - - - crab-eating macaque - - - - - - cynomolgus monkey - - - - - - cynomolgus monkeys - - - - - - long-tailed macaque - - - - - - Macaca cynomolgus - - - - - - Macaca irus - - - - - - cynomolgus macaque - - - - - - - - - - Rhesus monkey - rhesus macaque - rhesus macaques - rhesus monkeys - Macaca mulatta - - - - - - - - - - - - - - - - - - - GC_ID:1 - dog, coyote, wolf, fox - ncbi_taxonomy - Canidae - - - - - dog, coyote, wolf, fox - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Canis - - - - - - - - - - GC_ID:1 - gray wolf - grey wolf - ncbi_taxonomy - Canis lupus - - - - - gray wolf - - - - - - grey wolf - - - - - - - - - - - GC_ID:1 - dog - dogs - ncbi_taxonomy - Canis canis - Canis domesticus - Canis familiaris - Canis lupus familiaris - - - - - dog - - - - - - dogs - - - - - - Canis canis - - - - - - Canis domesticus - - - - - - Canis familiaris - - - - - - - - - - - GC_ID:1 - odd-toed ungulates - ncbi_taxonomy - odd-toed ungulates - Perissodactyla - - - - - odd-toed ungulates - - - - - - odd-toed ungulates - - - - - - - - - - - GC_ID:1 - horses - ncbi_taxonomy - Equidae - - - - - horses - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Equus - - - - - - - - - - GC_ID:1 - domestic horse - equine - horse - ncbi_taxonomy - Equus ferus caballus - Equus przewalskii f. caballus - Equus przewalskii forma caballus - Equus caballus - - - - - domestic horse - - - - - - equine - - - - - - horse - - - - - - Equus ferus caballus - - - - - - Equus przewalskii f. caballus - - - - - - Equus przewalskii forma caballus - - - - - - - - - - - NCBITaxon:39423 - GC_ID:1 - boars - pigs - ncbi_taxonomy - Suidae - - - - - boars - - - - - - pigs - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Sus - - - - - - - - - - GC_ID:1 - pig - pigs - swine - wild boar - ncbi_taxonomy - Sus scrofus - Sus scrofa - - - - - pig - - - - - - pigs - - - - - - swine - - - - - - wild boar - - - - - - Sus scrofus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Artiodactyla - Ruminantia - - - - - Artiodactyla - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Bovidae - - - - - - - - - - GC_ID:1 - oxen, cattle - ncbi_taxonomy - Bos - - - - - oxen, cattle - - - - - - - - - - - NCBITaxon:272461 - GC_ID:1 - bovine - cattle - cow - domestic cattle - domestic cow - ncbi_taxonomy - Bos Tauurus - Bos bovis - Bos primigenius taurus - Bos taurus - - - - - bovine - - - - - - cattle - - - - - - cow - - - - - - domestic cattle - - - - - - domestic cow - - - - - - Bos Tauurus - - - - - - Bos bovis - - - - - - Bos primigenius taurus - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Capra - - - - - - - - - - NCBITaxon:57076 - GC_ID:1 - domestic goat - goat - goats - ncbi_taxonomy - Capra aegagrus hircus - Carpa hircus - South African angora goat - Capra hircus - - - - - domestic goat - - - - - - goat - - - - - - goats - - - - - - Capra aegagrus hircus - - - - - - Carpa hircus - - - - - - South African angora goat - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ovis - - - - - - - - - - NCBITaxon:9936 - GC_ID:1 - domestic sheep - lambs - sheep - wild sheep - ncbi_taxonomy - Ovis ammon aries - Ovis orientalis aries - Ovis ovis - Ovis aries - - - - - domestic sheep - - - - - - lambs - - - - - - sheep - - - - - - wild sheep - - - - - - Ovis ammon aries - - - - - - Ovis orientalis aries - - - - - - Ovis ovis - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Caprinae - - - - - - - - - A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment. - http://en.wikipedia.org/wiki/Contraindication - http://purl.obolibrary.org/obo/dideo/dev/dideo.owl - contraindication + + 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 - + - - + + + - + - - - - - - + + + + + + - - + + - - - - + + + + - - - planned process - Injecting mice with a vaccine in order to test its efficacy - - A processual entity that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some - objectives is a planned process. - Bjoern Peters - branch derived - - planned process + + 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 - + - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material + + + A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic. + William R. Hogan + cumulative epidemic infection count - + - - + + + An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval. + William R. Hogan + incident epidemic infection count - + - - - intervention design - PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. - - An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. - Philppe Rocca-Serra - OBI branch derived - http://purl.obolibrary.org/obo/obi.owl - intervention design + + + A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic. + William R. Hogan + cumulative epidemic death count - + - - - data encoding - storage of measurement results from an assay into a text file, such as - - a documenting process to encode an information entity into a digital document - PlanAndPlannedProcess Branch - OBI branch derived - We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE - http://purl.obolibrary.org/obo/obi.owl - data encoding + + + An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval. + William R. Hogan + incident epidemic death count - - - - organization - PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. - - An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. - BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: - -1) there are organization_member_roles (president, treasurer, branch -editor), with individual persons as bearers - -2) there are organization_roles (employer, owner, vendor, patent holder) - -3) an organization has a charter / rules / bylaws, which specify what roles -there are, how they should be realized, and how to modify the -charter/rules/bylaws themselves. - -It is debatable what the organization itself is (some kind of dependent -continuant or an aggregate of people). This also determines who/what the -bearer of organization_roles' are. My personal favorite is still to define -organization as a kind of 'legal entity', but thinking it through leads to -all kinds of questions that are clearly outside the scope of OBI. - -Interestingly enough, it does not seem to matter much where we place -organization itself, as long as we can subclass it (University, Corporation, -Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, -W3C, University of Oklahoma), and have it play roles. + -This leads to my proposal: We define organization through the statements 1 - -3 above, but without an 'is a' statement for now. We can leave it in its -current place in the is_a hierarchy (material entity) or move it up to -'continuant'. We leave further clarifications to BFO, and close this issue -for now. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra - PERSON: Susanna Sansone - GROUP: OBI - organization + + + A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic. + William R. Hogan + cumulative epidemic hospitalization count - + - - - averaging objective - A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. - - An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. - Elisabetta Manduchi - James Malone - PERSON: Elisabetta Manduchi - http://purl.obolibrary.org/obo/obi.owl - averaging objective + + + An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval. + William R. Hogan + incident epidemic hospitalization count - + - - + + + A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic. + William R. Hogan + cumulative epidemic vaccination count - + - - - scattered molecular aggregate - the sodium and chloride ions in a glass of salt water - - a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates - PERSON: Alan Ruttenberg - Collective - Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 - http://purl.obolibrary.org/obo/obi.owl - scattered molecular aggregate + + + An incident vaccination count 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 reference interval. + William R. Hogan + incident epidemic vaccination count - + - - - data representational model - gene regulatory graph model - phylogenetic tree - protein interaction network - - Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. - Melanie Courtot - data structure - data structure specification - GROUP: OBI - 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 - http://purl.obolibrary.org/obo/obi.owl - data representational model + + + 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 - + - - - center value - - A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. - PERSON: James Malone - PERSON: Monnie McGee - median - http://purl.obolibrary.org/obo/obi.owl - median - center value + + + 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 - + - - - - - - - - - - - - - - average value - - A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. - PERSON: James Malone - PERSON: Monnie McGee - arithmetic mean - false - http://purl.obolibrary.org/obo/obi.owl - A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. - mean - average value + + + A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. + William R. Hogan + vaccination with nirsevimab - + - - - graph of vertices - For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. - - A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. - Bjoern Peters - Chris Stoeckert - James Malone - WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html - http://purl.obolibrary.org/obo/obi.owl - graph of vertices + + + A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative vaccination count - + - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - - A device is a processed material which is designed to perform some function or functions - 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 - would include reagents - device + + + A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident vaccination count - + - - - computer cluster - - A group of linked computers, working together closely so that in many respects they form a single computer. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Cluster_(computing) - http://purl.obolibrary.org/obo/obi.owl - computer cluster + + + A count of infections in a population that is the total number of infections that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative infection count - + - - - service - providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony - - A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. - Carlo; Matt - OBI workshop San Diego 2011 - http://purl.obolibrary.org/obo/obi.owl - service + + + A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident infection count - + - - - environmental history design - - A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. - Person: Chris Stoeckert, Jie Zheng - MO_698 environmental_history_design - http://purl.obolibrary.org/obo/obi.owl - environmental history design + + + A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative hospitalization count - + - - - disease state design - - A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. - Person: Chris Stoeckert, Jie Zheng - MO_902 disease_state_design - http://purl.obolibrary.org/obo/obi.owl - disease state design + + + A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident hospitalization count - + - - - pathogenicity design - - A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. - Person: Chris Stoeckert, Jie Zheng - MO_807 pathogenicity_design - http://purl.obolibrary.org/obo/obi.owl - pathogenicity design + + + A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative death count - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data service - Data analysis service such statistical abalysis or storage service such data backup. - - A service that has some information content entity as input and output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - http://purl.obolibrary.org/obo/obi.owl - Information content entity was used as specified input and output since it was more appropriate then data item or dataset. - data service + + + A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident death count - + - - - rate measurement datum - The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. - - A scalar measurement datum that represents the number of events occuring over a time interval - PERSON: Bjoern Peters, Randi Vita - IEDB - http://purl.obolibrary.org/obo/obi.owl - rate measurement datum + + + A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative case count - + - - - investigation description - - A textual entity that describes an investigation. - Person: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - http://purl.obolibrary.org/obo/obi.owl - study description - project description - investigationDescription - NIAID GSCID-BRC - investigation description + + + A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident case count - + - - - investigation identifier - - A CRID symbol used to identify an investigation. - Person: Chris Stoeckert, Jie Zhneg - NIAID GSCID-BRC metadata working group - http://purl.obolibrary.org/obo/obi.owl - project ID - investigationLabel - NIAID GSCID-BRC - investigation identifier + + + guardian's intent to have a ward under their care vaccinated + An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role. + William R. Hogan + The intent of a guardian to have a ward under their care vaccinated in the near future. + Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. + intent to have a ward vaccinated - + - - - grant identifier - - A CRID symbol used to identify a grant. - Person: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - http://purl.obolibrary.org/obo/obi.owl - grant ID - NIAID GSCID-BRC - grant identifier + + + An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child. + William R. Hogan + Intent to have one's child vaccinated. + The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. + intent to have a child vaccinated - - - - - - - - - - - - - + - - - systematic review study design - Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/ar\ -ticles/PMC4090399/ - The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic re\ -view. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ - - A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according \ -to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were no\ -t justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. - PERSON: Bill Hogan - systematic review study design + + + epidemic simulator action specification + William R. Hogan + epidemic simulator action specification - + - - - digital object identifier - The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 - - A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. - Discussed on Aug 22, 2016 OBI dev call. Details see tracker: -https://sourceforge.net/p/obi/obi-terms/818/ - OBI developers - DOI - https://en.wikipedia.org/wiki/Digital_object_identifier -https://www.doi.org/ - http://purl.obolibrary.org/obo/obi.owl - digital object identifier + + + infectious disease control strategy action specification + William R. Hogan + infectious disease control strategy action specification - + - - organism - - 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. - Individual - organism + + + individual treatment control strategy action specification + William R. Hogan + individual treatment control strategy action specification - + - + + + + + + + + + + + + - - + + - data transformation - The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. - - A data transformation is a process which produces output data from input data - Elisabetta Manduchi - Helen Parkinson - James Malone - Melanie Courtot - Philippe Rocca-Serra - Richard Scheuermann - Ryan Brinkman - Tina Hernandez-Boussard - data analysis - data processing - Branch editors - http://purl.obolibrary.org/obo/obi.owl - data transformation - - - - - - - - - data transformation objective - normalize objective - - A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed. - James Malone - PERSON: James Malone - http://purl.obolibrary.org/obo/obi.owl - data transformation objective + creating a data set + A planned process that has a data set as its specified output. + William R. Hogan + data set creation + dataset creation + dataset creating - + - + - + + - - - - - + - + - - averaging data transformation - - An averaging data transformation is a data transformation that has objective averaging. - James Malone - PERSON: James Malone - http://purl.obolibrary.org/obo/obi.owl - averaging data transformation - - - - - - - - - observation design - PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. - - observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. - Philippe Rocca-Serra - OBI branch derived - http://purl.obolibrary.org/obo/obi.owl - observation design + + + + + + + + creating a copyright license + A planned process that has a copyright license as its specified output. + William R. Hogan + copyright license creation + Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time. + creating a copyright license - + - - - predicted data item - - A data item that was generated on the basis of a calculation or logical reasoning - BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. - Philippe Rocca-Serra; Bjoern Peters - http://purl.obolibrary.org/obo/obi.owl - APOLLO DEVELOPERS: We need to check whether OBI changes the label and the hierarchical place of this class. - calculated datum - predicted data item + + + copyright license for a creative work + A document that is about the legal rights, claims, and obligations of a legal person (person or organization) under copyright law, and how that legal person intends for those rights, claims, and obligations to be handled/managed by users of the creative work to which this document is attached. + William R. Hogan + Can be for any creative work including fiction. But the license itself is an ICE, and refers to real claims and obligations. + copyright license - + - - - digital curation - PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44. - - Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally. - Philippe Rocca-Serra - wikipedia - http://purl.obolibrary.org/obo/obi.owl - digital curation + + + data service software application + A software application that implements a data service. + William R. Hogan + data service software - + - - - computer - Apple PowerBook, Dell OptiPlex - - A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. - Melanie Courtot - Trish Whetzel - http://en.wikipedia.org/wiki/Computer - computer + + + TODO - + - - - study design - a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. - - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. - PERSON: Chris Stoeckert - experimental design - rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. - - http://purl.obolibrary.org/obo/obi.owl - study design + + + facultative role + A role borne by an organism in virtue of the fact that it is in intimate association with one or more organisms of different species, and is realized by bodily benefit to that organism as an occurrent part of a symbiosis with the other organisms. This bodily benefit takes the place of the organism or some relatively isolated part of the organism realizing some normal homeostasis disposition itself. + facultative role - + - - - time series design - PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. - - Groups of assays that are related as part of a time series. - Philippe Rocca-Serra on behalf of MO - MO_887 - http://purl.obolibrary.org/obo/obi.owl - time series design - + - + - - - A planned process that realizes the concretization of a software. - ITPPR - operation - ITPPR - http://purl.obolibrary.org/obo/OBIws.owl - software execution - + - + - - - A software execution that is provided by the web service, and involves invoking software execution over network. - ITPPR - web service operation - ITPPR - http://purl.obolibrary.org/obo/OBIws.owl - web service execution - + - + - - - A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. - Albert Goldfain - http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf - creation date: 2010-07-19T10:18:02Z - http://purl.obolibrary.org/obo/ogms.owl - clinical finding - + - + - - - A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. - Albert Goldfain - http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf - creation date: 2009-06-23T10:21:58Z - http://purl.obolibrary.org/obo/ogms.owl - result - laboratory finding - + - + - - - A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. - Albert Goldfain - http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf - creation date: 2010-07-19T11:13:49Z - http://purl.obolibrary.org/obo/ogms.owl - phenotype - + - + - - - A clinically abnormal phenotype. - Albert Goldfain - http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf - creation date: 2009-06-23T11:18:05Z - http://purl.obolibrary.org/obo/ogms.owl - clinical phenotype - + - + - - - A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. - Albert Goldfain - http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf - creation date: 2009-06-23T11:21:20Z - disease - disease - + - - - - - A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning. - Albert Goldfain - Barry Smith - Richard H. Scheuermann - Werner Ceusters - Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. + -Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ - creation date: 2009-06-23T11:22:01Z - http://purl.obolibrary.org/obo/ogms.owl - homeostasis - + - + - - - A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. - 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 - + - + - - - disease course - The totality of all processes through which a given disease instance is realized. - 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 - + - + - - - 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. - 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 - extended organism - + - + - - - A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder - Albert Goldfain - http://code.google.com/p/ogms/issues/detail?id=35 - creation date: 2010-03-31T04:51:11Z - http://purl.obolibrary.org/obo/ogms.owl - Treatment - Apollo-SV currently defines two subclasses of treatment. -See vaccination and antiviral treatment. - - treatment - + - + - - - A processual entity which has as parts all the processes in which a given organism is participant. - Albert Goldfain - http://code.google.com/p/ogms/issues/detail?id=38 - creation date: 2010-03-31T04:51:11Z - http://purl.obolibrary.org/obo/ogms.owl - A processual entity which has as parts all the processes in which a given organism is participant. - LifeCycle - life course - + - + - - - A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process - Albert Goldfain - http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 - creation date: 2011-02-21T09:57:44Z - http://purl.obolibrary.org/obo/ogms.owl - health care process - + - + - - - A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter - Albert Goldfain - http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 - creation date: 2011-02-21T09:57:44Z - http://purl.obolibrary.org/obo/ogms.owl - health care encounter - + - + - - - Albert Goldfain - http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 - creation date: 2011-02-21T09:57:44Z - http://purl.obolibrary.org/obo/ogms.owl - hospitalization - hospitalization - + - + - - - Albert Goldfain - http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 - creation date: 2011-02-21T09:57:44Z - http://purl.obolibrary.org/obo/ogms.owl - outpatient encounter - + - + - - - Albert Goldfain - http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 - creation date: 2011-02-21T09:57:44Z - http://purl.obolibrary.org/obo/ogms.owl - inpatient encounter - + - + - - - Albert Goldfain - http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 - creation date: 2011-02-21T09:57:44Z - http://purl.obolibrary.org/obo/ogms.owl - ED encounter - + - + - - - A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course. - Albert Goldfain - http://code.google.com/p/ogms/issues/detail?id=73 - http://purl.obolibrary.org/obo/ogms.owl - relapse - + - + - - - A CRID that constitutes a reference to an Internet resource. - Mathias Brochhausen - uri - http://en.wikipedia.org/wiki/Uniform_resource_locator - http://purl.obolibrary.org/obo/omiabis.owl - url - unique resource locator - + - + - - - - - - - - - A social role inhering in a human being. - Mathias Brochhausen - - William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl - human social role - + - + - - - A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Gender_role - http://purl.obolibrary.org/obo/omrse.owl - sex - gender role - + - + - - - A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question. - Mathias Brochhausen - male gender - http://purl.obolibrary.org/obo/omrse.owl - male gender role - + - + - - - A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question. - Mathias Brochhausen - female gender - http://purl.obolibrary.org/obo/omrse.owl - female gender role - + - + - - - A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. - William R. Hogan - health care role - http://purl.obolibrary.org/obo/omrse.owl - Mathias Brochhausen - human health care role - + - + - - - A human health care role that inheres in an organism [human?] as the recipient of a health care service. - A role borne by an organism being as the recipient of a health care service. - Amanda Hicks - Mathias Brochhausen - patient - http://en.wikipedia.org/wiki/Patient - http://purl.obolibrary.org/obo/omrse.owl - patient role - + - + - - - http://purl.obolibrary.org/obo/omrse.owl - Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). - health care provider organization role - + - + - - - - - - - - - - - - - - - - - - - An object aggregate of organisms. - This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species. - Any arbitrary collection of organisms. They need not be of the same taxonomic class. - collection of organisms - + - + - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/omrse.owl - An object aggregate all of whose components are human beings. - collection of humans - + - - - - - A role in human social processes that inheres in an organization. - William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl - Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. + -Ditto for its current descendants. - organization social role - + - - - - - - - - - - - A role in human social processes that inheres in an organism. - William R. Hogan -Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. + -Ditto for its current descendants. - 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. - Previous definition: A role in human social processes played by an organism. - organism social role - + - + - - - An organization social role that is realized by a health care process. - http://purl.obolibrary.org/obo/omrse.owl - Previous definition: An organization social role played by an organization in health care processes. - organization health care role - + - + - - - - - - - - - - - - - - - - - - An aggregate of organizations that have some feature in common, but is not itself an organization. - William R. Hogan - It is often convenient to group organizations together that otherwise might not even interact with one another. - aggregate of organizations - + - + - - - A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - hospital function - + - + - - - A function inhering in a facility that manifests by the facility participating in providing formal education to a student population. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - school function - + - + - - - A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - hospital role - + - + - - - An organization social role that inheres in an organization and is realized by providing formal education to students. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - school role - + - + - - - - - - - - - - - - - - An organization that is the bearer of a hospital role. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - hospital organization - + - - - - - - - - - - - - - - - - - An organization that is the bearer of a school role. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - school organization - + + + + - + - - - A human social role that is realized by the process of formal education that the bearer undergoes. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - student role - + - + - - - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - preschool - Key motivating use case was Synthia synthetic population data. - - nursery school role - + - + - - - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - primarySchool - Key motivating use case was Synthia synthetic population data. - primary school role - + - + - - - A material entity that is a human made strcuture with firm connection between its foundation and the ground. - Mathias Brochhausen - http://de.wikipedia.org/wiki/Bauwerk - http://purl.obolibrary.org/obo/omrse.owl - "Building" is a subclass of this. - This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". - architectural structure - + - + - - - An architectural structure that bears some function. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - facility - + - + - - - A facility that is run by a hospital organization and is the bearer of a hospital function. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - HealthcareFacility - hospital facility - + - + - - - A facility that is run by a school organization and is the bearer of a school function. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - SchoolFacility - school facility - + - + - - - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - secondarySchool - Key motivating use case was Synthia synthetic population data. - secondary school role - + - + - - - A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function. - Amanda Hicks - https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household - http://purl.obolibrary.org/obo/omrse.owl - houses - Housing units are individuated by their residence functions. - housing unit - + - + - - - A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function. - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - Household - household - + - + - - - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - workplace - workplace facility - + - + - - - a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - workplace function - + - + - - - A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. - http://purl.obolibrary.org/obo/omrse.owl - race - racial identity datum - + - + - - - A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population. - http://purl.obolibrary.org/obo/omrse.owl - health care facility - + - + - - - http://purl.obolibrary.org/obo/omrse.owl - Amanda Hicks - An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method. - identity datum - + - + - - - A role inhering in an entity realized by social interactions in human society. - Matthew Diller - http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl - Mathias Brochhausen - Previous definition: A role played by an entity in human social processes. - role in human social processes - + - + - - - A quality that is the extent of space between two entities. - http://purl.obolibrary.org/obo/pato.owl - Distance - quality - PATO:0000040 - - - - distance - + - + - - - biological sex - An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. - http://purl.obolibrary.org/obo/obi.owl - biologicalSex - biological sex - + - + - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0000051 - - morphology - + - + - - - + - + - - - - + - + - - - - + - + - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - http://purl.obolibrary.org/obo/pato.owl - PATO:0001452 - conformation - relational structural quality - quality - PATO:0000141 - - structure - + - + - - - A physical quality of the thermal energy of a system. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0000146 - - - temperature - + - + - - - female - A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. - http://purl.obolibrary.org/obo/obi.owl - female - + - + - - - male - A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. - http://purl.obolibrary.org/obo/obi.owl - male - + - + - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - http://purl.obolibrary.org/obo/pato.owl - PATO:0002079 - Wikipedia:Physical_property - relational physical quality - quality - PATO:0001018 - - physical quality - + - + - - - A quality which inheres in a continuant. - http://purl.obolibrary.org/obo/pato.owl - PATO:0001237 - PATO:0001238 - snap:Quality - monadic quality of a continuant - multiply inhering quality of a physical entity - quality of a continuant - quality of a single physical entity - quality of an object - quality of continuant - monadic quality of an object - monadic quality of continuant - quality - PATO:0001241 - Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. - physical object quality - + - + - - - A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. - http://purl.obolibrary.org/obo/pato.owl - 1-D size - quality - PATO:0001708 - - 1-D extent - + - + - - - A structural quality inhering in a bearer by virtue of the bearer's touching another entity. - http://purl.obolibrary.org/obo/pato.owl - quality - contiguous - PATO:0001961 - - - in contact with - + - + - - - A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter. - http://purl.obolibrary.org/obo/pato.owl - radius - gkoutos - 2012-11-15T05:17:15Z - quality - PATO:0002390 - - - radius - + - + - - - Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. - A material entity that consists of two or more organisms, viruses, or viroids. - group of organisms - organism collection - May be of the same or different species. - PCO:collection of organisms - + - + - - - - - - - - - A collection of organisms, all of the same species, that live in the same place. - Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific. - ISBN:0878932739 - Population - It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used. - population - + - + - - - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. - collection of organisms of the same species - + - + - - - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/ - - effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval - Alejandra Gonzalez-Beltran - Orlaith Burke - Philippe Rocca-Serra - AGB,PRS - http://purl.obolibrary.org/obo/stato.owl - effect size - effect size estimate - + - + - - - - statistical sample size is a count evaluating the number of individual experimental units - Alejandra Gonzalez-Beltran - Orlaith Burke - Philippe Rocca-Serra - AGB-PRS - http://purl.obolibrary.org/obo/stato.owl - - statistical sample size - sampleSize - study group population size - + - + - - - - specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1 - Alejandra Gonzalez-Beltran - Orlaith Burke - Philippe Rocca-Serra - specificity - true negative rate - + - + - - - - sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1 - Alejandra Gonzalez-Beltran - Orlaith Burke - Philippe Rocca-Serra - recall - sensitivity - adapted from: -http://en.wikipedia.org/wiki/Sensitivity_and_specificity -and -http://mathworld.wolfram.com/Sensitivity.html - true positive rate - + - + - - - Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group. - Alejandra Gonzalez-Beltran - Orlaith Burke - Philippe Rocca-Serra - risk ratio - - http://purl.obolibrary.org/obo/stato.owl - - relative risk - + - + - - - - - a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories - Alejandra Gonzalez-Beltran - Orlaith Burke - Philippe Rocca-Serra - discrete variable - nominal variable - qualitative factor - http://udel.edu/~mcdonald/statvartypes.html - http://purl.obolibrary.org/obo/stato.owl - - categoricalVariable - https://onlinecourses.science.psu.edu/stat503/node/7 - categorical variable - + - + - - - - a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation. - Alejandra Gonzalez-Beltran - Orlaith Burke - Philippe Rocca-Serra - STATO - adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. + + -and from Oxford English Dictionary: -http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1 - http://purl.obolibrary.org/obo/stato.owl - - variable - variable - + + + + - + - - - - Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution. - Camille Maumet - Karl Helmer - Philippe Rocca-Serra - Thomas Nichols - http://purl.obolibrary.org/obo/stato.owl - NonparametricProbabilityDistribution - Initially discussed at https://github.com/incf-nidash/nidm/pull/191 - non-parametric distribution - + - + - - - - The weighted arithmetic mean is a measure of central tendency that is the sum of the products of each observed value and their respective non-negative weights, divided by the sum of the weights, such that the contribution of each observed value to the mean may defer according to its respective weight. It is defined by the formula: A = sum(vi*wi)/sum(wi), where 'i' ranges from 1 to n, 'vi' is the value of each observation, and 'wi' is the value of the respective weight for each observed value. + + -The weighted arithmetic mean is a kind of mean similar to an ordinary arithmetic mean (the most common type of average), except that instead of each of the data points contributing equally to the final average, some data points are weighted, meaning they contribute more than others. -The weighted arithmetic mean is often used if one wants to combine average values from samples of the same population with different sample sizes. - Alejandra Gonzalez-Beltran - Matthew Diller - Orlaith Burke - Philippe Rocca-Serra - https://en.wikipedia.org/wiki/Weighted_arithmetic_mean - - https://docs.scipy.org/doc/numpy/reference/generated/numpy.average.html + -np.average(range(1,11), weights=range(10,0,-1)) - https://github.com/ISA-tools/stato/issues/59 - weighted arithmetic mean - + - + - - - Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. - http://purl.obolibrary.org/obo/uberon.owl - AAO:0010825 - AEO:0000003 - BILA:0000003 - CARO:0000003 - EHDAA2:0003003 - EMAPA:0 - FBbt:00007001 - FMA:67135 - GAID:781 - HAO:0000003 - MA:0003000 - MESH:A13 - SCTID:362889002 - TAO:0000037 - TGMA:0001823 - VHOG:0001759 - WBbt:0000100 - XAO:0003000 - ZFA:0000037 - http://dbpedia.org/ontology/AnatomicalStructure - biological structure - uberon - UBERON:0000061 - - anatomical structure - - - - - - - - - Anatomical entity that has mass. - http://purl.obolibrary.org/obo/uberon.owl - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FBbt:00007016 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - uberon - UBERON:0000465 - - material anatomical entity - - - - - - - - - Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. - http://purl.obolibrary.org/obo/uberon.owl - Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO] - Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO] - Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO] - system - AAO:0000007 - AEO:0000011 - BILA:0000011 - BSA:0000049 - CALOHA:TS-2088 - CARO:0000011 - EHDAA2:0003011 - EHDAA:392 - EMAPA:16103 - EV:0100000 - FBbt:00004856 - FMA:7149 - HAO:0000011 - MA:0000003 - NIF_GrossAnatomy:birnlex_14 - OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ - SCTID:278195005 - TAO:0001439 - TGMA:0001831 - UMLS:C0460002 - VHOG:0001725 - WBbt:0005746 - WBbt:0005763 - Wikipedia:Organ_system - XAO:0003002 - ZFA:0001439 - galen:AnatomicalSystem - ncithesaurus:Organ_System - body system - organ system - uberon - UBERON:0000467 - - - anatomical system - - + - + - - - Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. - http://purl.obolibrary.org/obo/uberon.owl - AAO:0000607 - AAO:0010054 - AEO:0000043 - BILA:0000043 - CALOHA:TS-2090 - CARO:0000043 - EHDAA2:0003043 - FBbt:00007003 - FMA:9637 - HAO:0000043 - MA:0003002 - MESH:A10 - NIF_GrossAnatomy:birnlex_19 - TAO:0001477 - TGMA:0001844 - UMLS:C0040300 - VHOG:0001757 - WBbt:0005729 - XAO:0003040 - ZFA:0001477 - galen:Tissue - ncithesaurus:Tissue - portion of tissue - tissue portion - simple tissue - uberon - UBERON:0000479 - - Editor note: changed label and definition to reflect CARO2 - tissue - - - - - - - - - Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. - http://purl.obolibrary.org/obo/uberon.owl - AAO:0010008 - AEO:0000054 - BILA:0000054 - CARO:0000054 - EHDAA2:0003054 - HAO:0000054 - TAO:0001512 - TGMA:0001846 - VHOG:0001724 - XAO:0003001 - ZFA:0001512 - uberon - UBERON:0000480 - - anatomical group - + - + - - - Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. - http://purl.obolibrary.org/obo/uberon.owl - The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] - AAO:0011003 - BILA:0000104 - FMA:9825 - GAID:328 - MA:0002711 - MESH:A15.382 - OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA - SCTID:362590003 - TAO:0001159 - UMLS:C0020962 - VHOG:0001247 - Wikipedia:Immune_system - XAO:0003152 - ZFA:0001159 - ncithesaurus:Immune_System - uberon - UBERON:0002405 - - - This class was created automatically from a combination of ontologies - immune system - - - - - - - - - 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 - - - - - - - - - A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. - http://purl.obolibrary.org/obo/uberon.owl - uberon - UBERON:0035943 - - life cycle temporal boundary - + - + - - - 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 - time of death - uberon - death - end of life - UBERON:0035944 - life-death temporal boundary - + - + - - - http://purl.org/obo/owl/unit - unit.ontology - unit - + - + - - - - unitOfTime - + - + - - - A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. - http://purl.org/obo/owl/unit - DimensionlessUnit - unit.ontology - - dimensionless unit - + - + - - - A dimensionless ratio unit which denotes numbers as fractions of 100. - http://purl.org/obo/owl/unit - Percent - unit.ontology - - percent - + - + - - - A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. - http://purl.org/obo/owl/unit - Ratio - unit.ontology - - ratio - + - + - - - A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). - http://purl.org/obo/owl/unit - Fraction - unit.ontology - - fraction - + - + - - - A unit which represents a standard measurement occurrence of a process per unit time. - http://purl.org/obo/owl/unit - Rate - unit.ontology - - rate unit - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. - Many vaccines are developed to protect against infectious pathogens. Many vaccines are also being developed against some diseases such as cancer and autoimmune diseases. Vaccine is developed against a disease. Allergy. - YH, BP, BS, MC, LC, XZ, RS - a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo. - http://purl.obolibrary.org/obo/vo.owl - Vaccine - vaccine - MeSH: D014612 - + - + - - - A vaccine contraindication is a contraindication that increases the risks of a vaccination. - YH - contraindication for vaccination - http://purl.obolibrary.org/obo/vo.owl - VaccineContraindications - vaccine contraindication - + - + - - - vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host. - PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term. - YH, MC, XZ, and AR - http://purl.obolibrary.org/obo/vo.owl - vaccine function - + - + - - - vaccine preparation is a manufacturing process to produce a vaccine. - YH, BP - vaccine generation - vaccine production - http://purl.obolibrary.org/obo/vo.owl - vaccine preparation - + - + - - The specificity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X. - William R. Hogan - The specificity of a process or system that detects organisms who satisfy a case definition. - specificityOfCaseDetection - deprecated due to malformed URI and created anew. - obsolete specificity of case detection - true - + - + - - the specificity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment - William R. Hogan - the specificity of the process or system that detects organisms that have undergone a particular treatment - specificityOfTreatmentDetection - Deprecated due to malformed URI and created anew. - obsolete specificity of treatment detection - true - + - + - - the sensitivity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment - William R. Hogan - the sensitivity of the process or system that detects organisms that have undergone a particular treatment - sensitivityOfTreatmentDetection - Deprecated due to malformed URI and created anew. - obsolete sensitivity of treatment detection - true - + - + - - - http://purl.org/obo/owl/flybase_vocab - pub_type - - Originally imported into Apollo-SV for purpose of indexing in OBC.ide news articles relevant to infectious disease epidemiology. - news article - + - + - - - - - - - - - Genomic data is data about the genomes of an organism. - James Malone - genomic data - + - - Obsolete Class - + @@ -27794,30 +14749,6 @@ np.average(range(1,11), weights=range(10,0,-1)) atmosphere of the Earth - - - - - - - - "A time unit which is equal to 7 days." [Wikipedia:Wikipedia] - week - - - - - - - - administrativeLocations - diff --git a/apollo_sv-full.json b/apollo_sv-full.json index 9272a70..d16c2c2 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" : "2024-02-23" + "val" : "2024-04-19" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-02-23/apollo_sv-full.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-04-19/apollo_sv-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", @@ -4069,7 +4069,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000238", - "lbl" : "host", + "lbl" : "host organism", "type" : "CLASS", "meta" : { "definition" : { @@ -11771,7 +11771,7 @@ "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." + "val" : "A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11784,7 +11784,7 @@ "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." + "val" : "An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11797,7 +11797,7 @@ "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." + "val" : "A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11810,7 +11810,7 @@ "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." + "val" : "An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11823,7 +11823,7 @@ "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." + "val" : "A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11836,7 +11836,7 @@ "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." + "val" : "An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11849,7 +11849,7 @@ "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." + "val" : "A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11862,7 +11862,7 @@ "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." + "val" : "An incident vaccination count 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 reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11914,6 +11914,183 @@ "val" : "William R. Hogan" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000640", + "lbl" : "cumulative vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000641", + "lbl" : "incident vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000642", + "lbl" : "cumulative infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population that is the total number of infections that occur during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000643", + "lbl" : "incident infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000644", + "lbl" : "cumulative hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000645", + "lbl" : "incident hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000646", + "lbl" : "cumulative death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000647", + "lbl" : "incident death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000648", + "lbl" : "cumulative case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000649", + "lbl" : "incident case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650", + "lbl" : "intent to have a ward vaccinated", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role." + }, + "comments" : [ "Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "guardian's intent to have a ward under their care vaccinated" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "The intent of a guardian to have a ward under their care vaccinated in the near future." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000652", + "lbl" : "intent to have a child vaccinated", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child." + }, + "comments" : [ "The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Intent to have one's child vaccinated." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -45454,10 +45631,18 @@ "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_00000622", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000648" }, { "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_00000623", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000649" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624", "pred" : "is_a", @@ -45481,35 +45666,35 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000629", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000642" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000630", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000643" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000631", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000646" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000632", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000647" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000633", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000644" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000634", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000645" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000635", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000640" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000636", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000641" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000637", "pred" : "is_a", @@ -45522,6 +45707,54 @@ "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_00000640", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000641", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000642", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000643", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000645", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000646", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000647", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000648", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000497" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000649", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000497" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/MF_0000073" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000652", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "pred" : "is_a", diff --git a/apollo_sv-full.obo b/apollo_sv-full.obo index 4d03cd8..161b1e6 100644 --- a/apollo_sv-full.obo +++ b/apollo_sv-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: apollo_sv/releases/2024-02-23/apollo_sv-full.owl +data-version: apollo_sv/releases/2024-04-19/apollo_sv-full.owl subsetdef: attribute_slim "" subsetdef: common_anatomy "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" @@ -26,7 +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 "2024-02-23" xsd:string +property_value: owl:versionInfo "2024-04-19" xsd:string property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -1563,8 +1563,8 @@ property_value: IAO:0000600 "A census that is the outcome of assessing control-s id: APOLLO_SV:00000190 name: contagious organism def: "A host who is able to transmit some infection to another organism." [] -is_a: APOLLO_SV:00000238 ! host -intersection_of: APOLLO_SV:00000238 ! host +is_a: APOLLO_SV:00000238 ! host organism +intersection_of: APOLLO_SV:00000238 ! host organism intersection_of: RO:0000053 APOLLO_SV:00000182 ! is bearer of contagiousness relationship: RO:0000053 APOLLO_SV:00000182 ! is bearer of contagiousness property_value: APOLLO_SV:0000040 "infectious" xsd:string @@ -1720,7 +1720,7 @@ property_value: IAO:0000600 "A specification of when an infectious disease contr id: APOLLO_SV:00000209 name: infected organism def: "An infectious agent host who is NOT able to transmit the infection to another organism of the same species." [] -is_a: APOLLO_SV:00000238 ! host +is_a: APOLLO_SV:00000238 ! host organism property_value: APOLLO_SV:0000040 "infected" xsd:string property_value: IAO:0000111 "organism in latent period of infection" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -1955,7 +1955,7 @@ property_value: IAO:0000600 "A population of organisms that are all immune." xsd [Term] id: APOLLO_SV:00000236 name: asymptomatic host -is_a: APOLLO_SV:00000238 ! host +is_a: APOLLO_SV:00000238 ! host organism [Term] id: APOLLO_SV:00000237 @@ -1970,7 +1970,7 @@ property_value: IAO:0000600 "An organism, virus, or prion that can infect anothe [Term] id: APOLLO_SV:00000238 -name: host +name: host organism def: "An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon." [] is_a: OBI:0100026 ! organism intersection_of: OBI:0100026 ! organism @@ -5585,6 +5585,7 @@ 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 +is_a: APOLLO_SV:00000648 ! cumulative case count 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 @@ -5595,6 +5596,7 @@ def: "A count of cases in an epidemic that is about a proper part of the tempora 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 +is_a: APOLLO_SV:00000649 ! incident case count 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 @@ -5645,57 +5647,57 @@ property_value: IAO:0000600 "A count of infections in a population during a part [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 +def: "A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000642 ! cumulative infection count 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 +def: "An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval." [] +is_a: APOLLO_SV:00000643 ! incident infection count 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 +def: "A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000646 ! cumulative death count 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 +def: "An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." [] +is_a: APOLLO_SV:00000647 ! incident death count 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 +def: "A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000644 ! cumulative hospitalization count 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 +def: "An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." [] +is_a: APOLLO_SV:00000645 ! incident hospitalization count 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 +def: "A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000640 ! cumulative vaccination count 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 +def: "An incident vaccination count 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 reference interval." [] +is_a: APOLLO_SV:00000641 ! incident vaccination count property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] @@ -5721,6 +5723,105 @@ def: "A vaccination against respiratory syncytial virus via the administration o is_a: APOLLO_SV:00000142 ! vaccination property_value: IAO:0000117 "William R. Hogan" xsd:string +[Term] +id: APOLLO_SV:00000640 +name: cumulative vaccination count +def: "A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000641 +name: incident vaccination count +def: "A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000642 +name: cumulative infection count +def: "A count of infections in a population that is the total number of infections that occur during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000643 +name: incident infection count +def: "A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000644 +name: cumulative hospitalization count +def: "A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +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:00000645 +name: incident hospitalization count +def: "A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +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:00000646 +name: cumulative death count +def: "A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000647 +name: incident death count +def: "A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000648 +name: cumulative case count +def: "A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000497 ! count of disease cases +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000649 +name: incident case count +def: "A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000497 ! count of disease cases +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000650 +name: intent to have a ward vaccinated +def: "An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role." [] +comment: Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. +is_a: MF:0000073 ! intentionality +property_value: IAO:0000111 "guardian's intent to have a ward under their care vaccinated" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "The intent of a guardian to have a ward under their care vaccinated in the near future." xsd:string + +[Term] +id: APOLLO_SV:00000652 +name: intent to have a child vaccinated +def: "An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child." [] +comment: The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. +is_a: APOLLO_SV:00000650 ! intent to have a ward vaccinated +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "Intent to have one's child vaccinated." xsd:string + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification @@ -7239,8 +7340,8 @@ 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 +property_value: IAO:0000412 "http://purl.obolibrary.org/obo/go.owl" xsd:string [Term] id: GO:0007617 diff --git a/apollo_sv-full.owl b/apollo_sv-full.owl index e923d0e..74d3f8b 100644 --- a/apollo_sv-full.owl +++ b/apollo_sv-full.owl @@ -26,7 +26,7 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -42,7 +42,7 @@ 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 - 2024-02-23 + 2024-04-19 @@ -11093,7 +11093,7 @@ can't recall whether we should use process or processual_entity for future An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. host - host + host organism @@ -18563,6 +18563,7 @@ 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. @@ -18576,6 +18577,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si + 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. @@ -18737,8 +18739,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic. William R. Hogan cumulative epidemic infection count @@ -18748,8 +18750,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic infection count @@ -18759,8 +18761,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic. William R. Hogan cumulative epidemic death count @@ -18770,8 +18772,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic death count @@ -18781,8 +18783,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic. William R. Hogan cumulative epidemic hospitalization count @@ -18792,8 +18794,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic hospitalization count @@ -18803,8 +18805,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic. William R. Hogan cumulative epidemic vaccination count @@ -18814,8 +18816,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + An incident vaccination count 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 reference interval. William R. Hogan incident epidemic vaccination count @@ -18857,6 +18859,153 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative vaccination count + + + + + + + + + A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident vaccination count + + + + + + + + + A count of infections in a population that is the total number of infections that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative infection count + + + + + + + + + A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident infection count + + + + + + + + + A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative hospitalization count + + + + + + + + + A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident hospitalization count + + + + + + + + + A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative death count + + + + + + + + + A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident death count + + + + + + + + + A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative case count + + + + + + + + + A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident case count + + + + + + + + + guardian's intent to have a ward under their care vaccinated + An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role. + William R. Hogan + The intent of a guardian to have a ward under their care vaccinated in the near future. + Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. + intent to have a ward vaccinated + + + + + + + + + An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child. + William R. Hogan + Intent to have one's child vaccinated. + The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. + intent to have a child vaccinated + + + + diff --git a/apollo_sv.json b/apollo_sv.json index 6dbc268..e0d7de6 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" : "2024-02-23" + "val" : "2024-04-19" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-02-23/apollo_sv.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-04-19/apollo_sv.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", @@ -4069,7 +4069,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000238", - "lbl" : "host", + "lbl" : "host organism", "type" : "CLASS", "meta" : { "definition" : { @@ -11771,7 +11771,7 @@ "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." + "val" : "A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11784,7 +11784,7 @@ "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." + "val" : "An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11797,7 +11797,7 @@ "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." + "val" : "A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11810,7 +11810,7 @@ "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." + "val" : "An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11823,7 +11823,7 @@ "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." + "val" : "A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11836,7 +11836,7 @@ "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." + "val" : "An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11849,7 +11849,7 @@ "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." + "val" : "A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11862,7 +11862,7 @@ "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." + "val" : "An incident vaccination count 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 reference interval." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -11914,6 +11914,183 @@ "val" : "William R. Hogan" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000640", + "lbl" : "cumulative vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000641", + "lbl" : "incident vaccination count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000642", + "lbl" : "cumulative infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population that is the total number of infections that occur during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000643", + "lbl" : "incident infection count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000644", + "lbl" : "cumulative hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000645", + "lbl" : "incident hospitalization count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000646", + "lbl" : "cumulative death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000647", + "lbl" : "incident death count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000648", + "lbl" : "cumulative case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval." + }, + "comments" : [ "The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000649", + "lbl" : "incident case count", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval." + }, + "comments" : [ "The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive \"epidemiological weeks\" as defined by CDC or another national or subnational public health organization." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650", + "lbl" : "intent to have a ward vaccinated", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role." + }, + "comments" : [ "Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "guardian's intent to have a ward under their care vaccinated" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "The intent of a guardian to have a ward under their care vaccinated in the near future." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000652", + "lbl" : "intent to have a child vaccinated", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child." + }, + "comments" : [ "The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Intent to have one's child vaccinated." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -45454,10 +45631,18 @@ "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_00000622", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000648" }, { "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_00000623", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000649" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000624", "pred" : "is_a", @@ -45481,35 +45666,35 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000629", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000642" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000630", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000643" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000631", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000646" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000632", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000647" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000633", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000644" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000634", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000645" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000635", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000640" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000636", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000641" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000637", "pred" : "is_a", @@ -45522,6 +45707,54 @@ "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_00000640", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000641", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000626" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000642", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000643", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000645", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000627" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000646", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000647", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000625" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000648", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000497" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000649", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000497" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/MF_0000073" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000652", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "pred" : "is_a", diff --git a/apollo_sv.obo b/apollo_sv.obo index 44c1268..c7c91ce 100644 --- a/apollo_sv.obo +++ b/apollo_sv.