prepare release files

PopulationAndCommunityOntology · Aug 26, 2020 · 13a3ceb · 13a3ceb
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diff --git a/imports/bfo_import.obo b/imports/bfo_import.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: pco/imports/bfo_import/pco/releases/2020-02-13/bfo_import.owl/pco/imports/bfo_import.obo
+data-version: pco/releases/2020-08-26/imports/bfo_import.obo
 ontology: pco/imports/bfo_import.obo
 
 [Term]

diff --git a/imports/bfo_import.owl b/imports/bfo_import.owl
@@ -8,7 +8,7 @@
      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/2020-02-13/bfo_import.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/pco/releases/2020-08-26/bfo_import.owl"/>
     </owl:Ontology>
 
 

diff --git a/imports/ecocore_import.obo b/imports/ecocore_import.obo
@@ -0,0 +1,31 @@
+format-version: 1.2
+data-version: pco/releases/2020-08-26/imports/ecocore_import.obo
+ontology: pco/imports/ecocore_import.obo
+
+[Term]
+id: ECOCORE:00000045
+name: symbiotroph
+def: "heterotroph that acquires nutrition from a symbiont" []
+property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string
+
+[Term]
+id: ECOCORE:00000146
+name: parasite
+def: "A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host" []
+xref: https://www.wikidata.org/entity/Q10253316
+is_a: ECOCORE:00000045 ! symbiotroph
+property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string
+
+[Typedef]
+id: editor_note
+name: editor note
+namespace: uberon
+def: "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." []
+xref: IAO:0000116
+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: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
+is_metadata_tag: true
+
diff --git a/imports/ecocore_import.owl b/imports/ecocore_import.owl
@@ -0,0 +1,246 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/pco/imports/ecocore_import.owl#"
+     xml:base="http://purl.obolibrary.org/obo/pco/imports/ecocore_import.owl"
+     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#"
+     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#"
+     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:Ontology>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+        <obo:IAO_0000111>editor preferred label</obo:IAO_0000111>
+        <obo:IAO_0000111 xml:lang="en">editor preferred label</obo:IAO_0000111>
+        <obo:IAO_0000111>editor preferred term</obo:IAO_0000111>
+        <obo:IAO_0000111 xml:lang="en">editor preferred term</obo:IAO_0000111>
+        <obo:IAO_0000111>editor preferred term~editor preferred label</obo:IAO_0000111>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115 xml:lang="en">The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)</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.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
+        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <rdfs:label>editor preferred label</rdfs:label>
+        <rdfs:label xml:lang="en">editor preferred label</rdfs:label>
+        <rdfs:label>editor preferred term</rdfs:label>
+        <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+        <rdfs:label>editor preferred term~editor preferred label</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
+        <obo:IAO_0000111 xml:lang="en">has curation status</obo:IAO_0000111>
+        <obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
+        <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:label>has curation status</rdfs:label>
+        <rdfs:label xml:lang="en">has curation status</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+        <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_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>
+        <obo:IAO_0000116 xml:lang="en">2012-04-05: 
+Barry Smith
+
+The official OBI definition, explaining the meaning of a class or property: &apos;Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions&apos;  is terrible.
+
+Can you fix to something like:
+
+A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
+
+Alan Ruttenberg
+
+Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can&apos;t be evaluated by those criteria. 
+
+On the specifics of the proposed definition:
+
+We don&apos;t have definitions of &apos;meaning&apos; or &apos;expression&apos; or &apos;property&apos;. For &apos;reference&apos; in the intended sense I think we use the term &apos;denotation&apos;. For &apos;expression&apos;, I think we you mean symbol, or identifier. For &apos;meaning&apos; it differs for class and property. For class we want documentation that let&apos;s the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let&apos;s the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The &apos;intended reader&apos; part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. 
+
+Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. 
+
+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.  </obo:IAO_0000116>
+        <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 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>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
+        <obo:IAO_0000111 xml:lang="en">editor note</obo:IAO_0000111>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <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>
+        <oboInOwl:hasDbXref>IAO:0000116</oboInOwl:hasDbXref>
+        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>editor_note</oboInOwl:id>
+        <oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
+        <oboInOwl:shorthand>editor_note</oboInOwl:shorthand>
+        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <rdfs:label>editor note</rdfs:label>
+        <rdfs:label xml:lang="en">editor note</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
+        <obo:IAO_0000111 xml:lang="en">term editor</obo:IAO_0000111>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115 xml:lang="en">Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.</obo:IAO_0000116>
+        <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>term editor</rdfs:label>
+        <rdfs:label xml:lang="en">term editor</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
+
+    <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_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 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>
+        <rdfs:label xml:lang="en">definition source</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
+        <rdfs:isDefinedBy rdf:resource="http://www.geneontology.org/formats/oboinowl.owl"/>
+        <rdfs:label>database_cross_reference</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- 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>
+
+
+
+    <!-- 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>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#is_metadata_tag -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#is_metadata_tag"/>
+
+
+
+    <!-- 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>
+
+
+
+    <!-- http://www.w3.org/2000/01/rdf-schema#isDefinedBy -->
+
+    <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#isDefinedBy"/>
+
+
+
+    <!-- http://www.w3.org/2000/01/rdf-schema#label -->
+
+    <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label">
+        <obo:IAO_0000111>label</obo:IAO_0000111>
+        <rdfs:isDefinedBy rdf:resource="http://www.w3.org/2000/01/rdf-schema.owl"/>
+        <rdfs:label>label</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/ECOCORE_00000045 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ECOCORE_00000045">
+        <obo:IAO_0000115>heterotroph that acquires nutrition from a symbiont</obo:IAO_0000115>
+        <obo:IAO_0000117>http://orcid.org/0000-0002-2908-3327</obo:IAO_0000117>
+        <rdfs:label>symbiotroph</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/ECOCORE_00000146 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ECOCORE_00000146">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ECOCORE_00000045"/>
+        <obo:IAO_0000115>A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host</obo:IAO_0000115>
+        <obo:IAO_0000117>http://orcid.org/0000-0002-2908-3327</obo:IAO_0000117>
+        <oboInOwl:hasDbXref>https://www.wikidata.org/entity/Q10253316</oboInOwl:hasDbXref>
+        <rdfs:label>parasite</rdfs:label>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
+