Merge pull request #58 from monarch-initiative/rel2022-08-10

New GENO release August 2022
monarch-initiative · Aug 10, 2022 · 630a86e · 630a86e
2 parents a9a6e4f + 161d0a4
commit 630a86e
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diff --git a/geno-base.json b/geno-base.json
diff --git a/geno-base.obo b/geno-base.obo
@@ -1,11 +1,11 @@
 format-version: 1.2
-data-version: geno/releases/2022-03-05/geno-base.owl
+data-version: geno/releases/2022-08-10/geno-base.owl
 ontology: geno/geno-base
 property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities.  At present many parts of the model are exploratory and set to undergo refactoring.  In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc).  Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string
 property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string
 property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
-property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by-sa/2.0/
-property_value: owl:versionInfo "2022-03-05" xsd:string
+property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/
+property_value: owl:versionInfo "2022-08-10" xsd:string
 
 [Term]
 id: BFO:0000001

diff --git a/geno-base.owl b/geno-base.owl
@@ -11,14 +11,14 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/geno/geno-base.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/geno/releases/2022-03-05/geno-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/geno/releases/2022-08-10/geno-base.owl"/>
         <dc:description>GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities.  At present many parts of the model are exploratory and set to undergo refactoring.  In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc).  Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. 
 
 Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013</dc:description>
         <dc:title>GENO ontology</dc:title>
         <dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
-        <terms:license rdf:resource="https://creativecommons.org/licenses/by-sa/2.0/"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-03-05</owl:versionInfo>
+        <terms:license rdf:resource="https://creativecommons.org/licenses/by/4.0/"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-10</owl:versionInfo>
     </owl:Ontology>
 
 

diff --git a/geno-full.json b/geno-full.json
diff --git a/geno-full.obo b/geno-full.obo
@@ -1,10 +1,10 @@
 format-version: 1.2
-data-version: geno/releases/2022-03-05/geno-full.owl
+data-version: geno/releases/2022-08-10/geno-full.owl
 ontology: geno/geno-full
 property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities.  At present many parts of the model are exploratory and set to undergo refactoring.  In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc).  Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string
 property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string
-property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by-sa/2.0/
-property_value: owl:versionInfo "2022-03-05" xsd:string
+property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/
+property_value: owl:versionInfo "2022-08-10" xsd:string
 
 [Term]
 id: BFO:0000001

diff --git a/geno-full.owl b/geno-full.owl
@@ -12,13 +12,13 @@
      xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/geno/geno-full.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/geno/releases/2022-03-05/geno-full.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/geno/releases/2022-08-10/geno-full.owl"/>
         <dc:description>GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities.  At present many parts of the model are exploratory and set to undergo refactoring.  In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc).  Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. 
 
 Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013</dc:description>
         <dc:title>GENO ontology</dc:title>
-        <terms:license rdf:resource="https://creativecommons.org/licenses/by-sa/2.0/"/>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-03-05</owl:versionInfo>
+        <terms:license rdf:resource="https://creativecommons.org/licenses/by/4.0/"/>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-08-10</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -189,12 +189,14 @@ We also have the outstanding issue of how to aim different definitions to differ
     <!-- http://purl.obolibrary.org/obo/IAO_0000118 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
-        <obo:IAO_0000111 xml:lang="en">alternative term</obo:IAO_0000111>
+        <obo:IAO_0000111 xml:lang="en">alternative label</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
-        <obo:IAO_0000115 xml:lang="en">An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)</obo:IAO_0000115>
+        <obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
+        <obo:IAO_0000117>OBO Operations committee</obo:IAO_0000117>
         <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:label xml:lang="en">alternative term</rdfs:label>
+        <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).</rdfs:comment>
+        <rdfs:label xml:lang="en">alternative label</rdfs:label>
     </owl:AnnotationProperty>
 
 
@@ -340,6 +342,7 @@ Annotations: expand_assertion_to &quot;DisjointClasses: (http://purl.obolibrary.
         <obo:IAO_0000115 xml:lang="en">Use boolean value xsd:true to indicate that the property is an antisymmetric property</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
         <rdfs:label xml:lang="en">antisymmetric property</rdfs:label>
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/OMO_0001001"/>
     </owl:AnnotationProperty>
 
