diff --git a/apollo_sv-base.json b/apollo_sv-base.json index 3881b9d..31ca33c 100644 --- a/apollo_sv-base.json +++ b/apollo_sv-base.json @@ -52,9 +52,9 @@ "val" : "2023-01-10" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-05-05" + "val" : "2023-06-02" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2023-05-05/apollo_sv-base.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2023-06-02/apollo_sv-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", @@ -11034,6 +11034,26 @@ "val" : "2022-09-18T18:51:00" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000616", + "lbl" : "wastewater disease surveillance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disease surveillance that detects evidence of the presence of pathogens in sewage." + }, + "comments" : [ "See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sewage disease surveillance" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000617", "lbl" : "population count", @@ -11047,6 +11067,74 @@ "val" : "Matthew Diller" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000618", + "lbl" : "wastewater surveillance data set", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disease surveillance data set that is about some wastewater disease surveillance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sewage surveillance data" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000619", + "lbl" : "population density datum", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000620", + "lbl" : "physical distancing infectious disease control measure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000621", + "lbl" : "lockdown infectious disease control measure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations." + }, + "comments" : [ "The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -31287,10 +31375,30 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000615", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/DOID_3292" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000616", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000545" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000617", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000618", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000554" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000619", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000620", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000194" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000621", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000229" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "pred" : "is_a", diff --git a/apollo_sv-base.obo b/apollo_sv-base.obo index 55e8bf6..0173acd 100644 --- a/apollo_sv-base.obo +++ b/apollo_sv-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: apollo_sv/releases/2023-05-05/apollo_sv-base.owl +data-version: apollo_sv/releases/2023-06-02/apollo_sv-base.owl remark: When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). ontology: apollo_sv/apollo_sv-base property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string @@ -15,7 +15,7 @@ property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string property_value: owl:versionInfo "2023-01-10" xsd:string -property_value: owl:versionInfo "2023-05-05" xsd:string +property_value: owl:versionInfo "2023-06-02" xsd:string property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -5436,6 +5436,16 @@ property_value: http://purl.org/dc/elements/1.1/date "2022-09-18T18:51:00" xsd:d property_value: IAO:0000111 "monkeypox disease inhering in a human being" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string +[Term] +id: APOLLO_SV:00000616 +name: wastewater disease surveillance +def: "A disease surveillance that detects evidence of the presence of pathogens in sewage." [] +comment: See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html. +is_a: APOLLO_SV:00000545 ! disease surveillance +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string +property_value: IAO:0000118 "sewage disease surveillance" xsd:string + [Term] id: APOLLO_SV:00000617 name: population count @@ -5443,6 +5453,40 @@ def: "A count of simulated or physical individuals in a population." [] is_a: APOLLO_SV:00000032 ! count property_value: IAO:0000117 "Matthew Diller" xsd:string +[Term] +id: APOLLO_SV:00000618 +name: wastewater surveillance data set +def: "A disease surveillance data set that is about some wastewater disease surveillance." [] +is_a: APOLLO_SV:00000554 ! disease surveillance data +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string +property_value: IAO:0000118 "sewage surveillance data" xsd:string + +[Term] +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 +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string + +[Term] +id: APOLLO_SV:00000620 +name: physical distancing infectious disease control measure +def: "An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act." [] +is_a: APOLLO_SV:00000194 ! individual treatment control strategy +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string + +[Term] +id: APOLLO_SV:00000621 +name: lockdown infectious disease control measure +def: "A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations." [] +comment: The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services. +is_a: APOLLO_SV:00000229 ! place closure control strategy +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification diff --git a/apollo_sv-base.owl b/apollo_sv-base.owl index 8c4e10b..7d18b5e 100644 --- a/apollo_sv-base.owl +++ b/apollo_sv-base.owl @@ -2,6 +2,7 @@ - + Amanda Hicks John Levander Josh Hanna @@ -33,7 +39,7 @@ 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). 2023-01-10 - 2023-05-05 + 2023-06-02 @@ -12974,6 +12980,20 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A disease surveillance that detects evidence of the presence of pathogens in sewage. + Matthew Diller + sewage disease surveillance + William R. Hogan + See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html. + wastewater disease surveillance + + + + @@ -12985,6 +13005,56 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A disease surveillance data set that is about some wastewater disease surveillance. + Matthew Diller + sewage surveillance data + William R. Hogan + wastewater surveillance data set + + + + + + + + + A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region. + Matthew Diller + William R. Hogan + population density datum + + + + + + + + + An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act. + Matthew Diller + William R. Hogan + physical distancing infectious disease control measure + + + + + + + + + A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations. + Matthew Diller + William R. Hogan + The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services. + lockdown infectious disease control measure + + + + diff --git a/apollo_sv-full.json b/apollo_sv-full.json index ded5942..74a8154 100644 --- a/apollo_sv-full.json +++ b/apollo_sv-full.json @@ -49,9 +49,9 @@ "val" : "2023-01-10" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-05-05" + "val" : "2023-06-02" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2023-05-05/apollo_sv-full.