Merge pull request #35 from Occupation-Ontology/credential_terms

Added credential and related terms

src/ontology/Ontofox_input/IAO_import_input.txt

@@ -0,0 +1,24 @@
+[URI of the OWL(RDF/XML) output file]
+http://purl.obolibrary.org/obo/occo/IAO_imports.owl
+
+[Source ontology]
+IAO
+
+[Low level source term URIs]
+http://purl.obolibrary.org/obo/IAO_0000310 #document
+http://purl.obolibrary.org/obo/IAO_0000030 #information content entity
+
+
+[Top level source term URIs and target direct superclass URIs]
+http://purl.obolibrary.org/obo/IAO_0000310 #document
+subClassOf http://purl.obolibrary.org/obo/IAO_0000030
+http://purl.obolibrary.org/obo/IAO_0000030 #information content entity
+subClassOf http://purl.obolibrary.org/obo/BFO_0000031 #generically dependent continuant
+
+[Source term retrieval setting]
+includeNoIntermediates
+
+[Source annotation URIs]
+includeAllAnnotationProperties
+
+[Source annotation URIs to be excluded]

src/ontology/Ontofox_input/OBI_import_input.txt

@@ -0,0 +1,23 @@
+[URI of the OWL(RDF/XML) output file]
+http://purl.obolibrary.org/obo/occo/OBI_imports.owl
+
+[Source ontology]
+OBI
+
+[Low level source term URIs]
+http://purl.obolibrary.org/obo/OBI_0000245 #organization
+http://purl.obolibrary.org/obo/OBI_0000011 #planned process
+
+[Top level source term URIs and target direct superclass URIs]
+http://purl.obolibrary.org/obo/OBI_0000245 #organization
+subClassOf http://purl.obolibrary.org/obo/BFO_0000040 #material entity
+http://purl.obolibrary.org/obo/OBI_0000011 #planned process
+subClassOf http://purl.obolibrary.org/obo/BFO_0000015
+
+[Source term retrieval setting]
+includeNoIntermediates
+
+[Source annotation URIs]
+includeAllAnnotationProperties
+
+[Source annotation URIs to be excluded]

src/ontology/Ontofox_input/OMRSE_import_input.txt

@@ -10,7 +10,7 @@ http://purl.obolibrary.org/obo/OMRSE_00000285 #occupation activity
 http://purl.obolibrary.org/obo/OMRSE_00000077 #job role
 http://purl.obolibrary.org/obo/OMRSE_00002072 #role in human social processes
 http://purl.obolibrary.org/obo/OMRSE_00000048 #material entity role
-
+http://purl.obolibrary.org/obo/OMRSE_00000087 #employer role
 
 [Top level source term URIs and target direct superclass URIs]
 http://purl.obolibrary.org/obo/OMRSE_00000284 #occupation disposition
@@ -23,6 +23,8 @@ http://purl.obolibrary.org/obo/OMRSE_00002072 #role in human social processes
 subClassOf http://purl.obolibrary.org/obo/OMRSE_00000048 #material entity role
 http://purl.obolibrary.org/obo/OMRSE_00000048 #material entity role
 subClassOf http://purl.obolibrary.org/obo/BFO_0000023
+http://purl.obolibrary.org/obo/OMRSE_00000087 #employer role
+subClassOf http://purl.obolibrary.org/obo/OMRSE_00002072 #role in human social processes
 
 [Source term retrieval setting]
 includeNoIntermediates

src/ontology/catalog-v001.xml

@@ -1,7 +1,10 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
         <uri name="http://purl.obolibrary.org/obo/occo/NCBITaxon_imports.owl" uri="imports/NCBITaxon_imports.owl"/>
+        <uri name="http://purl.obolibrary.org/obo/occo/IAO_imports.owl" uri="imports/IAO_imports.owl"/>
+        <uri name="http://purl.obolibrary.org/obo/occo/OBI_imports.owl" uri="imports/OBI_imports.owl"/>
         <uri name="http://purl.obolibrary.org/obo/occo/OMRSE_imports.owl" uri="imports/OMRSE_imports.owl"/>
+        <uri name="http://purl.obolibrary.org/obo/occo/externalByHand.owl" uri="imports/externalByHand.owl"/>
         <uri name="http://purl.obolibrary.org/obo/occo/dev/ability_types.owl" uri="Modules/ability_types.owl"/>
         <uri name="http://purl.obolibrary.org/obo/occo/dev/job_zones.owl" uri="Modules/job_zones.owl"/>
         <uri name="http://purl.obolibrary.org/obo/occo/dev/job_zones_equivalent.owl" uri="Modules/job_zones_equivalent.owl"/>

src/ontology/imports/IAO_imports.owl

@@ -0,0 +1,205 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/occo/IAO_imports.owl#"
+     xml:base="http://purl.obolibrary.org/obo/occo/IAO_imports.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#">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/occo/IAO_imports.owl"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+        <obo:IAO_0000111 xml:lang="en">editor preferred term</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 xml:lang="en">editor preferred term</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112">
+        <obo:IAO_0000111 xml:lang="en">example of usage</obo:IAO_0000111>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115 xml:lang="en">A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.</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 xml:lang="en">example of usage</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>
+        <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_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <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>
+    </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.obofoundry.org/obo/obi&gt;</obo:IAO_0000119>
+        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <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 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 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 xml:lang="en">definition source</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+        <rdfs:label xml:lang="en">imported from</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000031 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000030 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
+        <obo:IAO_0000111 xml:lang="en">information content entity</obo:IAO_0000111>
+        <obo:IAO_0000112 xml:lang="en">Examples of information content entites include journal articles, data, graphical layouts, and graphs.</obo:IAO_0000112>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115 xml:lang="en">A generically dependent continuant that is about some thing.</obo:IAO_0000115>
+        <obo:IAO_0000116 xml:lang="en">2014-03-10: The use of &quot;thing&quot; is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).</obo:IAO_0000116>
+        <obo:IAO_0000116 xml:lang="en">information_content_entity &apos;is_encoded_in&apos; some digital_entity in obi before split (040907). information_content_entity &apos;is_encoded_in&apos; some physical_document in obi before split (040907).
+
+Previous. An information content entity is a non-realizable information entity that &apos;is encoded in&apos; some digital or physical entity.</obo:IAO_0000116>
+        <obo:IAO_0000117 xml:lang="en">PERSON: Chris Stoeckert</obo:IAO_0000117>
+        <obo:IAO_0000119 xml:lang="en">OBI_0000142</obo:IAO_0000119>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <rdfs:label xml:lang="en">information content entity</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000310 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000310">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+        <obo:IAO_0000111 xml:lang="en">document</obo:IAO_0000111>
+        <obo:IAO_0000112 xml:lang="en">A journal article, patent application, laboratory notebook, or a book</obo:IAO_0000112>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+        <obo:IAO_0000115 xml:lang="en">A collection of information content entities intended to be understood together as a whole</obo:IAO_0000115>
+        <obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <rdfs:label xml:lang="en">document</rdfs:label>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+