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Merge pull request #233 from ApolloDev/release-2023-06-02
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Preparing release 2023-06-02.
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dillerm committed Jun 2, 2023
2 parents 3a875e4 + 37f34dc commit c4e610b
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112 changes: 110 additions & 2 deletions apollo_sv-base.json
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Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
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48 changes: 46 additions & 2 deletions apollo_sv-base.obo
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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

Expand Down Expand Up @@ -5436,13 +5436,57 @@ 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
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
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74 changes: 72 additions & 2 deletions apollo_sv-base.owl
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Expand Up @@ -2,6 +2,7 @@
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/apollo_sv/apollo_sv-base.owl#"
xml:base="http://purl.obolibrary.org/obo/apollo_sv/apollo_sv-base.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:uo="http://purl.obolibrary.org/obo/uo#"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
Expand All @@ -10,13 +11,18 @@
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:doap="http://usefulinc.com/ns/doap#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:pato="http://purl.obolibrary.org/obo/pato#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:apollo_sv="http://purl.obolibrary.org/obo/apollo_sv.owl/"
xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/apollo_sv/apollo_sv-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/apollo_sv/releases/2023-05-05/apollo_sv-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/apollo_sv/releases/2023-06-02/apollo_sv-base.owl"/>
<dc:contributor>Amanda Hicks</dc:contributor>
<dc:contributor>John Levander</dc:contributor>
<dc:contributor>Josh Hanna</dc:contributor>
Expand All @@ -33,7 +39,7 @@
<www:RTS_00000002>082D5D78-D916-457E-B4FD-365F86F45B30</www:RTS_00000002>
<rdfs:comment xml:lang="en">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&apos;s Uniform Resource Identifier (URI).</rdfs:comment>
<owl:versionInfo>2023-01-10</owl:versionInfo>
<owl:versionInfo>2023-05-05</owl:versionInfo>
<owl:versionInfo>2023-06-02</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -12974,6 +12980,20 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si



<!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000616 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000616">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000545"/>
<obo:IAO_0000115 xml:lang="en">A disease surveillance that detects evidence of the presence of pathogens in sewage.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Matthew Diller</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">sewage disease surveillance</obo:IAO_0000118>
<dc:contributor xml:lang="en">William R. Hogan</dc:contributor>
<rdfs:comment xml:lang="en">See the CDC&apos;s explanation of wastewater surveillance, and how it uses the term &apos;wastewater&apos; synonymously with &apos;sewage&apos;, here: https://www.cdc.gov/nwss/wastewater-surveillance.html.</rdfs:comment>
<rdfs:label xml:lang="en">wastewater disease surveillance</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000617 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000617">
Expand All @@ -12985,6 +13005,56 @@ By &quot;similar vaccines&quot; we typically mean same pathogen, but could be si



<!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000618 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000618">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000554"/>
<obo:IAO_0000115 xml:lang="en">A disease surveillance data set that is about some wastewater disease surveillance.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Matthew Diller</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">sewage surveillance data</obo:IAO_0000118>
<dc:contributor xml:lang="en">William R. Hogan</dc:contributor>
<rdfs:label xml:lang="en">wastewater surveillance data set</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000619 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000619">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000032"/>
<obo:IAO_0000115 xml:lang="en">A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Matthew Diller</obo:IAO_0000117>
<dc:contributor xml:lang="en">William R. Hogan</dc:contributor>
<rdfs:label xml:lang="en">population density datum</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000620 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000620">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000194"/>
<obo:IAO_0000115 xml:lang="en">An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Matthew Diller</obo:IAO_0000117>
<dc:contributor xml:lang="en">William R. Hogan</dc:contributor>
<rdfs:label xml:lang="en">physical distancing infectious disease control measure</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000621 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000621">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/APOLLO_SV_00000229"/>
<obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Matthew Diller</obo:IAO_0000117>
<dc:contributor xml:lang="en">William R. Hogan</dc:contributor>
<rdfs:comment xml:lang="en">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.</rdfs:comment>
<rdfs:label xml:lang="en">lockdown infectious disease control measure</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/APOLLO_SV_00000793 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/APOLLO_SV_00000793">
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