latest ontology and update code

productMods/WEB-INF/filegraph/tbox/scires-1.4.owl

@@ -13,6 +13,11 @@
     xmlns:j.5="http://purl.org/dc/terms/"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" > 
+  <rdf:Description rdf:nodeID="A0">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
+    <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ERO_0000460"/>
+    <owl:allValuesFrom rdf:resource="http://purl.org/ontology/bibo/Document"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://purl.obolibrary.org/obo/">
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Ontology"/>
   </rdf:Description>
@@ -64,11 +69,6 @@
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
     <vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In Phase 2 trials, an experimental study drug or treatment is given to a larger group of people (100-300) to see if it is effective and to further evaluate its safety.</vitro:descriptionAnnot>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A0">
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
-    <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ERO_0000460"/>
-    <owl:allValuesFrom rdf:resource="http://purl.org/ontology/bibo/Document"/>
-  </rdf:Description>
   <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000392">
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
     <vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A service in which a service consumer provides some material or data as input which a service provider stores and returns as output.</vitro:descriptionAnnot>
@@ -136,10 +136,10 @@ NOTE that we are not addressing for now the issue of whether a foaf:Person is a
 </vitro:descriptionAnnot>
   </rdf:Description>
   <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000004">
-    <rdfs:subClassOf rdf:nodeID="A0"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
     <vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An implement used to facilitate work, especially precision work.</vitro:descriptionAnnot>
     <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An implement used to facilitate work, especially precision work.</vitro:shortDef>
+    <rdfs:subClassOf rdf:nodeID="A0"/>
     <rdfs:subClassOf rdf:resource="http://vivoweb.org/ontology/core#Equipment"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000029">

productMods/WEB-INF/ontologies/update/diff.tab.txt

@@ -5,8 +5,8 @@ http://vivoweb.org/ontology/core#subjectAreaFor		No	Delete	Delete
 http://vivoweb.org/ontology/core#researchAreaOf		No	Delete	Delete
 http://vivoweb.org/ontology/core#roleIn		No	Delete	Delete
 http://vivoweb.org/ontology/core#relatedRole		No	Delete	Delete
-http://vivoweb.org/ontology/core#VocabularySourceReference	http://vivoweb.org/ontology/core#URLLink	Yes	Map	Directly-changed
+http://vivoweb.org/ontology/core#URLLink		No	Delete	Delete
-http://vivoweb.org/ontology/core#sourceVocabularyReference	http://vivoweb.org/ontology/core#webpage	Yes	Map	Directly-changed
+http://vivoweb.org/ontology/core#sourceVocabularyReference		No	Delete	Delete
-http://vivoweb.org/ontology/core#vocabularyReferenceFor	http://vivoweb.org/ontology/core#webpageOf	Yes	Map	Directly-changed
+http://vivoweb.org/ontology/core#vocabularyReferenceFor		No	Delete	Delete
 http://vivoweb.org/ontology/core#addressStreet	http://vivoweb.org/ontology/core#address1	Yes	Map	Directly-changed
 http://vivoweb.org/ontology/core#addressDepartment	http://vivoweb.org/ontology/core#address2	Yes	Map	Directly-changed

productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/ExternalConcept.sparql

@@ -0,0 +1,27 @@
+PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:  <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX xsd:   <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl:   <http://www.w3.org/2002/07/owl#>
+PREFIX swrl:  <http://www.w3.org/2003/11/swrl#>
+PREFIX swrlb: <http://www.w3.org/2003/11/swrlb#>
+PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>
+PREFIX vivo:  <http://vivo.library.cornell.edu/ns/0.1#>
+PREFIX bibo: <http://purl.org/ontology/bibo/>   
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX event: <http://purl.org/NET/c4dm/event.owl#>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+PREFIX vivo: <http://vivoweb.org/ontology/core#>
+
+Construct {
+     ?something vivo:hasAssociatedConcept ?uri .
+     ?uri vivo:conceptAssociatedWith ?something 
+} where {
+     {?something vivo:hasSubjectArea ?concept}
+     union
+     {?something vivo:hasResearchArea ?concept}
+     
+     ?concept rdf:type vivo:SubjectArea .
+     ?concept vivo:vocabularySourceReference ?urllink .
+     ?urllink vivo:linkURI ?uri
+}

productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/InternalConcept.sparql

@@ -14,17 +14,20 @@ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 PREFIX vivo: <http://vivoweb.org/ontology/core#>
 
 Construct {
-     ?something vivo:terminologyAnnotation _:terminologyAnnotation .
+     ?something vivo:hasAssociatedConcept _:concept .
-     _:terminologyAnnotation rdf:type vivo:TerminologyAnnotation .
+     _:concept vivo:conceptAssociatedWith ?something .
-     _:terminologyAnnotation vivo:referencedTerm _:concept .
      _:concept rdf:type skos:Concept .
      _:concept rdfs:label ?label
 } where {
-     {?something vivo:hasSubjectArea ?area}
+     {?something vivo:hasSubjectArea ?concept}
      union
-     {?something vivo:hasResearchArea ?area}
+     {?something vivo:hasResearchArea ?concept}
      
-     ?something rdf:type vivo:SubjectArea
+     ?concept rdf:type vivo:SubjectArea .
      
