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PopulationAndCommunityOntology · May 3, 2021 · 76be344 · 76be344
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diff --git a/imports/bfo_import.obo b/imports/bfo_import.obo
@@ -1,6 +1,5 @@
 format-version: 1.2
-data-version: pco/releases/2020-08-26/imports/bfo_import.obo
-ontology: pco/imports/bfo_import.obo
+ontology: pco/imports/bfo_import
 
 [Term]
 id: BFO:0000001
@@ -12,7 +11,7 @@ property_value: IAO:0000112 "the Second World War" xsd:string
 property_value: IAO:0000112 "Verdi’s Requiem" xsd:string
 property_value: IAO:0000112 "your body mass index" xsd:string
 property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string
-property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf", comment="per discussion with Barry Smith"}
+property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"}
 property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"}
 property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
 

diff --git a/imports/bfo_import.owl b/imports/bfo_import.owl
@@ -7,9 +7,7 @@
      xmlns:xml="http://www.w3.org/XML/1998/namespace"
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
-    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/pco/imports/bfo_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/pco/releases/2020-08-26/bfo_import.owl"/>
-    </owl:Ontology>
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/pco/imports/bfo_import.owl"/>
 
 
 
@@ -778,5 +776,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
 
diff --git a/imports/ecocore_import.obo b/imports/ecocore_import.obo
@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: pco/releases/2020-08-26/imports/ecocore_import.obo
-ontology: pco/imports/ecocore_import.obo
+data-version: ecocore/releases/2021-02-17/ecocore.owl
+ontology: pco/imports/ecocore_import
 
 [Term]
 id: ECOCORE:00000045
@@ -26,6 +26,7 @@ property_value: IAO:0000111 "editor note" xsd:string
 property_value: IAO:0000114 IAO:0000122
 property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string
 property_value: IAO:0000119 GROUP:OBI:<http://purl.obfoundry.org/obo/obi> xsd:string
+property_value: IAO:0000119 GROUP:OBI:<http://purl.obofoundry.org/obo/obi> xsd:string
 property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
 is_metadata_tag: true
 
diff --git a/imports/ecocore_import.owl b/imports/ecocore_import.owl
@@ -9,7 +9,7 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/pco/imports/ecocore_import.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/pco/releases/2020-08-26/imports/ecocore_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ecocore/releases/2021-02-17/ecocore.owl"/>
     </owl:Ontology>
 
 
@@ -55,6 +55,7 @@
         <obo:IAO_0000117 xml:lang="en">PERSON:Bill Bug</obo:IAO_0000117>
         <obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
         <obo:IAO_0000119 xml:lang="en">OBI_0000281</obo:IAO_0000119>
+        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
         <rdfs:label>has curation status</rdfs:label>
         <rdfs:label xml:lang="en">has curation status</rdfs:label>
     </owl:AnnotationProperty>
@@ -64,9 +65,9 @@
     <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+        <obo:IAO_0000111>definition</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">definition</obo:IAO_0000111>
-        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</obo:IAO_0000111>
-        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">textual definition</obo:IAO_0000111>
+        <obo:IAO_0000111>textual definition</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
         <obo:IAO_0000115 xml:lang="en">The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
@@ -93,9 +94,9 @@ We also have the outstanding issue of how to aim different definitions to differ
         <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <rdfs:label>definition</rdfs:label>
         <rdfs:label xml:lang="en">definition</rdfs:label>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</rdfs:label>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">textual definition</rdfs:label>
+        <rdfs:label>textual definition</rdfs:label>
     </owl:AnnotationProperty>
 
 
@@ -108,6 +109,7 @@ We also have the outstanding issue of how to aim different definitions to differ
         <obo:IAO_0000115 xml:lang="en">An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obfoundry.org/obo/obi&gt;</obo:IAO_0000119>
+        <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obofoundry.org/obo/obi&gt;</obo:IAO_0000119>
         <oboInOwl:hasDbXref>IAO:0000116</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <oboInOwl:id>editor_note</oboInOwl:id>
@@ -141,9 +143,11 @@ We also have the outstanding issue of how to aim different definitions to differ
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
         <obo:IAO_0000111 xml:lang="en">definition source</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115 xml:lang="en">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</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">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</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
-        <obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w</obo:IAO_0000119>
+        <obo:IAO_0000119>Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w</obo:IAO_0000119>
+        <obo:IAO_0000119 xml:lang="en">Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w</obo:IAO_0000119>
         <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
         <rdfs:label>definition source</rdfs:label>
@@ -163,18 +167,13 @@ We also have the outstanding issue of how to aim different definitions to differ
 
     <!-- http://www.geneontology.org/formats/oboInOwl#hasOBONamespace -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace">
-        <rdfs:isDefinedBy rdf:resource="http://www.geneontology.org/formats/oboinowl.owl"/>
-        <rdfs:label>has_obo_namespace</rdfs:label>
-    </owl:AnnotationProperty>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"/>
 
 
 
     <!-- http://www.geneontology.org/formats/oboInOwl#id -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
-        <rdfs:isDefinedBy rdf:resource="http://www.geneontology.org/formats/oboinowl.owl"/>
-    </owl:AnnotationProperty>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
 
 
 
@@ -186,9 +185,7 @@ We also have the outstanding issue of how to aim different definitions to differ
 
