Merge pull request #22 from VirtualFlyBrain/release_2023-08-15

release 2023-08-15

VFB_drivers-base.owl

@@ -17,14 +17,14 @@
      xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/VFB_drivers/VFB_drivers-base.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/VFB_drivers/releases/2023-08-14/VFB_drivers-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/VFB_drivers/releases/2023-08-15/VFB_drivers-base.owl"/>
         <dc:description>An ontology of Drosophila melanogaster drivers and expression patterns. Split expression pattern classes are taken from Virtual Fly Brain, where these were created and linked to FlyBase terms for hemidrivers. Hemidriver classes are created using data taken directly from FlyBase. Other driver classes are retrieved from Virtual Fly Brain, which creates these using data from FlyBase.</dc:description>
         <dc:title>VFB Driver Ontology</dc:title>
         <dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
         <terms:contributor>http://orcid.org/0000-0002-1373-1705</terms:contributor>
         <terms:license>https://creativecommons.org/licenses/by/4.0/</terms:license>
-        <oboInOwl:date>14:08:2023 01:09</oboInOwl:date>
-        <owl:versionInfo>2023-08-14</owl:versionInfo>
+        <oboInOwl:date>15:08:2023 11:09</oboInOwl:date>
+        <owl:versionInfo>2023-08-15</owl:versionInfo>
     </owl:Ontology>
 
 

VFB_drivers-simple.owl

@@ -11,13 +11,13 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/VFB_drivers/VFB_drivers-simple.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/VFB_drivers/releases/2023-08-14/VFB_drivers-simple.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/VFB_drivers/releases/2023-08-15/VFB_drivers-simple.owl"/>
         <dc:description>An ontology of Drosophila melanogaster drivers and expression patterns. Split expression pattern classes are taken from Virtual Fly Brain, where these were created and linked to FlyBase terms for hemidrivers. Hemidriver classes are created using data taken directly from FlyBase. Other driver classes are retrieved from Virtual Fly Brain, which creates these using data from FlyBase.</dc:description>
         <dc:title>VFB Driver Ontology</dc:title>
         <terms:contributor>http://orcid.org/0000-0002-1373-1705</terms:contributor>
         <terms:license>https://creativecommons.org/licenses/by/4.0/</terms:license>
-        <oboInOwl:date>14:08:2023 01:09</oboInOwl:date>
-        <owl:versionInfo>2023-08-14</owl:versionInfo>
+        <oboInOwl:date>15:08:2023 11:10</oboInOwl:date>
+        <owl:versionInfo>2023-08-15</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -41,6 +41,12 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
+
+
+
     <!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
@@ -50,14 +56,55 @@
     <!-- 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_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
-        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <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:label xml:lang="en">definition</rdfs:label>
         <rdfs:label>definition</rdfs:label>
     </owl:AnnotationProperty>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
+
+
+
     <!-- http://purl.org/dc/elements/1.1/description -->
 
     <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
@@ -90,6 +137,12 @@
 
 
 
+    <!-- http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
+
+
+
     <!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by"/>