-     optional {?area rdfs:label ?label}
+     optional {?concept rdfs:label ?label}
+     
+     optional {?concept vivo:vocabularySourceReference ?urllink}
+      
+     filter (!bound(?urllink))
 }

productMods/WEB-INF/ontologies/user/tbox/vivo-core-1.4-annotations.rdf

@@ -783,6 +783,11 @@
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#nobody"/>
   </rdf:Description>
+  <rdf:Description rdf:about="http://vivoweb.org/ontology/core#conceptAssociatedWith">
+    <rdfs:label xml:lang="en-US">concept for</rdfs:label>
+    <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</vitro:displayLimitAnnot>
+    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">20</vitro:displayRankAnnot>
+  </rdf:Description>
   <rdf:Description rdf:about="http://aims.fao.org/aos/geopolitical.owl#nameOfficialIT">
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#nobody"/>
@@ -1094,16 +1099,6 @@
     <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">-1</vitro:displayRankAnnot>
     <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">-1</vitro:displayLimitAnnot>
   </rdf:Description>
-  <rdf:Description rdf:about="http://vivoweb.org/ontology/core#terminologyAnnotation">
-    <rdfs:label xml:lang="en-US">terminology annotation</rdfs:label>
-    <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</vitro:displayLimitAnnot>
-    <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
-    <vitro:selectFromExistingAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</vitro:selectFromExistingAnnot>
-    <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
-    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">20</vitro:displayRankAnnot>
-    <vitro:customEntryFormAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">terminologyAnnotation.jsp</vitro:customEntryFormAnnot>
-    <vitro:offerCreateNewOptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</vitro:offerCreateNewOptionAnnot>
-  </rdf:Description>
   <rdf:Description rdf:about="http://vivoweb.org/ontology/core#address3">
     <rdfs:label xml:lang="en-US">address3</rdfs:label>
     <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">10</vitro:displayRankAnnot>
@@ -1588,6 +1583,15 @@
     <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">-1</vitro:displayLimitAnnot>
     <rdfs:label xml:lang="en-US">Museum</rdfs:label>
   </rdf:Description>
+  <rdf:Description rdf:about="http://vivoweb.org/ontology/core#hasAssociatedConcept">
+    <rdfs:label xml:lang="en-US">associated concept</rdfs:label>
+    <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</vitro:displayLimitAnnot>
+    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">20</vitro:displayRankAnnot>
+    <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
+    <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
+    <vitro:selectFromExistingAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</vitro:selectFromExistingAnnot>
+    <vitro:inPropertyGroupAnnot rdf:resource="http://vivoweb.org/ontology#vitroPropertyGroupoverview"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://purl.org/ontology/bibo/affirmedBy">
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#nobody"/>
     <rdfs:label xml:lang="en-US">affirmedBy</rdfs:label>
@@ -1787,13 +1791,6 @@
     <vitro:offerCreateNewOptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</vitro:offerCreateNewOptionAnnot>
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
   </rdf:Description>
-  <rdf:Description rdf:about="http://vivoweb.org/ontology/core#referencedTerm">
-    <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
-    <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
-    <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">-1</vitro:displayLimitAnnot>
-    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">4</vitro:displayRankAnnot>
-    <rdfs:label xml:lang="en-US">referenced term</rdfs:label>
-  </rdf:Description>
   <rdf:Description rdf:about="http://vivoweb.org/ontology/core#TransnationalRegion">
     <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">-1</vitro:displayRankAnnot>
     <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">-1</vitro:displayLimitAnnot>
@@ -1825,8 +1822,8 @@
     <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <vitro:inPropertyGroupAnnot rdf:resource="http://vivoweb.org/ontology#vitroPropertyGroupoverview"/>
-    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayRankAnnot>
     <rdfs:label xml:lang="en-US">term label</rdfs:label>
+    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayRankAnnot>
   </rdf:Description>
   <rdf:Description rdf:about="http://vivoweb.org/ontology/core#degreeOutcomeOf">
     <rdfs:label xml:lang="en-US">degree outcome of</rdfs:label>
@@ -2732,14 +2729,6 @@
     <vitro:inPropertyGroupAnnot rdf:resource="http://vivoweb.org/ontology#vitroPropertyGroupoverview"/>
     <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">59</vitro:displayRankAnnot>
   </rdf:Description>
-  <rdf:Description rdf:about="http://vivoweb.org/ontology/core#TerminologyAnnotation">
-    <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
-    <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
-    <vitro:inClassGroup rdf:resource="http://vivoweb.org/ontology#vitroClassGrouppublications"/>
-    <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayLimitAnnot>
-    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayRankAnnot>
-    <rdfs:label xml:lang="en-US">Terminology Annotation</rdfs:label>
-  </rdf:Description>
   <rdf:Description rdf:about="http://vivoweb.org/ontology/core#School">
     <rdfs:label xml:lang="en-US">School</rdfs:label>
     <vitro:inClassGroup rdf:resource="http://vivoweb.org/ontology#vitroClassGrouporganizations"/>
@@ -4930,8 +4919,8 @@
     <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <vitro:inPropertyGroupAnnot rdf:resource="http://vivoweb.org/ontology#vitroPropertyGroupoverview"/>
-    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayRankAnnot>
     <rdfs:label xml:lang="en-US">term type</rdfs:label>
+    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayRankAnnot>
   </rdf:Description>
   <rdf:Description rdf:about="http://vivoweb.org/ontology/core#advisor">
     <vitro:selectFromExistingAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</vitro:selectFromExistingAnnot>
@@ -5103,8 +5092,8 @@
     <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <vitro:inPropertyGroupAnnot rdf:resource="http://vivoweb.org/ontology#vitroPropertyGroupoverview"/>
-    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">40</vitro:displayRankAnnot>
     <rdfs:label xml:lang="en-US">entry term</rdfs:label>
+    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">40</vitro:displayRankAnnot>
   </rdf:Description>
   <rdf:Description rdf:about="http://purl.org/ontology/bibo/status">
     <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</vitro:displayLimitAnnot>