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2023-06-02/apollo_sv-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", @@ -11498,6 +11498,26 @@ "val" : "2022-09-18T18:51:00" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000616", + "lbl" : "wastewater disease surveillance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disease surveillance that detects evidence of the presence of pathogens in sewage." + }, + "comments" : [ "See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sewage disease surveillance" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000617", "lbl" : "population count", @@ -11511,6 +11531,74 @@ "val" : "Matthew Diller" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000618", + "lbl" : "wastewater surveillance data set", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disease surveillance data set that is about some wastewater disease surveillance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sewage surveillance data" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000619", + "lbl" : "population density datum", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000620", + "lbl" : "physical distancing infectious disease control measure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000621", + "lbl" : "lockdown infectious disease control measure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations." + }, + "comments" : [ "The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -43771,10 +43859,30 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000615", "pred" : "http://purl.obolibrary.org/obo/RO_0000052", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000616", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000545" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000617", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000618", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000554" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000619", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000620", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000194" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000621", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000229" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "pred" : "is_a", diff --git a/apollo_sv-full.obo b/apollo_sv-full.obo index 996c1b8..33e424c 100644 --- a/apollo_sv-full.obo +++ b/apollo_sv-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: apollo_sv/releases/2023-05-05/apollo_sv-full.owl +data-version: apollo_sv/releases/2023-06-02/apollo_sv-full.owl subsetdef: attribute_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -24,7 +24,7 @@ property_value: http://purl.org/dc/elements/1.1/title "Apollo Structured Vocabul property_value: http://purl.org/dc/terms/description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string property_value: owl:versionInfo "2023-01-10" xsd:string -property_value: owl:versionInfo "2023-05-05" xsd:string +property_value: owl:versionInfo "2023-06-02" xsd:string property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -5526,6 +5526,16 @@ property_value: http://purl.org/dc/elements/1.1/date "2022-09-18T18:51:00" xsd:d property_value: IAO:0000111 "monkeypox disease inhering in a human being" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string +[Term] +id: APOLLO_SV:00000616 +name: wastewater disease surveillance +def: "A disease surveillance that detects evidence of the presence of pathogens in sewage." [] +comment: See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html. +is_a: APOLLO_SV:00000545 ! disease surveillance +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string +property_value: IAO:0000118 "sewage disease surveillance" xsd:string + [Term] id: APOLLO_SV:00000617 name: population count @@ -5533,6 +5543,40 @@ def: "A count of simulated or physical individuals in a population." [] is_a: APOLLO_SV:00000032 ! count property_value: IAO:0000117 "Matthew Diller" xsd:string +[Term] +id: APOLLO_SV:00000618 +name: wastewater surveillance data set +def: "A disease surveillance data set that is about some wastewater disease surveillance." [] +is_a: APOLLO_SV:00000554 ! disease surveillance data +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string +property_value: IAO:0000118 "sewage surveillance data" xsd:string + +[Term] +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 +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string + +[Term] +id: APOLLO_SV:00000620 +name: physical distancing infectious disease control measure +def: "An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act." [] +is_a: APOLLO_SV:00000194 ! individual treatment control strategy +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string + +[Term] +id: APOLLO_SV:00000621 +name: lockdown infectious disease control measure +def: "A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations." [] +comment: The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services. +is_a: APOLLO_SV:00000229 ! place closure control strategy +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification diff --git a/apollo_sv-full.owl b/apollo_sv-full.owl index c367991..5c3f37c 100644 --- a/apollo_sv-full.owl +++ b/apollo_sv-full.owl @@ -24,7 +24,7 @@ xmlns:apollo_sv="http://purl.obolibrary.org/obo/apollo_sv.owl/" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + Amanda Hicks John Levander Josh Hanna @@ -40,7 +40,7 @@ 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). 2023-01-10 - 2023-05-05 + 2023-06-02 @@ -18334,6 +18334,20 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A disease surveillance that detects evidence of the presence of pathogens in sewage. + Matthew Diller + sewage disease surveillance + William R. Hogan + See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html. + wastewater disease surveillance + + + + @@ -18345,6 +18359,56 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A disease surveillance data set that is about some wastewater disease surveillance. + Matthew Diller + sewage surveillance data + William R. Hogan + wastewater surveillance data set + + + + + + + + + A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region. + Matthew Diller + William R. Hogan + population density datum + + + + + + + + + An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act. + Matthew Diller + William R. Hogan + physical distancing infectious disease control measure + + + + + + + + + A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations. + Matthew Diller + William R. Hogan + The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services. + lockdown infectious disease control measure + + + + diff --git a/apollo_sv.json b/apollo_sv.json index 0b8c27e..8a3045d 100644 --- a/apollo_sv.json +++ b/apollo_sv.json @@ -49,9 +49,9 @@ "val" : "2023-01-10" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-05-05" + "val" : "2023-06-02" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2023-05-05/apollo_sv.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2023-06-02/apollo_sv.