 
@@ -577,6 +580,47 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OMO_0001001 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0001001">
+        <obo:IAO_0000115>This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.</obo:IAO_0000115>
+        <obo:IAO_0000119>OBO Operations call</obo:IAO_0000119>
+        <oboInOwl:created_by rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+        <rdfs:label>logical characteristic of object property</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/OMO_0002000 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0002000">
+        <obo:IAO_0000112>&apos;part disjoint with&apos; &apos;defined by construct&apos; &quot;&quot;&quot;
+    PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;
+    PREFIX : &lt;http://example.org/
+    CONSTRUCT {
+      [
+        a owl:Restriction ;
+        owl:onProperty :part_of ;
+        owl:someValuesFrom ?a ;
+        owl:disjointWith [
+          a owl:Restriction ;
+          owl:onProperty :part_of ;
+          owl:someValuesFrom ?b
+        ]
+      ]
+    }
+    WHERE {
+      ?a :part_disjoint_with ?b .
+    }</obo:IAO_0000112>
+        <obo:IAO_0000115>Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.</obo:IAO_0000115>
+        <obo:IAO_0000233 rdf:resource="https://github.com/ontodev/robot/issues/963"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
+        <dc:contributor rdf:resource="https://orcid.org/0000-0002-8688-6599"/>
+        <rdfs:label>defined by construct</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
     <!-- http://purl.org/dc/elements/1.1/contributor -->
 
     <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
@@ -691,12 +735,64 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
 
 
 
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym">
+        <obo:IAO_0000115>An alternative label for a class or property which has a more general meaning than the preferred name/primary label.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+        <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/18</obo:IAO_0000233>
+        <rdfs:label xml:lang="en">has broad synonym</rdfs:label>
+        <rdfs:seeAlso>https://github.com/information-artifact-ontology/ontology-metadata/issues/18</rdfs:seeAlso>
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
+    </owl:AnnotationProperty>
+
+
+
     <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
 
 
 
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym">
+        <obo:IAO_0000115>An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+        <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/20</obo:IAO_0000233>
+        <rdfs:label xml:lang="en">has exact synonym</rdfs:label>
+        <rdfs:seeAlso>https://github.com/information-artifact-ontology/ontology-metadata/issues/20</rdfs:seeAlso>
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym">
+        <obo:IAO_0000115>An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+        <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/19</obo:IAO_0000233>
+        <rdfs:label xml:lang="en">has narrow synonym</rdfs:label>
+        <rdfs:seeAlso>https://github.com/information-artifact-ontology/ontology-metadata/issues/19</rdfs:seeAlso>
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym">
+        <obo:IAO_0000115>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.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+        <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/21</obo:IAO_0000233>
+        <rdfs:label xml:lang="en">has related synonym</rdfs:label>
+        <rdfs:seeAlso>https://github.com/information-artifact-ontology/ontology-metadata/issues/21</rdfs:seeAlso>
+        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
+    </owl:AnnotationProperty>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -7394,6 +7490,7 @@ Previous. An information content entity is a non-realizable information entity t
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000227"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000228"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000229"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OMO_0001000"/>
                 </owl:oneOf>
             </owl:Class>
         </owl:equivalentClass>
@@ -9369,6 +9466,20 @@ Codes for: http://www.uniprot.org/uniprot/Q15465</rdfs:comment>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OMO_0001000 -->
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/OMO_0001000">
+        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
+        <obo:IAO_0000115 xml:lang="en">The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.</obo:IAO_0000116>
+        <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0001-5208-3432"/>
+        <obo:IAO_0000233>https://github.com/information-artifact-ontology/ontology-metadata/issues/77</obo:IAO_0000233>
+        <obo:IAO_0000234>https://orcid.org/0000-0001-5208-3432</obo:IAO_0000234>
+        <rdfs:label>out of scope</rdfs:label>
+    </owl:NamedIndividual>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //