updates for NIHVIVO-3271 and NIHVIVO-3207

productMods/WEB-INF/ontologies/app/loadedAtStartup/vivoListViewConfig.rdf

@@ -161,8 +161,8 @@
         <display:listViewConfigFile rdf:datatype="http://www.w3.org/2001/XMLSchema#string">listViewConfig-webpage.xml</display:listViewConfigFile>
     </rdf:Description>    
   
-    <rdf:Description rdf:about="http://vivoweb.org/ontology/core#terminologyAnnotation">
+    <rdf:Description rdf:about="http://vivoweb.org/ontology/core#hasAssociatedConcept">
-        <display:listViewConfigFile rdf:datatype="http://www.w3.org/2001/XMLSchema#string">listViewConfig-terminologyAnnotation.xml</display:listViewConfigFile>
+        <display:listViewConfigFile rdf:datatype="http://www.w3.org/2001/XMLSchema#string">listViewConfig-hasAssociatedConcept.xml</display:listViewConfigFile>
-    </rdf:Description>            
+    </rdf:Description>
-    
+        
 </rdf:RDF>

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

@@ -1,10 +1,8 @@
-http://vivoweb.org/ontology/core#SubjectArea		No	Delete	Delete
 http://vivoweb.org/ontology/core#hasSubjectArea		No	Delete	Delete
 http://vivoweb.org/ontology/core#subjectAreaFor		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		No	Delete	Delete
 http://vivoweb.org/ontology/core#sourceVocabularyReference		No	Delete	Delete
 http://vivoweb.org/ontology/core#vocabularyReferenceFor		No	Delete	Delete
+http://vivoweb.org/ontology/core#SubjectArea	http://www.w3.org/2004/02/skos/core#Concept	Yes	Map	Directly-changed
 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/InternalConcept.sparql

@@ -14,10 +14,10 @@ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 PREFIX vivo: <http://vivoweb.org/ontology/core#>
 
 Construct {
-     ?something vivo:hasAssociatedConcept _:concept .
+     ?something vivo:hasAssociatedConcept ?concept .
-     _:concept vivo:conceptAssociatedWith ?something .
+     ?concept vivo:conceptAssociatedWith ?something .
-     _:concept rdf:type skos:Concept .
+     ?concept rdf:type skos:Concept .
-     _:concept rdfs:label ?label
+     ?concept rdfs:label ?label
 } where {
      ?something vivo:hasSubjectArea ?concept .     
      ?concept rdf:type vivo:SubjectArea .

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

@@ -14,15 +14,14 @@ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 PREFIX vivo: <http://vivoweb.org/ontology/core#>
 
 Construct {
-     ?person vivo:hasResearchArea _:concept .
+     ?something vivo:hasSubjectArea ?concept .
-     _:concept vivo:researchAreaOf ?person .
+     ?concept ?property ?object .
-     _:concept rdf:type skos:Concept .
+     ?subject ?property2 ?concept . 
-     _:concept rdfs:label ?label
 } where {
-     ?person vivo:hasResearchArea ?concept .
+     ?something vivo:hasSubjectArea ?concept .
      ?concept rdf:type vivo:SubjectArea .
-     optional {?concept rdfs:label ?label}
+     ?concept vivo:sourceVocabularyReference ?urllink .
-     optional {?concept vivo:sourceVocabularyReference ?urllink}
+     ?urllink vivo:linkURI ?uri .
-      
+     ?concept ?property ?object .
-     filter (!bound(?urllink))
+     ?subject ?property2 ?concept
 }

productMods/WEB-INF/ontologies/update/sparqlConstructs/deletions/ExternalResearchArea.sparql

@@ -15,8 +15,13 @@ PREFIX vivo: <http://vivoweb.org/ontology/core#>
 
 Construct {
      ?person vivo:hasResearchArea ?concept .
-     ?concept vivo:researchAreaOf ?person 
+     ?concept ?property ?object .
+     ?subject ?property2 ?concept . 
 } where {
      ?person vivo:hasResearchArea ?concept .
      ?concept rdf:type vivo:SubjectArea .
+     ?concept vivo:sourceVocabularyReference ?urllink .
+     ?urllink vivo:linkURI ?uri .
+     ?concept ?property ?object .
+     ?subject ?property2 ?concept .
 }

productMods/WEB-INF/ontologies/update/sparqlConstructs/deletions/contributingRole.sparql

@@ -0,0 +1,31 @@
+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 {
+     ?role vivo:roleIn ?something .
+     ?something vivo:relatedRole ?role
+} where {
+     {?role vivo:roleIn ?something}
+        union
+     {?something vivo:relatedRole ?role}
+     
+     {?something rdf:type vivo:Service}
+        union
+     {?something rdf:type foaf:Agent}
+        union
+     {?something rdf:type vivo:Agreement}
+        union
+     {?something rdf:type vivo:InformationResource}
+}

productMods/WEB-INF/ontologies/update/sparqlConstructs/deletions/realizedRole.sparql