     <!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand">
-        <rdfs:label>shorthand</rdfs:label>
-    </owl:AnnotationProperty>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand"/>
 
 
 
@@ -242,5 +239,5 @@ We also have the outstanding issue of how to aim different definitions to differ
 
 
 
-<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
 
diff --git a/imports/envo_import.obo b/imports/envo_import.obo
@@ -1,6 +1,22 @@
 format-version: 1.2
-data-version: pco/releases/2020-08-26/imports/envo_import.owl
+data-version: envo/releases/2020-06-10/envo.owl
+default-namespace: ENVO
+remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 499 Logical Axioms: 88]
+remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 114 Logical Axioms: 19]
+remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 135 Logical Axioms: 22]
+remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>) VersionIRI(<null>))) [Axioms: 40 Logical Axioms: 6]
+remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>) VersionIRI(<null>))) [Axioms: 21 Logical Axioms: 2]
 ontology: pco/imports/envo_import
+property_value: bug-database https://github.com/EnvironmentOntology/envo/issues/ xsd:anyURI
+property_value: GitRepository https://github.com/EnvironmentOntology/envo/ xsd:anyURI
+property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-4366-3088
+property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-6601-2165 xsd:string
+property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8343-612X xsd:string
+property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0003-1604-1512 xsd:string
+property_value: http://purl.org/dc/elements/1.1/description "ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities" xsd:string
+property_value: http://purl.org/dc/elements/1.1/title "The Environment Ontology" xsd:string
+property_value: http://xmlns.com/foaf/0.1/homepage http://environmentontology.org/ xsd:anyURI
+property_value: owl:versionInfo "2020-06-10" xsd:string
 
 [Term]
 id: BFO:0000040

diff --git a/imports/envo_import.owl b/imports/envo_import.owl
@@ -12,8 +12,25 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/pco/imports/envo_import.obo">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/pco/imports/envo_import.obo/pco/releases/2020-08-26/imports/ecocore_import.obo"/>
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/pco/imports/envo_import.owl">
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/envo/releases/2020-06-10/envo.owl"/>
+        <dc:creator rdf:resource="http://orcid.org/0000-0002-4366-3088"/>
+        <dc:creator>http://orcid.org/0000-0002-6601-2165</dc:creator>
+        <dc:creator>http://orcid.org/0000-0002-8343-612X</dc:creator>
+        <dc:creator>http://orcid.org/0000-0003-1604-1512</dc:creator>
+        <dc:description>ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities</dc:description>
+        <dc:title>The Environment Ontology</dc:title>
+        <terms:license>https://creativecommons.org/publicdomain/zero/1.0/</terms:license>
+        <doap:GitRepository rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/EnvironmentOntology/envo/</doap:GitRepository>
+        <doap:bug-database rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/EnvironmentOntology/envo/issues/</doap:bug-database>
+        <oboInOwl:default-namespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ENVO</oboInOwl:default-namespace>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 499 Logical Axioms: 88]</rdfs:comment>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 114 Logical Axioms: 19]</rdfs:comment>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 135 Logical Axioms: 22]</rdfs:comment>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 40 Logical Axioms: 6]</rdfs:comment>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 21 Logical Axioms: 2]</rdfs:comment>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2020-06-10</owl:versionInfo>
+        <foaf:homepage rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://environmentontology.org/</foaf:homepage>
     </owl:Ontology>
 
 
@@ -190,5 +207,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
 
diff --git a/imports/go_import.obo b/imports/go_import.obo
@@ -1,6 +1,5 @@
 format-version: 1.2
-data-version: pco/releases/2020-08-26/imports/go_import.obo
-ontology: pco/imports/go_import.obo
+ontology: pco/imports/go_import
 
 [Term]
 id: GO:0007610
@@ -61,31 +60,37 @@ synonym: "cooperative behavior" RELATED []
 synonym: "social behaviour" EXACT []
 xref: Wikipedia:Social_behavior
 is_a: GO:0007610 ! behavior
-is_a: GO:0051703 ! intraspecies interaction between organisms
+is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms
 property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl
 
 [Term]
 id: GO:0044419
-name: interspecies interaction between organisms
+name: biological process involved in interspecies interaction between organisms
 namespace: biological_process
-def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc]
+def: "Any process evolved to enable an interaction with an organism of a different species." [GOC:cc]
+subset: gocheck_do_not_annotate
 subset: goslim_candida
 subset: goslim_pir
 synonym: "interaction with another species" EXACT []
 synonym: "interspecies interaction" EXACT []
+synonym: "interspecies interaction between organisms" EXACT []
 synonym: "interspecies interaction with other organisms" EXACT []
 is_a: GO:0008150 ! biological_process
+property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI
 property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl
 property_value: RO:0002161 NCBITaxon:4895
 
 [Term]
 id: GO:0051703
-name: intraspecies interaction between organisms
+name: biological process involved in intraspecies interaction between organisms
 namespace: biological_process
 def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai]
+subset: gocheck_do_not_annotate
 subset: goslim_pir
+synonym: "intraspecies interaction between organisms" EXACT []
 synonym: "intraspecies interaction with other organisms" EXACT []
 is_a: GO:0008150 ! biological_process
+property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI
 property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl
 
 [Term]