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-02-23 +data-version: releases/2024-04-19 subsetdef: attribute_slim "" subsetdef: common_anatomy "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" @@ -26,7 +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 "2024-02-23" xsd:string +property_value: owl:versionInfo "2024-04-19" xsd:string property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -1563,8 +1563,8 @@ property_value: IAO:0000600 "A census that is the outcome of assessing control-s id: APOLLO_SV:00000190 name: contagious organism def: "A host who is able to transmit some infection to another organism." [] -is_a: APOLLO_SV:00000238 ! host -intersection_of: APOLLO_SV:00000238 ! host +is_a: APOLLO_SV:00000238 ! host organism +intersection_of: APOLLO_SV:00000238 ! host organism intersection_of: RO:0000053 APOLLO_SV:00000182 ! is bearer of contagiousness relationship: RO:0000053 APOLLO_SV:00000182 ! is bearer of contagiousness property_value: APOLLO_SV:0000040 "infectious" xsd:string @@ -1720,7 +1720,7 @@ property_value: IAO:0000600 "A specification of when an infectious disease contr id: APOLLO_SV:00000209 name: infected organism def: "An infectious agent host who is NOT able to transmit the infection to another organism of the same species." [] -is_a: APOLLO_SV:00000238 ! host +is_a: APOLLO_SV:00000238 ! host organism property_value: APOLLO_SV:0000040 "infected" xsd:string property_value: IAO:0000111 "organism in latent period of infection" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -1955,7 +1955,7 @@ property_value: IAO:0000600 "A population of organisms that are all immune." xsd [Term] id: APOLLO_SV:00000236 name: asymptomatic host -is_a: APOLLO_SV:00000238 ! host +is_a: APOLLO_SV:00000238 ! host organism [Term] id: APOLLO_SV:00000237 @@ -1970,7 +1970,7 @@ property_value: IAO:0000600 "An organism, virus, or prion that can infect anothe [Term] id: APOLLO_SV:00000238 -name: host +name: host organism def: "An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon." [] is_a: OBI:0100026 ! organism intersection_of: OBI:0100026 ! organism @@ -5585,6 +5585,7 @@ 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 +is_a: APOLLO_SV:00000648 ! cumulative case count 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 @@ -5595,6 +5596,7 @@ def: "A count of cases in an epidemic that is about a proper part of the tempora 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 +is_a: APOLLO_SV:00000649 ! incident case count 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 @@ -5645,57 +5647,57 @@ property_value: IAO:0000600 "A count of infections in a population during a part [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 +def: "A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000642 ! cumulative infection count 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 +def: "An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval." [] +is_a: APOLLO_SV:00000643 ! incident infection count 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 +def: "A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000646 ! cumulative death count 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 +def: "An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." [] +is_a: APOLLO_SV:00000647 ! incident death count 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 +def: "A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000644 ! cumulative hospitalization count 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 +def: "An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval." [] +is_a: APOLLO_SV:00000645 ! incident hospitalization count 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 +def: "A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic." [] +is_a: APOLLO_SV:00000640 ! cumulative vaccination count 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 +def: "An incident vaccination count 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 reference interval." [] +is_a: APOLLO_SV:00000641 ! incident vaccination count property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] @@ -5721,6 +5723,105 @@ def: "A vaccination against respiratory syncytial virus via the administration o is_a: APOLLO_SV:00000142 ! vaccination property_value: IAO:0000117 "William R. Hogan" xsd:string +[Term] +id: APOLLO_SV:00000640 +name: cumulative vaccination count +def: "A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000641 +name: incident vaccination count +def: "A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000626 ! count of vaccinations in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000642 +name: cumulative infection count +def: "A count of infections in a population that is the total number of infections that occur during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000643 +name: incident infection count +def: "A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000628 ! count of infections in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000644 +name: cumulative hospitalization count +def: "A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +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:00000645 +name: incident hospitalization count +def: "A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +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:00000646 +name: cumulative death count +def: "A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000647 +name: incident death count +def: "A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000625 ! count of deaths in a population +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000648 +name: cumulative case count +def: "A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval." [] +comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000497 ! count of disease cases +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000649 +name: incident case count +def: "A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval." [] +comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. +is_a: APOLLO_SV:00000497 ! count of disease cases +property_value: IAO:0000117 "William R. Hogan" xsd:string + +[Term] +id: APOLLO_SV:00000650 +name: intent to have a ward vaccinated +def: "An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role." [] +comment: Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. +is_a: MF:0000073 ! intentionality +property_value: IAO:0000111 "guardian's intent to have a ward under their care vaccinated" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "The intent of a guardian to have a ward under their care vaccinated in the near future." xsd:string + +[Term] +id: APOLLO_SV:00000652 +name: intent to have a child vaccinated +def: "An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child." [] +comment: The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. +is_a: APOLLO_SV:00000650 ! intent to have a ward vaccinated +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "Intent to have one's child vaccinated." xsd:string + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification @@ -16851,8 +16952,8 @@ 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 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001025 diff --git a/apollo_sv.owl b/apollo_sv.owl index da97fef..18fd31a 100644 --- a/apollo_sv.owl +++ b/apollo_sv.owl @@ -26,7 +26,7 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -42,7 +42,7 @@ 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 - 2024-02-23 + 2024-04-19 @@ -11093,7 +11093,7 @@ can't recall whether we should use process or processual_entity for future An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. host - host + host organism @@ -18563,6 +18563,7 @@ 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. @@ -18576,6 +18577,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si + 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. @@ -18737,8 +18739,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic. William R. Hogan cumulative epidemic infection count @@ -18748,8 +18750,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic infection count @@ -18759,8 +18761,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic. William R. Hogan cumulative epidemic death count @@ -18770,8 +18772,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic death count @@ -18781,8 +18783,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic. William R. Hogan cumulative epidemic hospitalization count @@ -18792,8 +18794,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval. William R. Hogan incident epidemic hospitalization count @@ -18803,8 +18805,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic. William R. Hogan cumulative epidemic vaccination count @@ -18814,8 +18816,8 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - 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. + + An incident vaccination count 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 reference interval. William R. Hogan incident epidemic vaccination count @@ -18857,6 +18859,153 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative vaccination count + + + + + + + + + A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident vaccination count + + + + + + + + + A count of infections in a population that is the total number of infections that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative infection count + + + + + + + + + A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident infection count + + + + + + + + + A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative hospitalization count + + + + + + + + + A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident hospitalization count + + + + + + + + + A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative death count + + + + + + + + + A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident death count + + + + + + + + + A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative case count + + + + + + + + + A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident case count + + + + + + + + + guardian's intent to have a ward under their care vaccinated + An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role. + William R. Hogan + The intent of a guardian to have a ward under their care vaccinated in the near future. + Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. + intent to have a ward vaccinated + + + + + + + + + An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child. + William R. Hogan + Intent to have one's child vaccinated. + The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. + intent to have a child vaccinated + + + + diff --git a/src/ontology/imports/geo_import.owl b/src/ontology/imports/geo_import.owl index 23078de..936a3f8 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 "2024-02-23") + +Annotation(owl:versionInfo "2024-04-19") Declaration(Class()) Declaration(Class()) @@ -599,8 +599,8 @@ AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "editor preferred label"@en) -AnnotationAssertion(rdfs:label "editor preferred term") AnnotationAssertion(rdfs:label "editor preferred term"@en) +AnnotationAssertion(rdfs:label "editor preferred term") AnnotationAssertion(rdfs:label "editor preferred term~editor preferred label") # Annotation Property: (example of usage) @@ -657,8 +657,8 @@ We also have the outstanding issue of how to aim different definitions to differ AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "definition") AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") AnnotationAssertion(rdfs:label "textual definition") # Annotation Property: (editor note) @@ -688,8 +688,8 @@ AnnotationAssertion(rdfs:label "ter AnnotationAssertion( "alternative label"@en) AnnotationAssertion( ) AnnotationAssertion( "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."@en) -AnnotationAssertion( "OBO Operations committee") AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "OBO Operations committee") AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") AnnotationAssertion(rdfs:label "alternative label"@en) @@ -1013,8 +1013,8 @@ SubAnnotationPropertyOf( (Source) -AnnotationAssertion(rdfs:label "Source") AnnotationAssertion(rdfs:label "Source"@en-us) +AnnotationAssertion(rdfs:label "Source") # Annotation Property: (has_alternative_id) @@ -1160,6 +1160,7 @@ AnnotationAssertion(rdfs:comment "P AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) InverseObjectProperties( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (contains process) @@ -1202,8 +1203,8 @@ ObjectPropertyRange( "c-has-part_at") AnnotationAssertion( "hasContinuantPartAt") -AnnotationAssertion( "[copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)") AnnotationAssertion( "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])"@en) +AnnotationAssertion( "[copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)") AnnotationAssertion( "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.") AnnotationAssertion( "[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'") AnnotationAssertion( "http://purl.obolibrary.org/obo/bfo.owl") @@ -1256,9 +1257,9 @@ AnnotationAssertion( "Mary’s arm continuant_part_of Mary in the time of her life prior to her operation"@en) AnnotationAssertion( "the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists."@en) AnnotationAssertion( "[copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)") -AnnotationAssertion( "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.") AnnotationAssertion( "BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])"@en) AnnotationAssertion( "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion."@en) +AnnotationAssertion( "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.") AnnotationAssertion( "BFO2 Reference: continuant") AnnotationAssertion( "BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.") AnnotationAssertion( "[copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'") @@ -1584,8 +1585,8 @@ ObjectPropertyRange( ObjectIntersect # Object Property: (has_specified_input) -AnnotationAssertion( "has_specified_input") AnnotationAssertion( "has_specified_input"@en) +AnnotationAssertion( "has_specified_input") AnnotationAssertion( "see is_input_of example_of_usage"@en) AnnotationAssertion( ) AnnotationAssertion( "The inverse property of is_specified_input_of"@en) @@ -1614,8 +1615,8 @@ SubObjectPropertyOf( (has_specified_output) -AnnotationAssertion( "has_specified_output") AnnotationAssertion( "has_specified_output"@en) +AnnotationAssertion( "has_specified_output") AnnotationAssertion( ) AnnotationAssertion( "The inverse property of is_specified_output_of"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) @@ -1631,8 +1632,8 @@ ObjectPropertyDomain( (is_specified_output_of) -AnnotationAssertion( "is_specified_output_of") AnnotationAssertion( "is_specified_output_of"@en) +AnnotationAssertion( "is_specified_output_of") AnnotationAssertion( ) AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion( "Alan Ruttenberg"@en) @@ -2360,9 +2361,9 @@ AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) AnnotationAssertion( "the restaurants in Palo Alto"@en) AnnotationAssertion( "your collection of Meissen ceramic plates."@en) +AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") -AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) AnnotationAssertion(Annotation( ) "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.") AnnotationAssertion(Annotation( ) "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])"@en) AnnotationAssertion(Annotation( ) "(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] ") @@ -2689,7 +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) @@ -3088,8 +3089,8 @@ AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000261") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000261") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_digital entity"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3151,8 +3152,8 @@ AnnotationAssertion( "digital_entity"@en) AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000244") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000244") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_binary digital entity"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3191,7 +3192,6 @@ AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) -AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some @@ -3199,6 +3199,7 @@ process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief"@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) AnnotationAssertion( "PERSON: Chris Stoeckert"@en) AnnotationAssertion( "PERSON: Jonathan Rees"@en) @@ -3301,12 +3302,12 @@ SubClassOf( "obsolete_study interpretation"@en) AnnotationAssertion( ) AnnotationAssertion( "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses"@en) +AnnotationAssertion( "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead."@en) AnnotationAssertion( "2009-03-16: definition was \"A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.\"") AnnotationAssertion( "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.") -AnnotationAssertion( "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead."@en) AnnotationAssertion( "Lawrence Hunter"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg") AnnotationAssertion( "PERSON: Jennifer Fostel"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg") AnnotationAssertion( "PERSON: Melanie Courtot") AnnotationAssertion( "conclusion") AnnotationAssertion( "OBI_0000005") @@ -3392,8 +3393,8 @@ AnnotationAssertion( "Replaced by defined version of figure"@en) AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "OBI_0000027") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000027") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_report figure"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3481,12 +3482,12 @@ SubClassOf( "report element"@en) AnnotationAssertion( ) AnnotationAssertion( "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)."@en) +AnnotationAssertion( "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text"@en) AnnotationAssertion( "2009-03-16: needs some more work (clarify relations).") AnnotationAssertion( "2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.") AnnotationAssertion( "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.") AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion") AnnotationAssertion( "Replaced by textual entity and figure") -AnnotationAssertion( "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) AnnotationAssertion( "PERSON: Allyson Lister"@en) AnnotationAssertion( "PERSON: Melanie Courtot") @@ -3504,8 +3505,8 @@ AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'"@en) AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "OBI_0000222") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000222") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_binary executable"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3532,8 +3533,8 @@ AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion") AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "OBI_0000265") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000265") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete_report table"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3625,8 +3626,8 @@ AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'"@en) AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "OBI_0000195") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000195") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_digital document"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -5216,8 +5217,8 @@ SubClassOf( "database extract, transform, and load process"@en) AnnotationAssertion( "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second."@en) -AnnotationAssertion( "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second") AnnotationAssertion( "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output."@en) +AnnotationAssertion( "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second") AnnotationAssertion( "PERSON:Alan Ruttenberg") AnnotationAssertion( "ETL"@en) AnnotationAssertion( "WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load") @@ -5892,7 +5893,7 @@ SubClassOf( (obsolete_class) AnnotationAssertion( "http://www.geneontology.org/formats/oboInOwl") -AnnotationAssertion( _:genid2147483648) +AnnotationAssertion( _:genid2147484124) AnnotationAssertion(rdfs:label "obsolete_class"@en) @@ -6092,8 +6093,8 @@ DifferentIndividuals( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl index 9e73feb..4932c20 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 "2024-02-23") +Annotation(owl:versionInfo "2024-04-19") Declaration(Class()) Declaration(Class()) @@ -262,8 +262,8 @@ We also have the outstanding issue of how to aim different definitions to differ AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "definition") AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") AnnotationAssertion(rdfs:label "textual definition") # Annotation Property: (editor note) @@ -276,7 +276,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "editor note"@en) -# Annotation Property: (definition editor) +# Annotation Property: (term editor) AnnotationAssertion( "term editor"@en) AnnotationAssertion( ) @@ -287,7 +287,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "term editor"@en) -# Annotation Property: (alternative label) +# Annotation Property: (alternative term) AnnotationAssertion( "alternative term"@en) AnnotationAssertion( ) @@ -303,8 +303,8 @@ AnnotationAssertion( ) AnnotationAssertion( "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w") AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "definition source"@en) @@ -513,6 +513,7 @@ AnnotationAssertion(rdfs:comment "P AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) InverseObjectProperties( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (contains process) @@ -527,7 +528,7 @@ AnnotationAssertion(rdfs:label "con AnnotationAssertion(rdfs:label "results_in"@en) -# Object Property: (characteristic of) +# Object Property: (inheres in) AnnotationAssertion( "inheres in"@en) AnnotationAssertion( "this fragility inheres in this vase"@en) @@ -539,7 +540,7 @@ AnnotationAssertion( "inheres in"@en) InverseObjectProperties( ) -# Object Property: (has characteristic) +# Object Property: (bearer of) AnnotationAssertion( "bearer of"@en) AnnotationAssertion( "this apple is bearer of this red color"@en) @@ -691,8 +692,8 @@ SubObjectPropertyOf( (results in formation of) -AnnotationAssertion( "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) +AnnotationAssertion( "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") AnnotationAssertion( ) AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "GOC:mtg_berkeley_2013") @@ -978,7 +979,7 @@ AnnotationAssertion(rdfs:isDefinedBy "role"@en) SubClassOf( ) -# Class: (fiat object part) +# Class: (fiat object) AnnotationAssertion( "fiat-object") AnnotationAssertion( "FiatObjectPart") @@ -1013,9 +1014,9 @@ AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) AnnotationAssertion( "the restaurants in Palo Alto"@en) AnnotationAssertion( "your collection of Meissen ceramic plates."@en) +AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") -AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) AnnotationAssertion(Annotation( ) "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.") AnnotationAssertion(Annotation( ) "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])"@en) AnnotationAssertion(Annotation( ) "(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] ") @@ -1321,8 +1322,8 @@ AnnotationAssertion( "Alexander Diehl") AnnotationAssertion( "Lindsay Cowell") AnnotationAssertion( "opportunitistic pathogenic disposition"@en) -AnnotationAssertion(rdfs:comment "The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.") AnnotationAssertion(rdfs:comment "This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin)."@en) +AnnotationAssertion(rdfs:comment "The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.") AnnotationAssertion(rdfs:label "opportunistic infectious disposition"@en) SubClassOf( ) SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectAllValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))))))) @@ -1678,7 +1679,7 @@ AnnotationAssertion( "Lindsay Cowell") AnnotationAssertion(rdfs:comment "An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA."@en) AnnotationAssertion(rdfs:label "establishment of localization in host"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectSomeValuesFrom( )) SubClassOf( ) # Class: (appearance of disorder) @@ -1803,7 +1804,7 @@ AnnotationAssertion( "life-death temporal boundary") SubClassOf( ) -# Class: (obsolete_class) +# Class: (Obsolete Class) AnnotationAssertion(rdfs:label "Obsolete Class") @@ -1857,7 +1858,7 @@ AnnotationAssertion(rdfs:label "unc AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) AnnotationAssertion(rdfs:label "pending final vetting"@en) -# Individual: (obsolete_core) +# Individual: (core) AnnotationAssertion( "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes."@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) diff --git a/src/ontology/imports/mf_import.owl b/src/ontology/imports/mf_import.owl index 4bcee0d..2038588 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 "2024-02-23") +Annotation(owl:versionInfo "2024-04-19") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pno_import.owl b/src/ontology/imports/pno_import.owl index be834d2..23ac377 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 "2024-02-23") +Annotation(owl:versionInfo "2024-04-19") Declaration(Class()) Declaration(Class()) @@ -476,8 +476,8 @@ AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "editor preferred label"@en) -AnnotationAssertion(rdfs:label "editor preferred term") AnnotationAssertion(rdfs:label "editor preferred term"@en) +AnnotationAssertion(rdfs:label "editor preferred term") # Annotation Property: (example of usage) @@ -545,7 +545,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "editor note"@en) -# Annotation Property: (definition editor) +# Annotation Property: (term editor) AnnotationAssertion( "term editor"@en) AnnotationAssertion( ) @@ -561,8 +561,8 @@ AnnotationAssertion(rdfs:label "ter AnnotationAssertion( "alternative label"@en) AnnotationAssertion( ) AnnotationAssertion( "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."@en) -AnnotationAssertion( "OBO Operations committee") AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "OBO Operations committee") AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") AnnotationAssertion(rdfs:label "alternative label"@en) @@ -990,6 +990,7 @@ AnnotationAssertion(rdfs:comment "P AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) InverseObjectProperties( ) +ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (contains process) @@ -1278,8 +1279,8 @@ IrreflexiveObjectProperty() # Object Property: (has_specified_input) -AnnotationAssertion( "has_specified_input") AnnotationAssertion( "has_specified_input"@en) +AnnotationAssertion( "has_specified_input") AnnotationAssertion( "see is_input_of example_of_usage"@en) AnnotationAssertion( ) AnnotationAssertion( "The inverse property of is_specified_input_of"@en) @@ -1300,8 +1301,8 @@ AnnotationAssertion(rdfs:label "is_ # Object Property: (has_specified_output) -AnnotationAssertion( "has_specified_output") AnnotationAssertion( "has_specified_output"@en) +AnnotationAssertion( "has_specified_output") AnnotationAssertion( ) AnnotationAssertion( "The inverse property of is_specified_output_of"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) @@ -1317,15 +1318,15 @@ ObjectPropertyDomain( (is_specified_output_of) -AnnotationAssertion( "is_specified_output_of") AnnotationAssertion( "is_specified_output_of"@en) +AnnotationAssertion( "is_specified_output_of") AnnotationAssertion( ) AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion( "Alan Ruttenberg"@en) AnnotationAssertion( "PERSON:Bjoern Peters") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "is_specified_output_of") AnnotationAssertion(rdfs:label "is_specified_output_of"@en) +AnnotationAssertion(rdfs:label "is_specified_output_of") EquivalentObjectProperties( ObjectInverseOf()) SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -1343,7 +1344,7 @@ AnnotationAssertion(rdfs:label "char InverseObjectProperties( ) FunctionalObjectProperty() -# Object Property: (has characteristic) +# Object Property: (bearer_of) AnnotationAssertion( "bearer of"@en) AnnotationAssertion( "this apple is bearer of this red color"@en) @@ -1371,7 +1372,7 @@ InverseObjectProperties( ) ObjectPropertyRange( ) -# Object Property: (has participant) +# Object Property: (has_participant) AnnotationAssertion( "has participant"@en) AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) @@ -2031,9 +2032,9 @@ AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) AnnotationAssertion( "the restaurants in Palo Alto"@en) AnnotationAssertion( "your collection of Meissen ceramic plates."