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", @@ -11498,6 +11498,26 @@ "val" : "2022-09-18T18:51:00" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000616", + "lbl" : "wastewater disease surveillance", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disease surveillance that detects evidence of the presence of pathogens in sewage." + }, + "comments" : [ "See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sewage disease surveillance" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000617", "lbl" : "population count", @@ -11511,6 +11531,74 @@ "val" : "Matthew Diller" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000618", + "lbl" : "wastewater surveillance data set", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A disease surveillance data set that is about some wastewater disease surveillance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sewage surveillance data" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000619", + "lbl" : "population density datum", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000620", + "lbl" : "physical distancing infectious disease control measure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000621", + "lbl" : "lockdown infectious disease control measure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations." + }, + "comments" : [ "The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Diller" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "William R. Hogan" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -43771,10 +43859,30 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000615", "pred" : "http://purl.obolibrary.org/obo/RO_0000052", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000616", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000545" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000617", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000618", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000554" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000619", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000032" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000620", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000194" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000621", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000229" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "pred" : "is_a", diff --git a/apollo_sv.obo b/apollo_sv.obo index 1b91147..078fd8d 100644 --- a/apollo_sv.obo +++ b/apollo_sv.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2023-05-05 +data-version: releases/2023-06-02 subsetdef: attribute_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -24,7 +24,7 @@ property_value: http://purl.org/dc/elements/1.1/title "Apollo Structured Vocabul property_value: http://purl.org/dc/terms/description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string property_value: owl:versionInfo "2023-01-10" xsd:string -property_value: owl:versionInfo "2023-05-05" xsd:string +property_value: owl:versionInfo "2023-06-02" xsd:string property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -5526,6 +5526,16 @@ property_value: http://purl.org/dc/elements/1.1/date "2022-09-18T18:51:00" xsd:d property_value: IAO:0000111 "monkeypox disease inhering in a human being" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string +[Term] +id: APOLLO_SV:00000616 +name: wastewater disease surveillance +def: "A disease surveillance that detects evidence of the presence of pathogens in sewage." [] +comment: See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html. +is_a: APOLLO_SV:00000545 ! disease surveillance +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string +property_value: IAO:0000118 "sewage disease surveillance" xsd:string + [Term] id: APOLLO_SV:00000617 name: population count @@ -5533,6 +5543,40 @@ def: "A count of simulated or physical individuals in a population." [] is_a: APOLLO_SV:00000032 ! count property_value: IAO:0000117 "Matthew Diller" xsd:string +[Term] +id: APOLLO_SV:00000618 +name: wastewater surveillance data set +def: "A disease surveillance data set that is about some wastewater disease surveillance." [] +is_a: APOLLO_SV:00000554 ! disease surveillance data +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string +property_value: IAO:0000118 "sewage surveillance data" xsd:string + +[Term] +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 +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string + +[Term] +id: APOLLO_SV:00000620 +name: physical distancing infectious disease control measure +def: "An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act." [] +is_a: APOLLO_SV:00000194 ! individual treatment control strategy +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string + +[Term] +id: APOLLO_SV:00000621 +name: lockdown infectious disease control measure +def: "A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations." [] +comment: The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services. +is_a: APOLLO_SV:00000229 ! place closure control strategy +property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string +property_value: IAO:0000117 "Matthew Diller" xsd:string + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification @@ -16123,8 +16167,8 @@ 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 fe471f2..a0ce076 100644 --- a/apollo_sv.owl +++ b/apollo_sv.owl @@ -24,7 +24,7 @@ xmlns:apollo_sv="http://purl.obolibrary.org/obo/apollo_sv.owl/" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + Amanda Hicks John Levander Josh Hanna @@ -40,7 +40,7 @@ 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). 2023-01-10 - 2023-05-05 + 2023-06-02 @@ -18334,6 +18334,20 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A disease surveillance that detects evidence of the presence of pathogens in sewage. + Matthew Diller + sewage disease surveillance + William R. Hogan + See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html. + wastewater disease surveillance + + + + @@ -18345,6 +18359,56 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A disease surveillance data set that is about some wastewater disease surveillance. + Matthew Diller + sewage surveillance data + William R. Hogan + wastewater surveillance data set + + + + + + + + + A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region. + Matthew Diller + William R. Hogan + population density datum + + + + + + + + + An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act. + Matthew Diller + William R. Hogan + physical distancing infectious disease control measure + + + + + + + + + A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations. + Matthew Diller + William R. Hogan + The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services. + lockdown infectious disease control measure + + + + diff --git a/src/ontology/imports/geo_import.owl b/src/ontology/imports/geo_import.owl index 3197210..d15ea22 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 "2023-05-05") + +Annotation(owl:versionInfo "2023-06-02") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pno_import.owl b/src/ontology/imports/pno_import.owl index ae33bd8..15d1dcb 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 "2023-05-05") +Annotation(owl:versionInfo "2023-06-02") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 2dbc2c5..4e8dc1e 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 "2023-05-05") +Annotation(owl:versionInfo "2023-06-02") Declaration(Class()) Declaration(Class())