@@ -0,0 +1,29 @@
+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 {
+     ?role vivo:roleIn ?something .
+     ?something vivo:relatedRole ?role
+} where {
+     {?role vivo:roleIn ?something}
+        union
+     {?something vivo:relatedRole ?role}
+     
+     {?something rdf:type vivo:Project}
+        union
+     {?something rdf:type event:Event}
+        union
+     {?something rdf:type vivo:EventSeries}
+}

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

@@ -399,13 +399,13 @@
     <rdfs:label xml:lang="en-US">administered by</rdfs:label>
   </rdf:Description>
   <rdf:Description rdf:about="http://xmlns.com/foaf/0.1/Person">
+    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">-1</vitro:displayRankAnnot>
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <vitro:customDisplayViewAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">individual--foaf-person.ftl</vitro:customDisplayViewAnnot>
     <rdfs:label xml:lang="en-US">Person</rdfs:label>
     <vitro:inClassGroup rdf:resource="http://vivoweb.org/ontology#vitroClassGrouppeople"/>
     <vitro:hiddenFromDisplayBelowRoleLevelAnnot 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">-1</vitro:displayRankAnnot>
   </rdf:Description>
   <rdf:Description rdf:about="http://aims.fao.org/aos/geopolitical.owl#isInGroup">
     <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
@@ -1990,8 +1990,8 @@
     <rdfs:label xml:lang="en-US">reviewer role of</rdfs:label>
   </rdf:Description>
   <rdf:Description rdf:about="http://vivoweb.org/ontology/core#IssuedCredential">
-    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</vitro:displayRankAnnot>
     <vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</vitro:displayLimitAnnot>
+    <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</vitro:displayRankAnnot>
     <vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
     <rdfs:label xml:lang="en-US">Issued Credential</rdfs:label>
     <vitro:inClassGroup rdf:resource="http://vivoweb.org/ontology#vitroClassGroupactivities"/>
@@ -3883,12 +3883,12 @@
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://vivoweb.org/ontology/core#hasResearchArea">
+    <rdfs:label xml:lang="en-US">research areas</rdfs:label>
     <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:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</vitro:displayLimitAnnot>
     <vitro:inPropertyGroupAnnot rdf:resource="http://vivoweb.org/ontology#vitroPropertyGroupoverview"/>
     <vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">10</vitro:displayRankAnnot>
-    <rdfs:label xml:lang="en-US">has research area</rdfs:label>
     <vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://vivoweb.org/ontology/core#Department">

productMods/config/listViewConfig-hasAssociatedConcept.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+
+<!-- See guidelines in vitro/doc/list_view_configuration_guidelines.txt -->
+
+<list-view-config>
+    <query-select>    
+        PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;    
+        PREFIX vivo: &lt;http://vivoweb.org/ontology/core#&gt;
+        PREFIX afn:  &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
+        PREFIX skos: &lt;http://www.w3.org/2004/02/skos/core#&gt;
+        PREFIX rdf:  &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
+        
+        SELECT ?conceptLabel ?concept
+        WHERE {
+         	?subject ?property ?concept .
+         	?concept rdf:type skos:Concept .
+         	?concept rdfs:label ?conceptLabel .
+
+        } ORDER BY ?conceptLabel                   
+    </query-select>
+
+    <template>propStatement-hasAssociatedConcept.ftl</template>
+</list-view-config>

productMods/config/listViewConfig-terminologyAnnotation.xml

@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="ISO-8859-1"?>
-<!-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
-
-<!-- See guidelines in vitro/doc/list_view_configuration_guidelines.txt -->
-
-<list-view-config>
-    <query-select>    
-        PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;    
-        PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
-        PREFIX afn:  &lt;http://jena.hpl.hp.com/ARQ/function#&gt;
-        
-        SELECT ?terminologyContextNode ?referencedTerm ?entryTerm ?termLabel ?termType WHERE {
-         	?subject ?property ?terminologyContextNode .
-    		?terminologyContextNode core:referencedTerm ?referencedTerm .
-    		?terminologyContextNode core:entryTerm ?entryTerm .
-    		?terminologyContextNode core:termLabel ?termLabel .
-    		?terminologyContextNode core:termType ?termType .
-        } ORDER BY ?termLabel                   
-    </query-select>
-
-    <template>propStatement-terminologyAnnotation.ftl</template>
-</list-view-config>

productMods/templates/freemarker/body/partials/individual/propStatement-hasAssociatedConcept.ftl

@@ -1,6 +1,6 @@
 <#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
 
-<#-- Custom object property statement view for http://vivoweb.org/ontology/core#authorInAuthorship. 
+<#-- Custom object property statement view for http://vivoweb.org/ontology/core#hasAssociatedConcept. 
     
      This template must be self-contained and not rely on other variables set for the individual page, because it
      is also used to generate the property statement during a deletion.  
@@ -14,5 +14,5 @@
 <#-- Use a macro to keep variable assignments local; otherwise the values carry over to the
      next statement -->
 <#macro showTerm statement>
-	<a href="${statement.referencedTerm}">${statement.termLabel} (${statement.termType})</a>  
+	<a href="${statement.concept}">${statement.conceptLabel}</a>  
 </#macro>