@en) +AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") -AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) AnnotationAssertion(Annotation( ) "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.") AnnotationAssertion(Annotation( ) "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])"@en) AnnotationAssertion(Annotation( ) "(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] ") @@ -2447,8 +2448,8 @@ AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000261") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000261") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_digital entity"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2510,8 +2511,8 @@ AnnotationAssertion( "digital_entity"@en) AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000244") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000244") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_binary digital entity"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2550,7 +2551,6 @@ AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) -AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some @@ -2558,6 +2558,7 @@ process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief"@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) AnnotationAssertion( "PERSON: Chris Stoeckert"@en) AnnotationAssertion( "PERSON: Jonathan Rees"@en) @@ -2657,12 +2658,12 @@ SubClassOf( "obsolete_study interpretation"@en) AnnotationAssertion( ) AnnotationAssertion( "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses"@en) +AnnotationAssertion( "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead."@en) AnnotationAssertion( "2009-03-16: definition was \"A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.\"") AnnotationAssertion( "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.") -AnnotationAssertion( "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead."@en) AnnotationAssertion( "Lawrence Hunter"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg") AnnotationAssertion( "PERSON: Jennifer Fostel"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg") AnnotationAssertion( "PERSON: Melanie Courtot") AnnotationAssertion( "conclusion") AnnotationAssertion( "OBI_0000005") @@ -2748,8 +2749,8 @@ AnnotationAssertion( "Replaced by defined version of figure"@en) AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "OBI_0000027") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000027") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_report figure"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2837,12 +2838,12 @@ SubClassOf( "report element"@en) AnnotationAssertion( ) AnnotationAssertion( "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)."@en) +AnnotationAssertion( "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text"@en) AnnotationAssertion( "2009-03-16: needs some more work (clarify relations).") AnnotationAssertion( "2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.") AnnotationAssertion( "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.") AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion") AnnotationAssertion( "Replaced by textual entity and figure") -AnnotationAssertion( "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) AnnotationAssertion( "PERSON: Allyson Lister"@en) AnnotationAssertion( "PERSON: Melanie Courtot") @@ -2860,8 +2861,8 @@ AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'"@en) AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "OBI_0000222") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000222") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_binary executable"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2888,8 +2889,8 @@ AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion") AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "OBI_0000265") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000265") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete_report table"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2981,8 +2982,8 @@ AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'"@en) AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "OBI_0000195") AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion( "OBI_0000195") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_digital document"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -4571,8 +4572,8 @@ SubClassOf( "database extract, transform, and load process"@en) AnnotationAssertion( "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second."@en) -AnnotationAssertion( "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second") AnnotationAssertion( "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output."@en) +AnnotationAssertion( "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second") AnnotationAssertion( "PERSON:Alan Ruttenberg") AnnotationAssertion( "ETL"@en) AnnotationAssertion( "WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load") @@ -4702,8 +4703,8 @@ AnnotationAssertion( "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en) AnnotationAssertion( "An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "proper name"@en) AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) AnnotationAssertion( "Mathias Brochhausen") @@ -4793,8 +4794,8 @@ SubClassOf( "A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."@en) AnnotationAssertion( "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "dubbing process"@en) AnnotationAssertion( "naming"@en) AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) @@ -4819,8 +4820,8 @@ SubClassOf( "A personal name is a proper name identifying an individual person."@en) AnnotationAssertion( "An identifier referring to an individual entity that is ascribed personhood by the user of the identifier."@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "http://en.wikipedia.org/wiki/Personal_name") AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) AnnotationAssertion(rdfs:comment "Personal names \"today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names.\" (http://en.wikipedia.org/wiki/Personal_name)"@en) @@ -4835,8 +4836,8 @@ SubClassOf( "A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name"@en) AnnotationAssertion( "A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name"@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "first name"@en) AnnotationAssertion( "http://en.wikipedia.org/wiki/Given_name") AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) @@ -4849,8 +4850,8 @@ SubClassOf( ObjectSomeValuesFrom( "A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children."@en) AnnotationAssertion( "An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children."@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "last name"@en) AnnotationAssertion( "surname"@en) AnnotationAssertion( "http://en.wikipedia.org/wiki/Family_name") @@ -4866,8 +4867,8 @@ AnnotationAssertion( "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things."@en) AnnotationAssertion( "Alan Ruttenberg"@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion( "code map"@en) AnnotationAssertion( "code system"@en) AnnotationAssertion( "codeset"@en) @@ -5181,7 +5182,7 @@ SubClassOf( (pressure) -AnnotationAssertion( _:genid2147483649) +AnnotationAssertion( _:genid2147484058) AnnotationAssertion( "quality") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pressure"@en) @@ -5382,8 +5383,8 @@ DifferentIndividuals( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 39a491f..82ab86b 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 "2024-02-23") +Annotation(owl:versionInfo "2024-04-19") Declaration(Class()) Declaration(Class()) @@ -262,8 +262,8 @@ AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "example of usage") AnnotationAssertion(rdfs:label "example of usage"@en) +AnnotationAssertion(rdfs:label "example of usage") # Annotation Property: (has curation status) @@ -300,8 +300,8 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "definition") AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") # Annotation Property: (editor note) @@ -312,7 +312,7 @@ AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:label "editor note"@en) -# Annotation Property: (definition editor) +# Annotation Property: (term editor) AnnotationAssertion( "term editor"@en) AnnotationAssertion( ) @@ -327,8 +327,8 @@ AnnotationAssertion(rdfs:label "ter AnnotationAssertion( "alternative label"@en) AnnotationAssertion( ) AnnotationAssertion( "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."@en) -AnnotationAssertion( "OBO Operations committee") AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "OBO Operations committee") AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") AnnotationAssertion(rdfs:label "alternative label"@en) @@ -453,7 +453,7 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (has broad synonym) +# Annotation Property: (has_broad_synonym) AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") AnnotationAssertion( ) @@ -484,7 +484,7 @@ AnnotationAssertion(rdfs:label "has_narrow_synonym") AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") -# Annotation Property: (has related synonym) +# Annotation Property: (has_related_synonym) AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") AnnotationAssertion( ) @@ -527,12 +527,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -554,8 +554,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has part") AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -627,10 +627,11 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:label "occurs in"@en) +AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) +ObjectPropertyDomain( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -666,8 +667,8 @@ AnnotationAssertion( "bearer_of"@en) AnnotationAssertion( "is bearer of"@en) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has characteristic") AnnotationAssertion(rdfs:label "has characteristic"@en) +AnnotationAssertion(rdfs:label "has characteristic") AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -695,8 +696,8 @@ AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) AnnotationAssertion( "has_participant"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") -AnnotationAssertion(rdfs:label "has participant") AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -941,7 +942,7 @@ AnnotationAssertion(rdfs:label "ends SubObjectPropertyOf( ) TransitiveObjectProperty() -# Object Property: (immediately_preceded_by) +# Object Property: (immediately preceded by) AnnotationAssertion( "David Osumi-Sutherland") AnnotationAssertion( "starts_at_end_of") @@ -950,7 +951,7 @@ AnnotationAssertion(rdfs:label "imme SubObjectPropertyOf( ) InverseObjectProperties( ) -# Object Property: (immediately_precedes) +# Object Property: (immediately precedes) AnnotationAssertion( ) AnnotationAssertion( "David Osumi-Sutherland") @@ -1090,7 +1091,7 @@ AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) -# Object Property: (has active participant) +# Object Property: (obsolete has active participant) AnnotationAssertion( "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y") AnnotationAssertion( ) @@ -1118,7 +1119,7 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (temporal relation) +# Object Property: (temporally related to) AnnotationAssertion( ) AnnotationAssertion( ) @@ -1347,8 +1348,8 @@ SubObjectPropertyOf( "inverse of enables") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enabled by") AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:label "enabled by") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1579,8 +1580,8 @@ SubObjectPropertyOf( (interacts with) AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) +AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") AnnotationAssertion( ) AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") AnnotationAssertion( "in pairwise interaction with") @@ -2085,7 +2086,7 @@ AnnotationAssertion(rdfs:label "qua SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) -# Class: (specifically dependent continuant) +# Class: (characteristic) AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) AnnotationAssertion(rdfs: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."@en) @@ -2492,10 +2493,10 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) @@ -2504,19 +2505,19 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) AnnotationAssertion( "## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally'