Merge branch 'develop' of github.com:vivo-project/VIVO into develop

languages/example/themes/wilma/i18n/all_es.properties

@@ -421,8 +421,8 @@ check_grants_to_exclude = Compruebe las subvenciones y proyectos que desea exclu
 manage_affiliated_people = Gestione personas afiliadas
 check_people_to_exclude = Compruebe las personas que desea excluir de la página de perfil.
 
-manage_grants = Gestione subvenciones para
+manage_publications = Gestione publicaciónes para
-check_pubs_to_exclude = Compruebe las subvenciones que desea excluir de la página de perfil.
+check_pubs_to_exclude = Compruebe las publicaciónes que desea excluir de la página de perfil.
 
 manage_web_pages = Gestionar páginas Web
 has_no_webpages = Este individuo no tiene actualmente las páginas web específicas. Añadir una nueva página web haciendo clic en el botón de abajo.
@@ -822,3 +822,6 @@ full_name = Nombre y apellidos
 full_name_for = nombre y apellidos para
 first_name = Primer nombre
 last_name = Apellido
+title_not_found = Título que no se encuentra.
+speeches_capitalized = Discursos
+theses_capitalized = Tesis

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

@@ -13,5 +13,6 @@ CONSTRUCT {
       ?person vivo:editorOf ?document
     } UNION {
       ?document vivo:editor ?person
+      FILTER NOT EXISTS { ?person vivo:editorOf ?document } 
     }
 }

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

@@ -11,5 +11,7 @@ CONSTRUCT {
 } WHERE {
     { ?person vivo:currentlyHeadOf ?org }
       UNION 
-    { ?org vivo:currentlyHeadedBy ?person }
+    { ?org vivo:currentlyHeadedBy ?person 
+      FILTER NOT EXISTS { ?person vivo:currentlyHeadOf ?org }
+    }
 }

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

@@ -11,5 +11,7 @@ CONSTRUCT {
 } WHERE {
      {  ?person vivo:currentMemberOf ?org }
        UNION 
-     { ?org vivo:hasCurrentMember ?person }
+     { ?org vivo:hasCurrentMember ?person 
+       FILTER NOT EXISTS { ?person vivo:currentMemberOf ?org }
+     }
 }

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

@@ -0,0 +1,17 @@
+PREFIX vivo: <http://vivoweb.org/ontology/core#> 
+PREFIX owl: <http://www.w3.org/2002/07/owl#Thing> 
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+
+CONSTRUCT {
+    ?person1 vivo:relatedBy _:relationship .
+    ?person2 vivo:relatedBy _:relationship .
+    _:relationship vivo:relates ?person1 .
+    _:relationship vivo:relates ?person2 .
+} WHERE {
+     {  ?person1 vivo:hasCollaborator ?person2 
+        FILTER NOT EXISTS {
+            ?person1 vivo:relatedBy ?relationship .
+            ?relationship vivo:relates ?person2
+        }
+     }
+}

productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/grant-pre.sparql

@@ -0,0 +1,11 @@
+PREFIX vivo: <http://vivoweb.org/ontology/core#> 
+PREFIX owl: <http://www.w3.org/2002/07/owl#Thing> 
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+
+CONSTRUCT {
+    ?role vivo:relatedBy ?grant .
+    ?grant vivo:relates ?role    
+} WHERE {
+    ?role vivo:roleContributesTo ?grant .
+    ?grant a vivo:Grant .
+}

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

@@ -13,5 +13,7 @@ CONSTRUCT {
 } WHERE {
     { ?agent vivo:administers ?grant }
       UNION
-    { ?grant vivo:administeredBy ?agent }
+    { ?grant vivo:administeredBy ?agent 
+      FILTER NOT EXISTS { ?agent vivo:administers ?grant } 
+    }
 }

productMods/WEB-INF/ontologies/update/sparqlConstructs/deletions/grant-pre-del.sparql

@@ -0,0 +1,11 @@
+PREFIX vivo: <http://vivoweb.org/ontology/core#> 
+PREFIX owl: <http://www.w3.org/2002/07/owl#Thing> 
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+
+CONSTRUCT {
+    ?role vivo:roleContributesTo ?grant . 
+    ?grant vivo:contributingRole ?role .
+} WHERE {
+    ?role vivo:roleContributesTo ?grant .
+    ?grant a vivo:Grant .
+}

productMods/config/listViewConfig-advisorIn.xml

@@ -25,11 +25,14 @@
                          ?dateTimeEnd
 
          WHERE {
-                     ?subject ?property ?advisory 
+                     ?subject ?property ?advisory .
+                     ?advisory core:relates ?advisor .
+                     ?advisor <http://purl.obolibrary.org/obo/RO_0000053> ?advisorRole .
                      LET ( ?localName := afn:localname(?advisory) )
                      OPTIONAL { ?advisory rdfs:label ?advisoryLabel  }
                      OPTIONAL { ?advisory core:relates ?advisee .
                                 ?advisee a foaf:Person .
+                                ?advisee <http://purl.obolibrary.org/obo/RO_0000053> ?adviseeRole
                                 OPTIONAL { ?advisee rdfs:label ?adviseeLabel }
                      }
                      OPTIONAL { ?advisory core:relates ?degree .
@@ -74,7 +77,10 @@
             ?subject ?property ?advisory .
             ?advisory a core:AdvisingRelationship .
             ?advisory ?advisoryProperty ?advisoryValue .
-            ?advisory rdfs:label ?advisoryLabel 
+            ?advisory rdfs:label ?advisoryLabel .
+            ?advisory core:relates ?advisor .
+            ?advisor <http://purl.obolibrary.org/obo/RO_0000053> ?advisorRole .
+            ?advisorRole a core:AdvisorRole
         } WHERE {
             {
                ?subject ?property ?advisory .
@@ -88,10 +94,23 @@
                ?advisory a core:AdvisingRelationship .
                ?advisory ?advisoryProperty ?advisoryValue . 
                ?advisory rdfs:label ?advisoryLabel
+            } UNION {
+               ?subject ?property ?advisory .
+               ?advisory a core:AdvisingRelationship .
+               ?advisory ?advisoryProperty ?advisoryValue . 
+               ?advisory core:relates ?advisor .
+               ?advisor <http://purl.obolibrary.org/obo/RO_0000053> ?advisorRole .
+               ?advisorRole a core:AdvisorRole
             } 
         }
     </query-construct>
     
+    OPTIONAL { ?advisory core:relates ?advisee .
+               ?advisee a foaf:Person .
+               ?advisee &lt;http://purl.obolibrary.org/obo/RO_0000053&gt; ?adviseeRole
+
+
+
     <query-construct>
             PREFIX bibo: &lt;http://purl.org/ontology/bibo/&gt;
             PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt; 
@@ -104,6 +123,8 @@
                 ?advisory core:relates ?advisee .
                 ?advisee a foaf:Person .
                 ?advisee rdfs:label ?adviseeLabel .
+                ?advisee &lt;http://purl.obolibrary.org/obo/RO_0000053&gt; ?adviseeRole .
+                ?adviseeRole a core:AdviseeRole .
                 ?advisory core:relates ?degree .
                 ?degree a core:AcademicDegree .
                 ?degree rdfs:label ?degreeLabel .
@@ -117,11 +138,15 @@
                     ?advisory a core:AdvisingRelationship .
                     ?advisory core:relates ?advisee .
                     ?advisee a foaf:Person .
+                    ?advisee &lt;http://purl.obolibrary.org/obo/RO_0000053&gt; ?adviseeRole .
+                    ?adviseeRole a core:AdviseeRole 
                 } UNION {
                     ?subject ?property ?advisory .
                     ?advisory a core:AdvisingRelationship .
                     ?advisory core:relates ?advisee .
                     ?advisee a foaf:Person .
+                    ?advisee &lt;http://purl.obolibrary.org/obo/RO_0000053&gt; ?adviseeRole .
+                    ?adviseeRole a core:AdviseeRole .
                     ?advisee rdfs:label ?adviseeLabel
                 } UNION {
                     ?subject ?property ?advisory .

productMods/config/listViewConfig-authorInAuthorship.xml

@@ -30,7 +30,7 @@
             ?subject ?property ?authorship .
             ?authorship core:relates ?infoResource .
             ?infoResource a bibo:Document .                      
-            ?infoResource rdfs:label ?infoResourceName 
+            ?infoResource rdfs:label ?infoResourceName .
             
                OPTIONAL { ?infoResource bibo:volume ?volume }
                OPTIONAL { ?infoResource bibo:pageStart ?startPage }
@@ -49,9 +49,7 @@
                OPTIONAL { ?infoResource core:partOf ?partOfObj .
                           ?partOfObj rdfs:label ?partOf
                }
-               OPTIONAL { ?infoResource vitro:mostSpecificType ?subclass .
+               OPTIONAL { ?infoResource vitro:mostSpecificType ?subclass }     
-                          ?subclass rdfs:subClassOf core:InformationResource
-               }     
                OPTIONAL { ?infoResource core:hasPublicationVenue ?publishedIn .
                           ?publishedIn  rdfs:label ?journal 
                }
@@ -67,12 +65,14 @@
     </query-select>
 
     <query-construct>
-        PREFIX core: &lt;http://vivoweb.org/ontology/core#&gt;
+        PREFIX bibo: &lt;http://purl.org/ontology/bibo/&gt;
-        PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;    
+        PREFIX vitro: &lt;http://vitro.mannlib.cornell.edu/ns/vitro/0.7#&gt;    
         CONSTRUCT {
-            ?subclass rdfs:subClassOf core:InformationResource 
+            ?infoResource a bibo:Document .
+            ?infoResource vitro:mostSpecificType ?subclass 
         } WHERE {
-            ?subclass rdfs:subClassOf core:InformationResource 
+            ?infoResource a bibo:Document .
+            ?infoResource vitro:mostSpecificType ?subclass 
         }
     </query-construct>
 

productMods/js/individual/individualUtils.js

@@ -122,19 +122,19 @@ $(document).ready(function(){
         
     // if there are no selected pubs, hide the manage link; same for grants
     // and affiliated people on the org profile page
-    if ( $('ul#authorInAuthorshipList').children('li').length < 1 && $('h3#authorInAuthorship').attr('class') != "hiddenPubs" ) {
+    if ( $('ul#relatedBy-Authorship-List').children('li').length < 1 && $('h3#relatedBy-Authorship').attr('class') != "hiddenPubs" ) {
         $('a#managePubLink').hide();
     }
 
-    if ( $('ul#hasResearcherRoleList').children('li').length < 1 &&
+    if ( $('ul#RO_0000053-ResearcherRole-List').children('li').length < 1 &&
-            $('ul#hasPrincipalInvestigatorRoleList').children('li').length < 1 &&
+            $('ul#RO_0000053-PrincipalInvestigatorRole-List').children('li').length < 1 &&
-            $('ul#hasCo-PrincipalInvestigatorRoleList').children('li').length < 1 &&
+            $('ul#RO_0000053-CoPrincipalInvestigatorRole-List').children('li').length < 1 &&
-            $('ul#hasInvestigatorRoleList').children('li').length < 1 &&
+            $('ul#RO_0000053-InvestigatorRole-List').children('li').length < 1 &&
-            $('h3#hasResearcherRole').attr('class') != "hiddenGrants" ) {
+            $('h3#RO_0000053-ResearcherRole').attr('class') != "hiddenGrants" ) {
                     $('a#manageGrantLink').hide();
     }
 
-    if ( $('ul#organizationForPositionList').children('li').length < 1 && $('h3#organizationForPosition').attr('class') != "hiddenPeople" ) {
+    if ( $('ul#relatedBy-Position-List').children('li').length < 1 && $('h3#relatedBy-Position').attr('class') != "hiddenPeople" ) {
         $('a#managePeopleLink').hide();
     }
    

productMods/templates/freemarker/body/individual/individual.ftl

@@ -15,7 +15,7 @@
     ${affiliatedResearchAreas!}
         </section> <!-- #individual-info -->
     </section> <!-- #individual-intro -->
-    <!--postindiviudal overiew tfl-->
+    <!--postindividual overiew ftl-->
 </#assign>
 
 <#include "individual-vitro.ftl">

productMods/templates/freemarker/body/individual/manageLabelsForIndividualAddForm.ftl

@@ -3,17 +3,17 @@
 <#assign isPersonType = editConfiguration.pageData.isPersonType />
 <form id="addLabelForm" name="addLabelForm" class="customForm" action="${submitUrl}">
            <h2>${i18n().add_label}</h2>
-           <#if isPersonType = "true">       
+           <#if isPersonType?has_content && isPersonType = "true">       
 	        <p>
 	            <label for="firstName">${i18n().first_name} ${requiredHint}</label>
 	            <input size="30"  type="text" id="firstName" name="firstName" value="${firstNameValue}" />
 	        </p>
 			<#--TODO: With ISF changes, add middle name input-->
 	
-			<!--p-->
+			<p>
-	            <!--label for="middleName">${i18n().middle_name} ${requiredHint}</label>
+	            <label for="middleName">${i18n().middle_name} </label>
 	            <input size="30"  type="text" id="middleName" name="middleName" value="${middleNameValue}" />
-	        </p-->
+	        </p>
 	
 	        <p>
 	            <label for="lastName">${i18n().last_name} ${requiredHint}</label>

productMods/templates/freemarker/body/individual/manageLabelsForIndividualSubmissionErrors.ftl

@@ -5,8 +5,7 @@
 <#--Get existing value for specific data literals and uris, in case the form is returned because of an error-->
 <#assign firstNameValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "firstName")/>
 <#assign lastNameValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "lastName")/>
-<#--With ISF changes, we also have a niddle name value, also add error field below-->
+<#assign middleNameValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "middleName") />
-<#--assign middleNameValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "middleName") /-->
 
 <#assign labelValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "label")/>
 <#assign newLabelLanguageValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "newLabelLanguage")/>

productMods/templates/freemarker/body/partials/individual/individual-visualizationFoafPerson.ftl

@@ -3,12 +3,14 @@
 <#-- Template for sparkline visualization on individual profile page -->
 
 <#-- Determine whether this person is an author -->
-<#assign isAuthor = p.hasStatements(propertyGroups, "${core}authorInAuthorship") />
+<#assign isAuthor = p.hasVisualizationStatements(propertyGroups, "${core}relatedBy", "${core}Authorship") />
 
 <#-- Determine whether this person is involved in any grants -->
-<#assign isInvestigator = ( p.hasStatements(propertyGroups, "${core}hasInvestigatorRole") ||
+<#assign obo_RO53 = "http://purl.obolibrary.org/obo/RO_0000053">
-                            p.hasStatements(propertyGroups, "${core}hasPrincipalInvestigatorRole") || 
+
-                            p.hasStatements(propertyGroups, "${core}hasCo-PrincipalInvestigatorRole") ) >
+<#assign isInvestigator = ( p.hasVisualizationStatements(propertyGroups, "${obo_RO53}", "${core}InvestigatorRole") ||
+                            p.hasVisualizationStatements(propertyGroups, "${obo_RO53}", "${core}PrincipalInvestigatorRole") || 
+                            p.hasVisualizationStatements(propertyGroups, "${obo_RO53}", "${core}CoPrincipalInvestigatorRole") ) >
 
 <#if (isAuthor || isInvestigator)>
  

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

@@ -18,8 +18,8 @@
     <span class="hideThis">&nbsp;</span>
     <script type="text/javascript" >
         $('span.hideThis').parent().parent().addClass("hideThis");
-        if ( $('h3#authorInAuthorship').attr('class').length == 0 ) {
+        if ( $('h3#relatedBy-Authorship').attr('class').length == 0 ) {
-            $('h3#authorInAuthorship').addClass('hiddenPubs');
+            $('h3#relatedBy-Authorship').addClass('hiddenPubs');
         }
         $('span.hideThis').parent().remove();
     </script>

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

@@ -16,8 +16,8 @@
     <span class="hideThis">&nbsp;</span>
     <script type="text/javascript" >
         $('span.hideThis').parent().parent().addClass("hideThis");
-        if ( $('h3#hasResearcherRole').attr('class').length == 0 ) {
+        if ( $('h3#RO_0000053-ResearcherRole').attr('class').length == 0 ) {
-            $('h3#hasResearcherRole').addClass('hiddenGrants');
+            $('h3#RO_0000053-ResearcherRole').addClass('hiddenGrants');
         }
         $('span.hideThis').parent().remove();
     </script>

productMods/templates/freemarker/edit/forms/manageGrantsForIndividual.ftl

@@ -25,7 +25,7 @@ ${i18n().check_grants_to_exclude}
         <ul >
             <#list grantList as grant>
             <li>
-                <input type="checkbox" class="grantCheckbox" <#if grant.hideThis??>checked</#if> />${grant.label!}
+                <input type="checkbox" class="grantCheckbox" <#if grant.hideThis??>checked</#if> />${grant.label!grant.activity!}
             </li>
             <script type="text/javascript">
                 grantData.push({

productMods/templates/freemarker/edit/forms/managePublicationsForIndividual.ftl

@@ -6,9 +6,9 @@
 <#if subjectName?contains(",") >
 <#assign lastName = subjectName?substring(0,subjectName?index_of(",")) />
 <#assign firstName = subjectName?substring(subjectName?index_of(",") + 1) />
-<h2>${i18n().manage_publications} ${firstName} ${lastName}</h2>
+<h2>${i18n().manage_publications_for} ${firstName} ${lastName}</h2>
 <#else>
-<h2>${i18n().manage_publications} ${subjectName}</h2>
+<h2>${i18n().manage_publications_for} ${subjectName}</h2>
 </#if>
 <p style="margin-left:25px;margin-bottom:12px">
 ${i18n().check_pubs_to_exclude}
@@ -25,9 +25,9 @@ ${i18n().check_pubs_to_exclude}
         <#if sub = "Software">
             ${sub}
         <#elseif sub = "Thesis">
-            Theses
+            ${i18n().theses_capitalized}
         <#elseif sub = "Speech">
-            Speeches
+            ${i18n().speeches_capitalized}
         <#else>
             ${sub}s
         </#if>
@@ -38,7 +38,7 @@ ${i18n().check_pubs_to_exclude}
             <#list pubs as pub>
             <li>
                 <input type="checkbox" class="pubCheckbox" <#if pub.hideThis??>checked</#if> />
-                <#if pub.title?has_content>${pub.title!}<#else>Title not found.</#if>
+                <#if pub.title?has_content>${pub.title!}<#else>${i18n().title_not_found}</#if>
             </li>
             <script type="text/javascript">
                 publicationData.push({

productMods/templates/freemarker/edit/forms/newIndividualForm.ftl

@@ -11,6 +11,8 @@
 <#--Get existing value for specific data literals and uris-->
 <#assign firstNameValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "firstName")/>
 <#assign lastNameValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "lastName")/>
+<#assign middleNameValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "middleName")/>
+
 <#assign labelValue = lvf.getFormFieldValue(editSubmission, editConfiguration, "label")/>
 
 <#--If edit submission exists, then retrieve validation errors if they exist-->
@@ -52,6 +54,11 @@
             <input size="30"  type="text" id="firstName" name="firstName" value="${firstNameValue}" />
         </p>
         
+        <p>
+            <label for="lastName">${i18n().middle_name} </label>
+            <input size="30"  type="text" id="middleName" name="middleName" value="${middleNameValue}" />
+        </p>
+
         <p>
             <label for="lastName">${i18n().last_name} ${requiredHint}</label>
             <input size="30"  type="text" id="lastName" name="lastName" value="${lastNameValue}" />

productMods/templates/freemarker/visualization/entitycomparison/entityComparisonErrorCommonBody.ftl

@@ -16,7 +16,7 @@
 <h1 id="noPubsOrGrants-header">${organizationLabel}</h1>
 
     <h3 id="alternative-vis-info">${textForCurrentEntityComparisonType?capitalize} ${i18n().temporal_graph_capitalized} 
-        <span id="noPubsOrGrants-span">|&nbsp;<a  href="${temporalGraphURL}" title="${i18n().view}">${i18n().view} ${textForOtherEntityComparisonType} ${i18n().temporal_graph}</a></span>
+        <span id="noPubsOrGrants-span">|&nbsp;<a  href="${temporalGraphURL}" title="${i18n().view}">${i18n().view}&nbsp${textForOtherEntityComparisonType}&nbsp;${i18n().temporal_graph}</a></span>
     </h3>
     <div id="error-body">
         <p>${i18n().entity_comp_error_text1} 

productMods/templates/freemarker/visualization/tools.ftl

@@ -5,7 +5,7 @@
 
 <h2>${i18n().visualization_tools}</h2>
 
-<a href="${refreshCacheURL}">${i18n().refresh_cached_vis_model}</a> 
+<a href="${refreshCacheURL}">${i18n().refresh_cached_vis_models}</a> 
 <section class="visualizationTools">
 <h3>${i18n().why_needed}</h3>
 <p>${i18n().vis_tools_note_one}</p>

rdf/display/everytime/PropertyConfig.n3

@@ -453,7 +453,7 @@ local:eventWithinConfig a :ObjectPropertyDisplayConfig ;
 
 local:includesEventContext a :ConfigContext ;
     :hasConfiguration local:includesEventConfig ;
-    :configContextFor <http://purl.obolibrary.org/obo/BFO_0000050> ;
+    :configContextFor <http://purl.obolibrary.org/obo/BFO_0000051> ;
     :qualifiedByDomain      <http://purl.org/NET/c4dm/event.owl#Event> ;
     :qualifiedBy      <http://purl.org/NET/c4dm/event.owl#Event> .
 
@@ -467,11 +467,11 @@ local:includesEventConfig a :ObjectPropertyDisplayConfig ;
 
 local:inEventSeriesContext a :ConfigContext ;
     :hasConfiguration local:inEventSeriesConfig ;
-    :configContextFor <http://purl.obolibrary.org/obo/BFO_0000051> ;
+    :configContextFor <http://purl.obolibrary.org/obo/BFO_0000050> ;
     :qualifiedByDomain      <http://purl.org/NET/c4dm/event.owl#Event> ;
     :qualifiedBy      <http://purl.org/NET/c4dm/event.owl#EventSeries> .
 
-local:includesEventConfig a :ObjectPropertyDisplayConfig ;
+local:inEventSeriesConfig a :ObjectPropertyDisplayConfig ;
     :listViewConfigFile "listViewConfig-default.xml"^^xsd:string ;
     :displayName "in event series" ;
     vitro:displayRankAnnot 3;
@@ -479,3 +479,16 @@ local:includesEventConfig a :ObjectPropertyDisplayConfig ;
     vitro:prohibitedFromUpdateBelowRoleLevelAnnot role:public ;
     :propertyGroup <http://vivoweb.org/ontology#vitroPropertyGroupoverview> .
 
+local:awardAssignedByContext a :ConfigContext ;
+    :hasConfiguration local:awardAssignedByConfig ;
+    :configContextFor <http://vivoweb.org/ontology/core#assignedBy> ;
+    :qualifiedByDomain      <http://vivoweb.org/ontology/core#Award> ;
+    :qualifiedBy      <http://vivoweb.org/ontology/core#Award> .
+
+local:awardAssignedByConfig a :ObjectPropertyDisplayConfig ;
+    :listViewConfigFile "listViewConfig-default.xml"^^xsd:string ;
+    :displayName "award conferred by" ;
+    vitro:displayRankAnnot 3;
+    vitro:hiddenFromDisplayBelowRoleLevelAnnot role:public ;
+    vitro:prohibitedFromUpdateBelowRoleLevelAnnot role:public ;
+    :propertyGroup <http://vivoweb.org/ontology#vitroPropertyGroupoverview> .

rdf/tbox/filegraph/classes-additional.owl

@@ -539,7 +539,6 @@
 
     <owl:Class rdf:about="http://purl.org/spar/c4o/BibliographicInformationSource">
         <rdfs:label xml:lang="en-us">Bibliographic Information Source</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://isf/deprecated_class"/>
         <vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A source of information about bibliographic citations, such as Google Scholar, Web of Science or Scopus.</vitro:descriptionAnnot>
     </owl:Class>
     
@@ -792,7 +791,6 @@
 
     <owl:Class rdf:about="http://vivoweb.org/ontology/core#EducationalProcess">
         <rdfs:label xml:lang="en-us">Educational Process</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://isf/deprecated_class"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://vivoweb.org/ontology/core#supplementalInformation"/>
@@ -805,8 +803,8 @@
                 <owl:allValuesFrom rdf:resource="http://vivoweb.org/ontology/core#DateTimeInterval"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <vitro:exampleAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Currently any abstract name is given to individuals of this class. This could change in the future.</vitro:exampleAnnot>
+        <obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Currently any abstract name is given to individuals of this class. This could change in the future.</obo:IAO_0000112>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Represents educational training that has been received.</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Represents educational training that has been received.</obo:IAO_0000115>
         <vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This connects person to their academic degree through this educational training, but can also be used when the training does not result in a degree.</vitro:descriptionAnnot>
     </owl:Class>
     
@@ -915,7 +913,7 @@
                 <owl:allValuesFrom rdf:resource="http://vivoweb.org/ontology/core#DateTimeValue"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The most general classification of an information resource</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The most general classification of an information resource</obo:IAO_0000115>
     </owl:Class>
     
 
@@ -1044,8 +1042,8 @@
                 <owl:allValuesFrom rdf:resource="http://vivoweb.org/ontology/core#DateTimeInterval"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A person&apos;s, group&apos;s or organization&apos;s role in an endeavor</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A person&apos;s, group&apos;s or organization&apos;s role in an endeavor</obo:IAO_0000115>
-        <vitro:exampleAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Only use if no specific subclasses of core:Role describe the role.</vitro:exampleAnnot>
+        <obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Only use if no specific subclasses of core:Role describe the role.</obo:IAO_0000112>
         <vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Only use this broad role class if no subclasses of role describe the item being classified.</vitro:descriptionAnnot>
     </owl:Class>
     
@@ -1056,7 +1054,6 @@
 
     <owl:Class rdf:about="http://vivoweb.org/ontology/core#Software">
         <rdfs:label xml:lang="en-us">Software</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://isf/deprecated_class"/>
         <rdfs:subClassOf rdf:resource="http://vivoweb.org/ontology/core#InformationResource"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -1064,7 +1061,7 @@
                 <owl:allValuesFrom rdf:resource="http://www.w3.org/2000/01/rdf-schema#Literal"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Computer program and its related documentation; directs the operation of a computer</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Computer program and its related documentation; directs the operation of a computer</obo:IAO_0000115>
     </owl:Class>
     
 

rdf/tbox/filegraph/object-properties.owl

@@ -1532,6 +1532,7 @@ there is a measurement process p that has specified output m, a measurement datu
     <owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#geographicFocusOf">
         <rdfs:label xml:lang="en">geographic focus of</rdfs:label>
         <rdfs:domain rdf:resource="http://vivoweb.org/ontology/core#GeographicRegion"/>
+        <owl:inverseOf rdf:resource="http://vivoweb.org/ontology/core#geographicFocus"/>
     </owl:ObjectProperty>
     
 

rdf/tbox/filegraph/other.owl

@@ -75,16 +75,6 @@
     
     
 
-    <!-- http://vivoweb.org/ontology/core#URLLink -->
-
-    <owl:Class rdf:about="http://vivoweb.org/ontology/core#URLLink">
-        <rdfs:label xml:lang="en">urllink</rdfs:label>
-        <obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The full URL.</obo:IAO_0000112>
-        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uniform Resource Locator (URL) specifies where an identified resource is available and the mechanism for retrieving it.</obo:IAO_0000115>
-        <obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://info.slis.indiana.edu/~katy/</obo:IAO_0000112>
-    </owl:Class>
-    
-
 
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////

rdf/tbox/filegraph/personTypes.n3

@@ -52,46 +52,46 @@ core:FacultyMember
       rdfs:subClassOf foaf:Person , <http://isf/deprecated_class> ;
       vitro:descriptionAnnot
               "Definition from here: http://research.carleton.ca/htr/defs.php."^^xsd:string ;
-      vitro:shortDef "A person with at least one academic appointment to a specific faculty of a university or institution of higher learning."^^xsd:string .
+      obo:IAO_0000115 "A person with at least one academic appointment to a specific faculty of a university or institution of higher learning."^^xsd:string .
 
 core:Postdoc
       a       owl:Class ;
       rdfs:label "Postdoc"@en-us ;
       rdfs:subClassOf <http://isf/deprecated_class> , core:NonFacultyAcademic ;
-      vitro:shortDef "A Person holding an academic employment appointment focused on research rather than teaching; temporary (or for some defined term)"^^xsd:string .
+      obo:IAO_0000115 "A Person holding an academic employment appointment focused on research rather than teaching; temporary (or for some defined term)"^^xsd:string .
 
 core:NonFacultyAcademic
       a       owl:Class ;
       rdfs:label "Non-Faculty Academic"@en-us ;
       rdfs:subClassOf foaf:Person , <http://isf/deprecated_class> ;
-      vitro:shortDef "A person not considered a faculty member but holding an academic appointment."^^xsd:string .
+      obo:IAO_0000115 "A person not considered a faculty member but holding an academic appointment."^^xsd:string .
 
 core:EmeritusLibrarian
       a       owl:Class ;
       rdfs:label "Librarian Emeritus"@en-us ;
       rdfs:subClassOf foaf:Person , <http://isf/deprecated_class> ;
-      vitro:shortDef "A retired librarian who has retained their rank, title and privileges."^^xsd:string .
+      obo:IAO_0000115 "A retired librarian who has retained their rank, title and privileges."^^xsd:string .
 
 core:EmeritusFaculty
       a       owl:Class ;
       rdfs:label "Faculty Member Emeritus"@en-us ;
       rdfs:subClassOf foaf:Person , <http://isf/deprecated_class> ;
-      vitro:shortDef "A retired faculty member who has retained their rank, title and privileges."^^xsd:string .
+      obo:IAO_0000115 "A retired faculty member who has retained their rank, title and privileges."^^xsd:string .
 
 core:Librarian
       a       owl:Class ;
       rdfs:label "Librarian"@en-us ;
       rdfs:subClassOf foaf:Person , <http://isf/deprecated_class> ;
-      vitro:shortDef "A person working in a position of librarian or information professional, or academic or technical expert in support of providing information services or materials."^^xsd:string .
+      obo:IAO_0000115 "A person working in a position of librarian or information professional, or academic or technical expert in support of providing information services or materials."^^xsd:string .
 
 core:EmeritusProfessor
       a       owl:Class ;
       rdfs:label "Professor Emeritus"@en-us ;
       rdfs:subClassOf core:EmeritusFaculty , foaf:Person , <http://isf/deprecated_class> ;
-      vitro:shortDef "A retired professor who has retained their rank, title and privileges."^^xsd:string .
+      obo:IAO_0000115 "A retired professor who has retained their rank, title and privileges."^^xsd:string .
 
 core:NonAcademic
       a       owl:Class ;
       rdfs:label "Non-Academic"@en-us ;
       rdfs:subClassOf foaf:Person , <http://isf/deprecated_class> ;
-      vitro:shortDef "A person holding a position that is not considered to be an academic appointment."^^xsd:string .
+      obo:IAO_0000115 "A person holding a position that is not considered to be an academic appointment."^^xsd:string .

rdf/tbox/filegraph/publication.owl

@@ -27,7 +27,6 @@
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
-    <owl:AnnotationProperty rdf:about="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#shortDef"/>
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
     
@@ -864,7 +863,7 @@
     <owl:Class rdf:about="http://purl.org/spar/fabio/ClinicalGuideline">
         <rdfs:label xml:lang="en">clinical guideline</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.org/ontology/bibo/Document"/>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A recommendation on the appropriate treatment and care of people with a specific disease or condition, based on the best available evidence, designed to help healthcare professionals in their work.</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A recommendation on the appropriate treatment and care of people with a specific disease or condition, based on the best available evidence, designed to help healthcare professionals in their work.</obo:IAO_0000115>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A recommendation on the appropriate treatment and care of people with a specific disease or condition, based on the best available evidence, designed to help healthcare professionals in their work.</obo:IAO_0000115>
     </owl:Class>
     
@@ -875,7 +874,7 @@
     <owl:Class rdf:about="http://purl.org/spar/fabio/Comment">
         <rdfs:label xml:lang="en">comment</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.org/ontology/bibo/Document"/>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A verbal or written remark concerning some entity. In written form, a comment is often appended to that entity and termed an annotation. Within computer programs or ontologies, comments are added to enhance human understanding, and are usually prefaced by</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A verbal or written remark concerning some entity. In written form, a comment is often appended to that entity and termed an annotation. Within computer programs or ontologies, comments are added to enhance human understanding, and are usually prefaced by</obo:IAO_0000115>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A verbal or written remark concerning some entity. In written form, a comment is often appended to that entity and termed an annotation. Within computer programs or ontologies, comments are added to enhance human understanding, and are usually prefaced by a special syntactic symbol that ensures they are ignored during execution of the program.
 
 has super-classes</obo:IAO_0000115>
@@ -888,7 +887,7 @@ has super-classes</obo:IAO_0000115>
     <owl:Class rdf:about="http://purl.org/spar/fabio/Erratum">
         <rdfs:label xml:lang="en">erratum</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.org/ontology/bibo/Document"/>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A formal correction to an error introduced by the publisher into a previously published document.</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A formal correction to an error introduced by the publisher into a previously published document.</obo:IAO_0000115>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A formal correction to an error introduced by the publisher into a previously published document.</obo:IAO_0000115>
     </owl:Class>
     
@@ -1142,12 +1141,6 @@ Contents
     
 
 
-    <!-- http://vivoweb.org/ontology/core#URLLink -->
-
-    <owl:Class rdf:about="http://vivoweb.org/ontology/core#URLLink"/>
-    
-
-
     <!-- http://vivoweb.org/ontology/core#Video -->
 
     <owl:Class rdf:about="http://vivoweb.org/ontology/core#Video">

rdf/tbox/filegraph/research.owl

@@ -25,7 +25,6 @@
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118"/>
-    <owl:AnnotationProperty rdf:about="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#shortDef"/>
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
     
@@ -93,7 +92,7 @@
     <owl:Class rdf:about="http://vivoweb.org/ontology/scientific-research#Phase0ClinicalTrial">
         <rdfs:label xml:lang="en">phase 0 clinical trial</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000016"/>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 0 Clinical Trial</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 0 Clinical Trial</obo:IAO_0000115>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 0 is a recent designation for exploratory, first-in-human trials  conducted in accordance with the United States Food and Drug Administration&apos;s (FDA) 2006 Guidance on Exploratory Investigational New Drug (IND) Studies.  Phase 0 trials are also known as human microdosing  studies and are designed to speed up the development of promising drugs or imaging agents by establishing very early on whether the drug or agent behaves in human subjects as was expected from preclinical studies.</obo:IAO_0000115>
     </owl:Class>
     
@@ -105,7 +104,7 @@
         <rdfs:label xml:lang="en">phase 1 clinical trial</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000016"/>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In Phase I trials, researchers test an experimental drug or treatment in a small group of people (20-80) for the first time to evaluate its safety, determine a safe dosage range, and identify side effects</obo:IAO_0000115>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 1 Clinical Trial</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 1 Clinical Trial</obo:IAO_0000115>
     </owl:Class>
     
 
@@ -116,7 +115,7 @@
         <rdfs:label xml:lang="en">phase 2 clinical trial</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000016"/>
         <obo:IAO_0000115 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.</obo:IAO_0000115>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 2 Clinical Trial</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 2 Clinical Trial</obo:IAO_0000115>
     </owl:Class>
     
 
@@ -128,7 +127,7 @@
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000016"/>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In Phase 3 trials, an experimental study drug or treatment is given to large groups of people (1,000-3,000) to confirm its effectiveness, monitor side effects, compare it to commonly used treatments, and collect information that will allow the experimental drug or treatment to be used safely.
 </obo:IAO_0000115>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 3 Clinical Trial</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 3 Clinical Trial</obo:IAO_0000115>
     </owl:Class>
     
 
@@ -139,7 +138,7 @@
         <rdfs:label xml:lang="en">phase 4 clinical trial</rdfs:label>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000016"/>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In Phase 4 trials, post marketing studies delineate additional information including the drug&apos;s or treatment&apos;s risks, benefits, and optimal use.</obo:IAO_0000115>
-        <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 4 Clinical Trial</vitro:shortDef>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phase 4 Clinical Trial</obo:IAO_0000115>
     </owl:Class>
 </rdf:RDF>
 

src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManageGrantsForIndividualController.java

@@ -67,13 +67,13 @@ public class ManageGrantsForIndividualController extends FreemarkerHttpServlet {
         + "PREFIX afn:  <http://jena.hpl.hp.com/ARQ/function#> \n"
         + "SELECT DISTINCT ?subclass ?role (str(?label2) as ?label) ?activity ?hideThis WHERE { \n"
         + "    ?subject ?roleProp ?role . \n"
-        + "    ?roleProp rdfs:subPropertyOf core:hasResearcherRole . \n"
+        + "    ?role a core:ResearcherRole . \n"
         + "    ?role vitro:mostSpecificType ?subclass \n"
-        + "    OPTIONAL { ?role core:roleRealizedIn ?activity . \n" 
+        + "    OPTIONAL { ?role core:relatedBy ?activity . \n" 
-        + "               ?activity rdfs:label ?label2  \n" 
+        + "               OPTIONAL {?activity rdfs:label ?label2}  \n" 
         + "    } \n"
-        + "    OPTIONAL { ?role core:roleContributesTo ?activity . \n" 
+        + "    OPTIONAL { ?role <http://purl.obolibrary.org/obo/BFO_0000054> ?activity . \n" 
-        + "               ?activity rdfs:label ?label2  \n" 
+        + "               OPTIONAL {?activity rdfs:label ?label2}  \n" 
         + "    } \n"
         + "    OPTIONAL { ?role core:hideFromDisplay ?hideThis } \n" 
         + "} ORDER BY ?subclass ?label2";

src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePeopleForOrganizationController.java

@@ -65,12 +65,14 @@ public class ManagePeopleForOrganizationController extends FreemarkerHttpServlet
         + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
         + "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n"
         + "PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n"
+        + "PREFIX foaf: <http://xmlns.com/foaf/0.1/> \n"
         + "SELECT DISTINCT ?subclass ?position (str(?label) as ?name) ?person ?hideThis WHERE { \n"
-        + "    ?subject core:organizationForPosition ?position . \n"
+        + "    ?subject core:relatedBy ?position . \n"
-        + "    OPTIONAL { ?position core:positionForPerson  ?person . " 
+        + "    ?position a core:Position . \n"
+        + "    OPTIONAL { ?position core:relates  ?person . " 
+        + "               ?person a foaf:Person . \n"
         + "               ?person rdfs:label ?label } \n"
-        + "    OPTIONAL { ?position vitro:mostSpecificType ?subclass . \n"
+        + "    OPTIONAL { ?position vitro:mostSpecificType ?subclass } \n"
-        + "              ?subclass rdfs:subClassOf core:Position } \n"
         + "    OPTIONAL { ?position core:hideFromDisplay ?hideThis } \n "
         + "} ORDER BY ?subclass ?name";    
        

src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java

@@ -66,11 +66,12 @@ public class ManagePublicationsForIndividualController extends FreemarkerHttpSer
         + "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n"
         + "PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n"
         + "SELECT DISTINCT ?subclass ?authorship (str(?label) as ?title) ?pub ?hideThis WHERE { \n"
-        + "    ?subject core:authorInAuthorship ?authorship . \n"
+        + "    ?subject core:relatedBy ?authorship . \n"
-        + "    OPTIONAL { ?authorship core:linkedInformationResource ?pub . " 
+        + "    ?authorship a core:Authorship  . \n"
+        + "    OPTIONAL { ?authorship core:relates ?pub . " 
+        + "               ?pub a <http://purl.org/ontology/bibo/Document> . \n"
         + "               ?pub rdfs:label ?label  \n"
-        + "               OPTIONAL { ?pub vitro:mostSpecificType ?subclass . \n"
+        + "               OPTIONAL { ?pub vitro:mostSpecificType ?subclass } \n"
-        + "                          ?subclass rdfs:subClassOf core:InformationResource } \n"
         + "    } \n" 
         + "    OPTIONAL { ?authorship core:hideFromDisplay ?hideThis } \n"
         + "} ORDER BY ?subclass ?title";

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageLabelsForPersonGenerator.java

@@ -54,6 +54,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTw
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.FoafNameToRdfsLabelPreprocessor;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.ManageLabelsForIndividualPreprocessor;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.ManageLabelsForPersonPreprocessor;
 import edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionDataGetter;
 import edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectorUtilities;
 import edu.cornell.mannlib.vitro.webapp.i18n.selection.SelectedLocale;
@@ -69,12 +70,7 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
     private static String template = "manageLabelsForPerson.ftl";
     private HashMap<String, List<LabelInformation>> labelsSortedByLanguage = null;
     private List<Literal> existingLabelLiterals = null;
-    //list of language names sorted alphabetically
-    private List<String> existingSortedLanguageNameList = null;
-    //This would be for the full list and can be used for the existing labels list as well
 
-    private HashMap<String, String> fullLanguageNameToCodeMap = null;
-    private static String predicateUri = RDFS.label.getURI();
     @Override
     public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) {
 
@@ -115,7 +111,7 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
         addFormSpecificData(config, vreq);
         //This preprocessor handles getting the correct label language and putting the attribute on the label
  	   config.addEditSubmissionPreprocessor(
-			   new ManageLabelsForIndividualPreprocessor(config));
+			   new ManageLabelsForPersonPreprocessor(config));
  	   //This will handle generating the label from the first name, middle, and last names and also make sure to associate
  	   //a language with that label
        config.addModelChangePreprocessor(new FoafNameToRdfsLabelPreprocessor());        
@@ -150,22 +146,20 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
 
 	private List<String> generateN3Optional(VitroRequest vreq) {
 		List<String> n3Optional = new ArrayList<String>();
-		String predicateUri = EditConfigurationUtils.getPredicateUri(vreq);
+		
-		String n3 = "?subject <" + predicateUri + "> ?label ";
+		String personFullNameN3 = this.N3_PREFIX + 
-		//n3 used if the subject is a person
-		//String personN3 = this.N3_PREFIX + "?subject foaf:firstName ?firstName ; foaf:lastName ?lastName .";
-		//This n3 will be different with the ISF changes
-		String personN3 = this.N3_PREFIX + 
 		 "?subject <http://purl.obolibrary.org/obo/ARG_2000028>  ?individualVcard . \n" +
 	        "?individualVcard a <http://www.w3.org/2006/vcard/ns#Individual> . \n" +              
 	        "?individualVcard <http://purl.obolibrary.org/obo/ARG_2000029> ?subject . \n" +
 	        "?individualVcard <http://www.w3.org/2006/vcard/ns#hasName> ?fullName . \n" +
-	        "?fullName a <http://www.w3.org/2006/vcard/ns#Name> . \n"  + 
+	        "?fullName a <http://www.w3.org/2006/vcard/ns#Name> .";
-	        "?fullName <http://www.w3.org/2006/vcard/ns#givenName> ?firstName . \n" + 
+		String personFirstNameN3 =  
+	        "?fullName <http://www.w3.org/2006/vcard/ns#givenName> ?firstName . ";
+		String personLastNameN3 = 
 	        "?fullName <http://www.w3.org/2006/vcard/ns#familyName> ?lastName .";
-       
+		String personMiddleNameN3 = "?fullName <http://www.w3.org/2006/vcard/ns#middleName> ?middleName .";
-		n3Optional.add(n3);
+  		n3Optional.add(personFullNameN3 + "\n " + personFirstNameN3 + "\n " + personLastNameN3);
-		n3Optional.add(personN3);
+		n3Optional.add(personMiddleNameN3);
 		return n3Optional;
 	}
 	
@@ -174,9 +168,7 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
 	private void setFields(EditConfigurationVTwo editConfiguration, VitroRequest vreq, String predicateUri) {
     	Map<String, FieldVTwo> fields = new HashMap<String, FieldVTwo>();
     	editConfiguration.setFields(fields);
-    	editConfiguration.addField(new FieldVTwo().
+    	
-                setName("label").
-                setValidators(getLabelValidators(vreq, editConfiguration)));    
     	editConfiguration.addField(new FieldVTwo(
     			).setName("newLabelLanguage"));
     	//no validators since all of this is optional
@@ -186,7 +178,7 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
     	        setValidators(getFirstNameValidators(vreq, editConfiguration)));
     	editConfiguration.addField(new FieldVTwo().
                 setName("middleName").
-                setValidators(getLastNameValidators(vreq, editConfiguration)));  
+                setValidators(getMiddleNameValidators(vreq, editConfiguration)));  
     	
     	editConfiguration.addField(new FieldVTwo().
                 setName("lastName").
@@ -199,39 +191,36 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
 	//first and last name have validators if is person is true
     private List<String> getFirstNameValidators(VitroRequest vreq, EditConfigurationVTwo config) {
 		List<String> validators = new ArrayList<String>();
-		if(isPersonType(vreq, config)) {
 			validators.add("nonempty");
+		
+		return validators;
 	}
+    
+    private List<String> getMiddleNameValidators(VitroRequest vreq, EditConfigurationVTwo config) {
+		List<String> validators = new ArrayList<String>();
+		
 		return validators;
 	}
 
 	private List<String> getLastNameValidators(VitroRequest vreq, EditConfigurationVTwo config) {
 		List<String> validators = new ArrayList<String>();
-		if(isPersonType(vreq, config)) {
 			validators.add("nonempty");
-		}
+		
 		return validators;
 	}
 
-	//validate label if person is not true
+	
-	private List<String> getLabelValidators(VitroRequest vreq, EditConfigurationVTwo config) {
-		List<String> validators = new ArrayList<String>();
-		if(!isPersonType(vreq, config)) {
-			validators.add("nonempty");
-		}
-		return validators;
-	}
     
 
     
 	private void setUrisAndLiteralsOnForm(EditConfigurationVTwo config,
 			VitroRequest vreq) {
 		List<String> literalsOnForm = new ArrayList<String>();
-		literalsOnForm.add("label");
 		literalsOnForm.add("newLabelLanguage");
 		//optional for person
 		literalsOnForm.add("firstName");
 		literalsOnForm.add("lastName");
+		literalsOnForm.add("middleName");
 		config.setLiteralsOnForm(literalsOnForm);
 		
 	}
@@ -253,17 +242,6 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
 	private void initExistingLabels(EditConfigurationVTwo config,
 			VitroRequest vreq) {
 		this.existingLabelLiterals = this.getExistingLabels(config.getSubjectUri(), vreq);
-    //	this.labelsSortedByLanguage = this.getLabelsSortedByLanguage(config,vreq);
-    	//language names sorted for the existing languages
-   // 	this.existingSortedLanguageNameList = getExistingSortedLanguageNamesList();
-    	
-    	//Generate a label to language code hash map
-    	//TODO: 
-    	
-    	//HashMap<String, String> labelToLanguageCode = new HashMap<String, String>();
-    	
-    	//this.labels = getExistingLabels(config.getSubjectUri(), vreq);
-    	//this.labelsSortedByLanguage = getLabelsSortedByLanguage(config.getSubjectUri(), vreq);
 		
 	}
     
@@ -318,15 +296,7 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
             config.addFormSpecificData("subjectName", null);
         }
         
-  //Put in whether or not person type
-  		if(isPersonType(vreq, config)) {
-  			//Doing this b/c unsure how freemarker will handle boolean value from JAVA
   		config.addFormSpecificData("isPersonType", "true");
-  		} else {
-  			config.addFormSpecificData("isPersonType", "false");
-
-  		}
-  		
   		//Include whether or not editable to enable edit/remove links and add to show up
   		config.addFormSpecificData("editable", isEditable(vreq, config));
 	}
@@ -376,7 +346,6 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
 
 
 	//Copied from NewIndividualFormGenerator
-	//TODO: Refactor so common code can be used by both generators
 	public String getFOAFPersonClassURI() {
 		return "http://xmlns.com/foaf/0.1/Person";
 	}

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/NewIndividualFormGenerator.java

@@ -41,6 +41,7 @@ public class NewIndividualFormGenerator extends BaseEditConfigurationGenerator i
     	));    
     	//Optional because user may have selected either person or individual of another kind
     	//Person uses first name and last name whereas individual of other class would use label 
+    	//middle name is also optional
     	config.setN3Optional(list(
     	        N3_PREFIX + "@prefix vcard:<http://www.w3.org/2006/vcard/ns#> .\n"
     	                  + " ?newInd <http://purl.obolibrary.org/obo/ARG_2000028> ?newVcardInd . \n"
@@ -50,6 +51,7 @@ public class NewIndividualFormGenerator extends BaseEditConfigurationGenerator i
     	                  + " ?newVcardName a <http://www.w3.org/2006/vcard/ns#Name> . \n"
     	                  + " ?newVcardName vcard:givenName ?firstName . \n"
     	                  + " ?newVcardName vcard:familyName ?lastName .",
+    	        "?newVcardName <http://www.w3.org/2006/vcard/ns#middleName> ?middleName .",
                 N3_PREFIX + " ?newInd <" + RDFS.label.getURI() + "> ?label ."
     	));
     	                    
@@ -58,7 +60,7 @@ public class NewIndividualFormGenerator extends BaseEditConfigurationGenerator i
     	config.addNewResource("newVcardName", vreq.getWebappDaoFactory().getDefaultNamespace());
     	    	
     	config.setUrisOnform(list ());
-        config.setLiteralsOnForm( list( "label", "firstName", "lastName" ));            	
+        config.setLiteralsOnForm( list( "label", "firstName", "lastName", "middleName" ));            	
     	setUrisAndLiteralsInScope(config);
     	//No SPARQL queries for existing since this is only used to create new, never for edit    	
     	    	
@@ -67,6 +69,11 @@ public class NewIndividualFormGenerator extends BaseEditConfigurationGenerator i
     	        setRangeDatatypeUri(XSD.xstring.getURI()).
     	        setValidators(getFirstNameValidators(vreq)));
     	
+    	config.addField(new FieldVTwo().
+    	        setName("middleName").
+    	        setRangeDatatypeUri(XSD.xstring.getURI()).
+    	        setValidators(getMiddleNameValidators(vreq)));
+    	
     	config.addField(new FieldVTwo().
                 setName("lastName").
     	        setRangeDatatypeUri(XSD.xstring.getURI()).
@@ -96,6 +103,11 @@ public class NewIndividualFormGenerator extends BaseEditConfigurationGenerator i
     	return config;
     }
     
+    private List<String> getMiddleNameValidators(VitroRequest vreq) {
+    	List<String> validators = new ArrayList<String>();
+		return validators;
+	}
+
 	//first and last name have validators if is person is true
     private List<String> getFirstNameValidators(VitroRequest vreq) {
 		List<String> validators = new ArrayList<String>();

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/PersonHasAwardOrHonorGenerator.java

@@ -209,25 +209,25 @@ public class PersonHasAwardOrHonorGenerator extends VivoBaseGenerator implements
         "?awardReceipt <"+ descriptionPred +"> ?description .";
 
     final static String n3ForExistingOrgNewAwardAssertion  =      
-        "?award <" + awardConferredByPred +"> ?existingOrg . \n" +
+        "?awardReceipt <" + awardConferredByPred +"> ?existingOrg . \n" +
-        "?existingOrg <" + awardConferredPred + "> ?award . \n" +
+        "?existingOrg <" + awardConferredPred + "> ?awardReceipt . \n" +
         "?award <"+ label + "> ?awardLabel .";    
 
     final static String n3ForExistingOrgExistingAwardAssertion  =      
-        "?existingAward <" + awardConferredByPred +"> ?existingOrg . \n" +
+        "?awardReceipt <" + awardConferredByPred +"> ?existingOrg . \n" +
-        "?existingOrg <" + awardConferredPred + "> ?existingAward . ";    
+        "?existingOrg <" + awardConferredPred + "> ?awardReceipt . ";    
 
     final static String n3ForNewOrgNewAwardAssertion  =      
         "?newOrg a <" + orgClass + "> . \n" +
-        "?award <" + awardConferredByPred +"> ?newOrg . \n" +
+        "?awardReceipt <" + awardConferredByPred +"> ?newOrg . \n" +
-        "?newOrg <" + awardConferredPred + "> ?award . \n" +
+        "?newOrg <" + awardConferredPred + "> ?awardReceipt . \n" +
         "?award <"+ label + "> ?awardLabel . \n" +   
         "?newOrg <"+ label + "> ?orgLabel .";    
 
     final static String n3ForNewOrgExistingAwardAssertion  =      
         "?newOrg a <" + orgClass + "> . \n" +
-        "?existingAward <" + awardConferredByPred +"> ?newOrg . \n" +
+        "?awardReceipt <" + awardConferredByPred +"> ?newOrg . \n" +
-        "?newOrg <" + awardConferredPred + "> ?existingAward . \n" +    
+        "?newOrg <" + awardConferredPred + "> ?awardReceipt . \n" +    
         "?newOrg <"+ label + "> ?orgLabel .";    
 
 	final static String n3ForYearAwarded = 

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/PersonHasEducationalTraining.java

@@ -240,6 +240,8 @@ public class PersonHasEducationalTraining  extends VivoBaseGenerator implements
         "?newOrg <http://vivoweb.org/ontology/core#assigns> ?newAwardedDegree . \n" +
         "?newOrg a ?orgType . \n" +
         "?newOrg <"+ label +"> ?orgLabel . \n" +
+        "?edTraining <http://purl.obolibrary.org/obo/RO_0000057> ?newOrg . \n" +
+        "?newOrg <http://purl.obolibrary.org/obo/RO_0000056> ?edTraining . \n" +
         "?newAwardedDegree <http://vivoweb.org/ontology/core#relates> ?degreeType .\n"+
         "?degreeType <http://vivoweb.org/ontology/core#relatedBy> ?newAwardedDegree . \n"+
         "?newAwardedDegree a core:AwardedDegree .";
@@ -254,6 +256,8 @@ public class PersonHasEducationalTraining  extends VivoBaseGenerator implements
         "?existingOrg  <http://vivoweb.org/ontology/core#assigns> ?newAwardedDegree . \n" +
         "?newAwardedDegree <http://vivoweb.org/ontology/core#assignedBy> ?existingOrg  . \n" +
         "?newAwardedDegree <http://vivoweb.org/ontology/core#relates> ?degreeType .\n"+
+        "?edTraining <http://purl.obolibrary.org/obo/RO_0000057> ?existingOrg . \n" +
+        "?existingOrg <http://purl.obolibrary.org/obo/RO_0000056> ?edTraining . \n" +
         "?degreeType <http://vivoweb.org/ontology/core#relatedBy> ?newAwardedDegree . \n"+
         "?newAwardedDegree a core:AwardedDegree .";
 

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/ManageLabelsForPersonPreprocessor.java

@@ -0,0 +1,105 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.servlet.http.HttpServletRequest;
+
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.ResIterator;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+/*
+ * This preprocessor is used to set the language attribute on the label based on the user selection
+ * on the manage labels page when adding a new label.
+ */
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.BaseEditSubmissionPreprocessorVTwo;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.MultiValueEditSubmission;
+
+public class ManageLabelsForPersonPreprocessor extends ManageLabelsForIndividualPreprocessor {
+
+	
+
+	
+	public ManageLabelsForPersonPreprocessor(EditConfigurationVTwo editConfig) {
+		super(editConfig);
+		
+	}
+	
+	@Override
+	public void preprocess(MultiValueEditSubmission inputSubmission, VitroRequest vreq) {
+		//Use the ManageLabelsForIndividualPreprocessor in addition to this code specific for person
+		super.preprocess(inputSubmission, vreq);
+		//First name and last name would also have a language selected so make sure those literals are also
+		//correctly typed
+		//Middle name is optional
+		if(inputSubmission.hasLiteralValue("firstName") && inputSubmission.hasLiteralValue("lastName") && inputSubmission.hasLiteralValue("newLabelLanguage")) {
+			Map<String, List<Literal>> literalsFromForm = inputSubmission.getLiteralsFromForm();
+			List<Literal> newLabelLanguages = literalsFromForm.get("newLabelLanguage");
+			List<Literal> firstNames = literalsFromForm.get("firstName");
+			List<Literal> lastNames = literalsFromForm.get("lastName");
+			List<Literal> middleNames = new ArrayList<Literal>();
+			if(inputSubmission.hasLiteralValue("middleName")) {
+				middleNames = literalsFromForm.get("middleName");
+			}
+			
+			
+			//Expecting only one language
+			if(firstNames.size() > 0 && lastNames.size() > 0 && newLabelLanguages.size() > 0) {
+				Literal newLabelLanguage = newLabelLanguages.get(0);
+				Literal firstNameLiteral = firstNames.get(0);
+				Literal lastNameLiteral = lastNames.get(0);
+				
+				//Get the string
+				String lang = this.getLanguage(newLabelLanguage.getString());
+				String firstNameValue = firstNameLiteral.getString();
+				String lastNameValue = lastNameLiteral.getString();
+				
+				//Now add the language category to the literal
+				Literal firstNameWithLanguage = inputSubmission.createLiteral(firstNameValue, 
+						null, 
+						lang);
+				Literal lastNameWithLanguage = inputSubmission.createLiteral(lastNameValue, 
+						null, 
+						lang);
+				
+				firstNames = new ArrayList<Literal>();
+				lastNames = new ArrayList<Literal>();
+				firstNames.add(firstNameWithLanguage);
+				lastNames.add(lastNameWithLanguage);
+				//replace the label with one with language, again assuming only one label being returned
+				literalsFromForm.put("firstName", firstNames);
+				literalsFromForm.put("lastName", lastNames);
+				
+				//Middle name handling
+				if(middleNames.size() > 0) {
+					Literal middleNameLiteral = middleNames.get(0);
+					String middleNameValue = middleNameLiteral.getString();
+					Literal middleNameWithLanguage = inputSubmission.createLiteral(middleNameValue, 
+							null, 
+							lang);
+					middleNames = new ArrayList<Literal>();
+					middleNames.add(middleNameWithLanguage);
+					literalsFromForm.put("middleName", middleNames);
+				}
+				
+				//Set literals
+				inputSubmission.setLiteralsFromForm(literalsFromForm);
+			}
+		}
+		
+	}
+	
+
+}

src/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java

@@ -398,11 +398,14 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CollaborationData> {
 			+ "WHERE { \n"
 			+ "<" + queryURI + "> rdf:type foaf:Person ;" 
 								+ " rdfs:label ?authorLabel ;" 
-								+ " core:authorInAuthorship ?authorshipNode . \n"
+								+ " core:relatedBy ?authorshipNode . \n"
 			+ "?authorshipNode rdf:type core:Authorship ;" 
-								+ " core:linkedInformationResource ?document . \n"
+								+ " core:relates ?document . \n"
-			+ "?document core:informationResourceInAuthorship ?coAuthorshipNode . \n" 
+            + "?document rdf:type bibo:Document . \n" 
-			+ "?coAuthorshipNode core:linkedAuthor ?coAuthorPerson . \n" 
+			+ "?document core:relatedBy ?coAuthorshipNode . \n" 
+			+ "?coAuthorshipNode rdf:type core:Authorship . \n" 
+			+ "?coAuthorshipNode core:relates ?coAuthorPerson . \n" 
+			+ "?coAuthorPerson rdf:type foaf:Person . \n"
 			+ "?coAuthorPerson rdfs:label ?coAuthorPersonLabel . \n"
 			+ "OPTIONAL {  ?document core:dateTimeValue ?dateTimeValue . \n" 
 			+ "				?dateTimeValue core:dateTime ?publicationDate } .\n" 

src/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountConstructQueryRunner.java

@@ -38,9 +38,9 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 			.getLog(CoPIGrantCountConstructQueryRunner.class.getName());
 
 	private static final String SPARQL_QUERY_COMMON_CONSTRUCT_AND_WHERE_STRING = 
-			"?Role core:roleContributesTo ?Grant . "
+			"?Role core:relatedBy ?Grant . "
-//			+ "?Grant rdfs:label ?GrantLabel . "
+			+ "?Grant rdf:type core:Grant ."
-			+ "?Grant core:contributingRole ?RelatedRole . ";
+			+ "?Grant core:relates ?RelatedRole . ";
 
 	public CoPIGrantCountConstructQueryRunner(String egoURI, Dataset dataset,
 			Log log) {
@@ -59,23 +59,31 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 	}
 
 	private String generateConstructQueryForInvestigatorRoleOfProperty(
-			String queryURI, String preboundProperty) {
+			String queryURI, String preboundProperty, String preboundRoleType) {
 
 		String sparqlQuery = "CONSTRUCT { " + "<" + queryURI + ">"
 				+ preboundProperty + " ?Role . "
+				+ "?Role rdf:type " + preboundRoleType + " . "
 				+ SPARQL_QUERY_COMMON_CONSTRUCT_AND_WHERE_STRING
-				+ "?RelatedRole core:investigatorRoleOf ?coInvestigator ."
+				+ "?RelatedRole rdf:type core:InvestigatorRole ."
+				+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?coInvestigator ."
+			    + "?coInvestigator rdf:type foaf:Person  ."
 				+ "?coInvestigator rdfs:label ?coInvestigatorLabel . " + "}"
-				+ "WHERE { " + "<" + queryURI + ">" + preboundProperty
+				+ "WHERE { " + "<" + queryURI + ">" + preboundProperty + " ?Role . "  
-				+ " ?Role . " + SPARQL_QUERY_COMMON_CONSTRUCT_AND_WHERE_STRING
+				+ "?Role rdf:type " + preboundRoleType + " . "
-				+ "?RelatedRole core:investigatorRoleOf ?coInvestigator ."
+				+ SPARQL_QUERY_COMMON_CONSTRUCT_AND_WHERE_STRING
-				+ "?coInvestigator rdfs:label ?coInvestigatorLabel . " + "}";
+				+ "?RelatedRole rdf:type core:InvestigatorRole ."
+				+ "?RelatedRole vitro:mostSpecificType ?subclass ."
+				+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?coInvestigator ."
+		        + "?coInvestigator rdf:type foaf:Person  ."
+				+ "?coInvestigator rdfs:label ?coInvestigatorLabel . " 
+				+ "FILTER (?subclass != core:PrincipalInvestigatorRole && ?subclass != core:CoPrincipalInvestigatorRole)}";
 
 		return sparqlQuery;
 	}
 
 	private String generateConstructQueryForPrincipalInvestigatorRoleOfProperty(
-			String queryURI, String preboundProperty) {
+			String queryURI, String preboundProperty, String preboundRoleType) {
 
 		String sparqlQuery = "CONSTRUCT { "
 				+ "<"
@@ -83,8 +91,11 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 				+ ">"
 				+ preboundProperty
 				+ " ?Role . "
+				+ "?Role rdf:type " + preboundRoleType + " . "
 				+ SPARQL_QUERY_COMMON_CONSTRUCT_AND_WHERE_STRING
-				+ "?RelatedRole core:principalInvestigatorRoleOf ?coInvestigator ."
+				+ "?RelatedRole rdf:type core:PrincipalInvestigatorRole ."
+				+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?coInvestigator ."
+		        + "?coInvestigator rdf:type foaf:Person  ."
 				+ "?coInvestigator rdfs:label ?coInvestigatorLabel . "
 				+ "}"
 				+ "WHERE { "
@@ -93,15 +104,18 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 				+ ">"
 				+ preboundProperty
 				+ " ?Role . "
+				+ "?Role rdf:type " + preboundRoleType + " . "
 				+ SPARQL_QUERY_COMMON_CONSTRUCT_AND_WHERE_STRING
-				+ "?RelatedRole core:principalInvestigatorRoleOf ?coInvestigator ."
+				+ "?RelatedRole rdf:type core:PrincipalInvestigatorRole ."
+				+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?coInvestigator ."
+		        + "?coInvestigator rdf:type foaf:Person  ."
 				+ "?coInvestigator rdfs:label ?coInvestigatorLabel . " + "}";
 
 		return sparqlQuery;
 	}
 
 	private String generateConstructQueryForCoPrincipalInvestigatorRoleOfProperty(
-			String queryURI, String preboundProperty) {
+			String queryURI, String preboundProperty, String preboundRoleType) {
 
 		String sparqlQuery = "CONSTRUCT { "
 				+ "<"
@@ -109,8 +123,11 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 				+ ">"
 				+ preboundProperty
 				+ " ?Role . "
+				+ "?Role rdf:type " + preboundRoleType + " . "
 				+ SPARQL_QUERY_COMMON_CONSTRUCT_AND_WHERE_STRING
-				+ "?RelatedRole core:co-PrincipalInvestigatorRoleOf ?coInvestigator ."
+				+ "?RelatedRole rdf:type core:CoPrincipalInvestigatorRole ."
+				+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?coInvestigator ."
+		        + "?coInvestigator rdf:type foaf:Person  ."
 				+ "?coInvestigator rdfs:label ?coInvestigatorLabel . "
 				+ "}"
 				+ "WHERE { "
@@ -119,18 +136,22 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 				+ ">"
 				+ preboundProperty
 				+ " ?Role . "
+				+ "?Role rdf:type " + preboundRoleType + " . "
 				+ SPARQL_QUERY_COMMON_CONSTRUCT_AND_WHERE_STRING
-				+ "?RelatedRole core:co-PrincipalInvestigatorRoleOf ?coInvestigator ."
+				+ "?RelatedRole rdf:type core:CoPrincipalInvestigatorRole ."
+				+ "?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?coInvestigator ."
+		        + "?coInvestigator rdf:type foaf:Person  ."
 				+ "?coInvestigator rdfs:label ?coInvestigatorLabel . " + "}";
 
 		return sparqlQuery;
 	}
 
 	private String generateConstructQueryForDateTimeValueofRole(
-			String queryURI, String preboundProperty) {
+			String queryURI, String preboundProperty, String preboundRoleType) {
 
 		String sparqlQuery = "CONSTRUCT { " + "<" + queryURI + ">"
 				+ preboundProperty + " ?Role . "
+				+ "?Role rdf:type " + preboundRoleType + " . "
 				+ "?Role core:dateTimeInterval ?dateTimeIntervalValue . "
 				+ "?dateTimeIntervalValue core:start ?startDate . "
 				+ "?startDate core:dateTime ?startDateTimeValue . "
@@ -139,6 +160,7 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 				+ "}"
 				+ "WHERE { " + "{" + "<" + queryURI + ">" + preboundProperty
 				+ " ?Role . "
+				+ "?Role rdf:type " + preboundRoleType + " . "
 				+ "?Role core:dateTimeInterval ?dateTimeIntervalValue . "
 				+ "?dateTimeIntervalValue core:start ?startDate . "
 				+ "?startDate core:dateTime ?startDateTimeValue . "
@@ -153,14 +175,16 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 	}
 
 	private String generateConstructQueryForDateTimeValueofGrant(
-			String queryURI, String preboundProperty) {
+			String queryURI, String preboundProperty, String preboundRoleType) {
 
 		String sparqlQuery = "CONSTRUCT { " + "<"
 				+ queryURI
 				+ ">"
 				+ preboundProperty
 				+ " ?Role . "
-				+ "?Role core:roleContributesTo ?Grant ."
+				+ "?Role rdf:type " + preboundRoleType + " . "
+				+ "?Role core:relatedBy ?Grant ."
+    			+ "?Grant rdf:type core:Grant ."
 				+ "?Grant core:dateTimeInterval ?dateTimeIntervalValueForGrant . "
 				+ "?dateTimeIntervalValueForGrant core:start ?startDateForGrant . "
 				+ "?startDateForGrant core:dateTime ?startDateTimeValueForGrant . "
@@ -174,7 +198,9 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 				+ ">"
 				+ preboundProperty
 				+ " ?Role . "
-				+ "?Role core:roleContributesTo ?Grant ."
+				+ "?Role rdf:type " + preboundRoleType + " . "
+				+ "?Role core:relatedBy ?Grant ."
+    			+ "?Grant rdf:type core:Grant ."
 				+ "?Grant core:dateTimeInterval ?dateTimeIntervalValueForGrant . "
 				+ "?dateTimeIntervalValueForGrant core:start ?startDateForGrant . "
 				+ "?startDateForGrant core:dateTime ?startDateTimeValueForGrant . "
@@ -268,45 +294,45 @@ public class CoPIGrantCountConstructQueryRunner implements ModelConstructor {
 				.add(generateConstructQueryForInvestigatorLabel(this.egoURI));
 		constructQueries
 				.add(generateConstructQueryForInvestigatorRoleOfProperty(
-						this.egoURI, "core:hasInvestigatorRole"));
+						this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:InvestigatorRole"));
 		constructQueries
 				.add(generateConstructQueryForCoPrincipalInvestigatorRoleOfProperty(
-						this.egoURI, "core:hasInvestigatorRole"));
+						this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:InvestigatorRole"));
 		constructQueries
 				.add(generateConstructQueryForPrincipalInvestigatorRoleOfProperty(
-						this.egoURI, "core:hasInvestigatorRole"));
+						this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:InvestigatorRole"));
 		constructQueries.add(generateConstructQueryForDateTimeValueofRole(
-				this.egoURI, "core:hasInvestigatorRole"));
+				this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:InvestigatorRole"));
 		constructQueries.add(generateConstructQueryForDateTimeValueofGrant(
-				this.egoURI, "core:hasInvestigatorRole"));
+				this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:InvestigatorRole"));
 
 		constructQueries
 				.add(generateConstructQueryForInvestigatorRoleOfProperty(
-						this.egoURI, "core:hasPrincipalInvestigatorRole"));
+						this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:PrincipalInvestigatorRole"));
 		constructQueries
 				.add(generateConstructQueryForCoPrincipalInvestigatorRoleOfProperty(
-						this.egoURI, "core:hasPrincipalInvestigatorRole"));
+						this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:PrincipalInvestigatorRole"));
 		constructQueries
 				.add(generateConstructQueryForPrincipalInvestigatorRoleOfProperty(
-						this.egoURI, "core:hasPrincipalInvestigatorRole"));
+						this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:PrincipalInvestigatorRole"));
 		constructQueries.add(generateConstructQueryForDateTimeValueofRole(
-				this.egoURI, "core:hasPrincipalInvestigatorRole"));
+				this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:PrincipalInvestigatorRole"));
 		constructQueries.add(generateConstructQueryForDateTimeValueofGrant(
-				this.egoURI, "core:hasPrincipalInvestigatorRole"));
+				this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:PrincipalInvestigatorRole"));
 
 		constructQueries
 				.add(generateConstructQueryForInvestigatorRoleOfProperty(
-						this.egoURI, "core:hasCo-PrincipalInvestigatorRole"));
+						this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:CoPrincipalInvestigatorRole"));
 		constructQueries
 				.add(generateConstructQueryForCoPrincipalInvestigatorRoleOfProperty(
-						this.egoURI, "core:hasCo-PrincipalInvestigatorRole"));
+						this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:CoPrincipalInvestigatorRole"));
 		constructQueries
 				.add(generateConstructQueryForPrincipalInvestigatorRoleOfProperty(
-						this.egoURI, "core:hasCo-PrincipalInvestigatorRole"));
+						this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:CoPrincipalInvestigatorRole"));
 		constructQueries.add(generateConstructQueryForDateTimeValueofRole(
-				this.egoURI, "core:hasCo-PrincipalInvestigatorRole"));
+				this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:CoPrincipalInvestigatorRole"));
 		constructQueries.add(generateConstructQueryForDateTimeValueofGrant(
-				this.egoURI, "core:hasCo-PrincipalInvestigatorRole"));
+				this.egoURI, "<http://purl.obolibrary.org/obo/RO_0000053>", "core:CoPrincipalInvestigatorRole"));
 
 	}
 }

src/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java

@@ -113,13 +113,21 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
 			+ 		"<" + queryURI + "> rdfs:label ?PILabel . "  	
 			+  		"{ "
 			        	
-			+			"<" + queryURI + "> core:hasCo-PrincipalInvestigatorRole ?Role . "
+			+			"<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
 
-			+			"?Role core:roleContributesTo ?Grant . "
+		    +			"?Role rdf:type core:CoPrincipalInvestigatorRole . "
 
-			+			"?Grant core:contributingRole ?RelatedRole . "
+			+			"?Role core:relatedBy ?Grant . "
 
-			+			"?RelatedRole core:principalInvestigatorRoleOf ?CoPI . " 
+			+			"?Grant rdf:type core:Grant . "
+
+			+			"?Grant core:relates ?RelatedRole . "
+
+			+			"?RelatedRole rdf:type core:PrincipalInvestigatorRole . " 
+
+			+			"?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . " 
+
+	        +			"?CoPI rdf:type foaf:Person .	"
 
 			+			"?CoPI rdfs:label ?CoPILabel .	"
 
@@ -133,13 +141,21 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
 
 			+  		"{ "
 			        	
-			+			"<" + queryURI + "> core:hasCo-PrincipalInvestigatorRole ?Role . "
+			+			"<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
 
-			+			"?Role core:roleContributesTo ?Grant . "
+	        +			"?Role rdf:type core:CoPrincipalInvestigatorRole . "
 
-			+			"?Grant core:contributingRole ?RelatedRole . "
+			+			"?Role core:relatedBy ?Grant . "
 
-			+			"?RelatedRole core:investigatorRoleOf ?CoPI . " 
+			+			"?Grant rdf:type core:Grant . "
+
+			+			"?Grant core:relates ?RelatedRole . "
+
+			+			"?RelatedRole rdf:type core:InvestigatorRole . " 
+
+			+			"?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . " 
+
+	        +			"?CoPI rdf:type foaf:Person .	"
 
 			+			"?CoPI rdfs:label ?CoPILabel .	"
 
@@ -154,13 +170,21 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
 					
 			+  		"{ "
 			        	
-			+			"<" + queryURI + "> core:hasCo-PrincipalInvestigatorRole ?Role . "
+			+			"<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
 
-			+			"?Role core:roleContributesTo ?Grant . "
+	        +			"?Role rdf:type core:CoPrincipalInvestigatorRole . "
 
-			+			"?Grant core:contributingRole ?RelatedRole . "
+			+			"?Role core:relatedBy ?Grant . "
 
-			+			"?RelatedRole core:co-PrincipalInvestigatorRoleOf ?CoPI . " 
+			+			"?Grant rdf:type core:Grant . "
+
+			+			"?Grant core:relates ?RelatedRole . "
+
+			+			"?RelatedRole rdf:type core:CoPrincipalInvestigatorRole  . " 
+
+			+			"?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . " 
+
+	        +			"?CoPI rdf:type foaf:Person .	"
 
 			+			"?CoPI rdfs:label ?CoPILabel .	"
 
@@ -176,13 +200,21 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
 			
 			+		"{ "
 			        	
-			+			"<" + queryURI + "> core:hasPrincipalInvestigatorRole ?Role . "
+			+			"<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
 
-			+			"?Role core:roleContributesTo ?Grant . "
+	        +			"?Role rdf:type core:PrincipalInvestigatorRole . "
 
-			+			"?Grant core:contributingRole ?RelatedRole . "
+			+			"?Role core:relatedBy ?Grant . "
 
-			+			"?RelatedRole core:principalInvestigatorRoleOf ?CoPI . " 
+			+			"?Grant rdf:type core:Grant . "
+
+			+			"?Grant core:relates ?RelatedRole . "
+
+			+			"?RelatedRole rdf:type core:PrincipalInvestigatorRole  . " 
+
+			+			"?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . " 
+
+	        +			"?CoPI rdf:type foaf:Person .	"
 
 			+			"?CoPI rdfs:label ?CoPILabel .	"
 
@@ -197,13 +229,21 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
 			
 			+		"{ "
 			        	
-			+			"<" + queryURI + "> core:hasPrincipalInvestigatorRole ?Role . "
+			+			"<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
 
-			+			"?Role core:roleContributesTo ?Grant . "
+	        +			"?Role rdf:type core:PrincipalInvestigatorRole . "
 
-			+			"?Grant core:contributingRole ?RelatedRole . "
+			+			"?Role core:relatedBy ?Grant . "
 
-			+			"?RelatedRole core:investigatorRoleOf ?CoPI . " 
+			+			"?Grant rdf:type core:Grant . "
+
+			+			"?Grant core:relates ?RelatedRole . "
+
+			+			"?RelatedRole rdf:type core:InvestigatorRole  . " 
+
+			+			"?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . " 
+
+	        +			"?CoPI rdf:type foaf:Person .	"
 
 			+			"?CoPI rdfs:label ?CoPILabel .	"
 
@@ -218,13 +258,21 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
 					
 			+		"{ "
 			        	
-			+			"<" + queryURI + "> core:hasPrincipalInvestigatorRole ?Role . "
+			+			"<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
 
-			+			"?Role core:roleContributesTo ?Grant . "
+	        +			"?Role rdf:type core:PrincipalInvestigatorRole . "
 
-			+			"?Grant core:contributingRole ?RelatedRole . "
+			+			"?Role core:relatedBy ?Grant . "
 
-			+			"?RelatedRole core:co-PrincipalInvestigatorRoleOf ?CoPI . " 
+			+			"?Grant rdf:type core:Grant . "
+
+			+			"?Grant core:relates ?RelatedRole . "
+
+			+			"?RelatedRole rdf:type core:CoPrincipalInvestigatorRole . " 
+
+			+			"?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . " 
+
+	        +			"?CoPI rdf:type foaf:Person .	"
 
 			+			"?CoPI rdfs:label ?CoPILabel .	"
 
@@ -239,13 +287,21 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
 					
 			+		"{ "
 			        	
-			+			"<" + queryURI + "> core:hasInvestigatorRole ?Role . "
+			+			"<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
 
-			+			"?Role core:roleContributesTo ?Grant . "
+	        +			"?Role rdf:type core:InvestigatorRole . "
 
-			+			"?Grant core:contributingRole ?RelatedRole . "
+			+			"?Role core:relatedBy ?Grant . "
 
-			+			"?RelatedRole core:investigatorRoleOf ?CoPI . " 
+			+			"?Grant rdf:type core:Grant . "
+
+			+			"?Grant core:relates ?RelatedRole . "
+
+			+			"?RelatedRole rdf:type core:InvestigatorRole  . " 
+
+			+			"?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . " 
+
+	        +			"?CoPI rdf:type foaf:Person .	"
 
 			+			"?CoPI rdfs:label ?CoPILabel .	"
 
@@ -260,13 +316,21 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
 			
 			+		"{ "
 			        	
-			+			"<" + queryURI + "> core:hasInvestigatorRole ?Role . "
+			+			"<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
 
-			+			"?Role core:roleContributesTo ?Grant . "
+	        +			"?Role rdf:type core:InvestigatorRole . "
 
-			+			"?Grant core:contributingRole ?RelatedRole . "
+			+			"?Role core:relatedBy ?Grant . "
 
-			+			"?RelatedRole core:co-PrincipalInvestigatorRoleOf ?CoPI . " 
+			+			"?Grant rdf:type core:Grant . "
+
+			+			"?Grant core:relates ?RelatedRole . "
+
+			+			"?RelatedRole rdf:type core:CoPrincipalInvestigatorRole  . " 
+
+			+			"?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . " 
+
+	        +			"?CoPI rdf:type foaf:Person .	"
 
 			+			"?CoPI rdfs:label ?CoPILabel .	"
 
@@ -281,13 +345,21 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CollaborationData>
 			
 			+		"{ "
 			        	
-			+			"<" + queryURI + "> core:hasInvestigatorRole ?Role . "
+			+			"<" + queryURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
 
-			+			"?Role core:roleContributesTo ?Grant . "
+	        +			"?Role rdf:type core:InvestigatorRole . "
 
-			+			"?Grant core:contributingRole ?RelatedRole . "
+			+			"?Role core:relatedBy ?Grant . "
 
-			+			"?RelatedRole core:principalInvestigatorRoleOf ?CoPI . " 
+			+			"?Grant rdf:type core:Grant . "
+
+			+			"?Grant core:relates ?RelatedRole . "
+
+			+			"?RelatedRole rdf:type core:PrincipalInvestigatorRole . " 
+
+			+			"?RelatedRole <http://purl.obolibrary.org/obo/RO_0000052> ?CoPI . " 
+
+		    +			"?CoPI rdf:type foaf:Person .	"
 
 			+			"?CoPI rdfs:label ?CoPILabel .	"
 

src/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/OrganizationAssociatedPeopleModelWithTypesConstructor.java

@@ -53,8 +53,9 @@ public class OrganizationAssociatedPeopleModelWithTypesConstructor implements Mo
 		+ "     <" + organizationURI + "> rdf:type foaf:Organization . "
 		+ "     <" + organizationURI + "> rdfs:label ?organizationLabel . "
 		+ "     OPTIONAL { "
-		+ "         <" + organizationURI + "> core:organizationForPosition ?Position .  "
+		+ "         <" + organizationURI + "> core:relatedBy ?Position .  "
-		+ "         ?Position core:positionForPerson ?Person .  "
+		+ "         ?Position rdf:type core:Position .  "
+		+ "         ?Position core:relates ?Person .  "
 		+ "         ?Person rdfs:label ?personLabel. "
 		+ "         ?Person rdf:type ?personType . "
 		+ "         ?personType rdfs:label ?personTypeLabel . "

src/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/OrganizationModelWithTypesConstructor.java

@@ -50,7 +50,8 @@ public class OrganizationModelWithTypesConstructor implements ModelConstructor {
 		+ " CONSTRUCT { "
 		+ "     ?organization rdf:type foaf:Organization . "
 		+ "     ?organization rdfs:label ?organizationLabel . "
-		+ "     ?organization core:hasSubOrganization ?subOrganization . "
+		+ "     ?organization <http://purl.obolibrary.org/obo/BFO_0000051> ?subOrganization . "
+        + "     ?subOrganization rdf:type foaf:Organization .  "
 		+ "     ?subOrganization rdfs:label ?subOrganizationLabel .     "
 		+ "     ?subOrganization rdf:type ?subOrganizationType . "
 		+ "     ?subOrganizationType rdfs:label ?subOrganizationTypeLabel . "
@@ -60,7 +61,8 @@ public class OrganizationModelWithTypesConstructor implements ModelConstructor {
 		+ "     ?organization rdfs:label ?organizationLabel . "
 		+ "      "
 		+ "     OPTIONAL { "
-		+ "         ?organization core:hasSubOrganization ?subOrganization . "
+		+ "         ?organization <http://purl.obolibrary.org/obo/BFO_0000051> ?subOrganization . "
+        + "         ?subOrganization rdf:type foaf:Organization .  "
 		+ "         ?subOrganization rdfs:label ?subOrganizationLabel . "
 		+ "         ?subOrganization rdf:type ?subOrganizationType . "
 		+ "         ?subOrganizationType rdfs:label ?subOrganizationTypeLabel . "

src/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/OrganizationToGrantsForSubOrganizationsModelConstructor.java

@@ -40,7 +40,7 @@ public class OrganizationToGrantsForSubOrganizationsModelConstructor implements
 		this.dataset = dataset;
 	}
 	
-	private Set<String> constructOrganizationGrantsQueryTemplate(String constructProperty, String roleTypeProperty) {
+	private Set<String> constructOrganizationGrantsQueryTemplate(String constructProperty, String roleType) {
 		
 		Set<String> differentPerspectiveQueries = new HashSet<String>();
 		
@@ -56,11 +56,16 @@ public class OrganizationToGrantsForSubOrganizationsModelConstructor implements
 		+ " } "
 		+ " WHERE { "
 		+ "     <" + organizationURI + "> rdfs:label ?organizationLabel . "
-		+ "     <" + organizationURI + "> core:hasSubOrganization* ?subOrganization . "
+		+ "     <" + organizationURI + "> <http://purl.obolibrary.org/obo/BFO_0000051>* ?subOrganization . "
-		+ "     ?subOrganization core:organizationForPosition ?Position .  "
+        + "     ?subOrganization rdf:type foaf:Organization .  "
-		+ "     ?Position core:positionForPerson ?Person .        "
+		+ "     ?subOrganization core:relatedBy ?Position .  "
-		+ "     ?Person core:" + roleTypeProperty + " ?Role .  "
+		+ "     ?Position rdf:type core:Position .  "
-		+ "     ?Role core:roleContributesTo ?Grant . "
+		+ "     ?Position core:relates ?Person .  "
+		+ "     ?Person  rdf:type foaf:Person .  "
+		+ "     ?Person <http://purl.obolibrary.org/obo/RO_0000053> ?Role .  "
+	    + "     ?Role rdf:type core:" + roleType + " . "
+		+ "     ?Role core:relatedBy ?Grant . "
+		+ "     ?Grant rdf:type core:Grant . "
 		+ "     ?Grant rdfs:label ?grantLabel . "
 		+ "      "
 		+ "     LET(?now := afn:now()) "
@@ -77,11 +82,16 @@ public class OrganizationToGrantsForSubOrganizationsModelConstructor implements
 			+ " } "
 			+ " WHERE { "
 			+ "     <" + organizationURI + "> rdfs:label ?organizationLabel . "
-			+ "     <" + organizationURI + "> core:hasSubOrganization* ?subOrganization . "
+			+ "     <" + organizationURI + "> <http://purl.obolibrary.org/obo/BFO_0000051>* ?subOrganization . "
-			+ "     ?subOrganization core:organizationForPosition ?Position .  "
+            + "     ?subOrganization rdf:type foaf:Organization .  "
-			+ "     ?Position core:positionForPerson ?Person .        "
+		    + "     ?subOrganization core:relatedBy ?Position .  "
-			+ "     ?Person core:" + roleTypeProperty + " ?Role .  "
+		    + "     ?Position rdf:type core:Position .  "
-			+ "     ?Role core:roleContributesTo ?Grant . "
+	        + "     ?Position core:relates ?Person .  "
+	        + "     ?Person  rdf:type foaf:Person .  "
+    		+ "     ?Person <http://purl.obolibrary.org/obo/RO_0000053> ?Role .  "
+    	    + "     ?Role rdf:type core:" + roleType + " . "
+    		+ "     ?Role core:relatedBy ?Grant . "
+    		+ "     ?Grant rdf:type core:Grant . "
 			+ "      "
 			+ "         ?Grant core:dateTimeInterval ?dateTimeIntervalValueForGrant .          "
 //			+ "         OPTIONAL { "
@@ -106,11 +116,16 @@ public class OrganizationToGrantsForSubOrganizationsModelConstructor implements
 			+ " } "
 			+ " WHERE { "
 			+ "     <" + organizationURI + "> rdfs:label ?organizationLabel . "
-			+ "     <" + organizationURI + "> core:hasSubOrganization* ?subOrganization . "
+			+ "     <" + organizationURI + "> <http://purl.obolibrary.org/obo/BFO_0000051>* ?subOrganization . "
-			+ "     ?subOrganization core:organizationForPosition ?Position .  "
+            + "     ?subOrganization rdf:type foaf:Organization .  "
-			+ "     ?Position core:positionForPerson ?Person .        "
+		    + "     ?subOrganization core:relatedBy ?Position .  "
-			+ "     ?Person core:" + roleTypeProperty + " ?Role .  "
+		    + "     ?Position rdf:type core:Position .  "
-			+ "     ?Role core:roleContributesTo ?Grant . "
+	        + "     ?Position core:relates ?Person .  "
+	        + "     ?Person  rdf:type foaf:Person .  "
+    		+ "     ?Person <http://purl.obolibrary.org/obo/RO_0000053> ?Role .  "
+    	    + "     ?Role rdf:type core:" + roleType + " . "
+    		+ "     ?Role core:relatedBy ?Grant . "
+    		+ "     ?Grant rdf:type core:Grant . "
 			+ "      "
 			+ "         ?Role core:dateTimeInterval ?dateTimeIntervalValue . "
 //			+ "         OPTIONAL { "
@@ -137,9 +152,9 @@ public class OrganizationToGrantsForSubOrganizationsModelConstructor implements
 
 		Set<String> differentInvestigatorTypeQueries = new HashSet<String>();
 		
-		Set<String> investigatorRoleQuery = constructOrganizationGrantsQueryTemplate("hasInvestigatorWithGrant", "hasInvestigatorRole");
+		Set<String> investigatorRoleQuery = constructOrganizationGrantsQueryTemplate("hasInvestigatorWithGrant", "InvestigatorRole");
-		Set<String> piRoleQuery = constructOrganizationGrantsQueryTemplate("hasPIWithGrant", "hasPrincipalInvestigatorRole");
+		Set<String> piRoleQuery = constructOrganizationGrantsQueryTemplate("hasPIWithGrant", "PrincipalInvestigatorRole");
-		Set<String> coPIRoleQuery = constructOrganizationGrantsQueryTemplate("hascoPIWithGrant", "hasCo-PrincipalInvestigatorRole");
+		Set<String> coPIRoleQuery = constructOrganizationGrantsQueryTemplate("hascoPIWithGrant", "CoPrincipalInvestigatorRole");
 
 		differentInvestigatorTypeQueries.addAll(investigatorRoleQuery);
 		differentInvestigatorTypeQueries.addAll(piRoleQuery);

src/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/OrganizationToPublicationsForSubOrganizationsModelConstructor.java

@@ -53,11 +53,16 @@ public class OrganizationToPublicationsForSubOrganizationsModelConstructor imple
 		+ " } "
 		+ " WHERE {  "
 		+ "         <" + organizationURI + "> rdfs:label ?organizationLabel .  "
-		+ "         <" + organizationURI + "> core:hasSubOrganization* ?subOrganization .  "
+		+ "         <" + organizationURI + "> <http://purl.obolibrary.org/obo/BFO_0000051>* ?subOrganization .  "
-		+ "         ?subOrganization core:organizationForPosition ?Position .  "
+	    + "         ?subOrganization rdf:type foaf:Organization .  "
-		+ "         ?Position core:positionForPerson ?Person .  "
+		+ "         ?subOrganization core:relatedBy ?Position .  "
-		+ "         ?Person  core:authorInAuthorship ?Resource .  "
+		+ "         ?Position rdf:type core:Position .  "
-		+ "         ?Resource core:linkedInformationResource ?Document .  "
+		+ "         ?Position core:relates ?Person .  "
+		+ "         ?Person  rdf:type foaf:Person .  "
+		+ "         ?Person  core:relatedBy ?Resource .  "
+		+ "         ?Resource  rdf:type core:Authorship .  "
+		+ "         ?Resource core:relates ?Document .  "
+		+ "         ?Document rdf:type bibo:Document . "
 		+ "         ?Document rdfs:label ?DocumentLabel . "
 		+ "          "
 		+ "         OPTIONAL { "

src/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/PeopleToGrantsModelConstructor.java

@@ -37,22 +37,24 @@ public class PeopleToGrantsModelConstructor implements ModelConstructor {
 		this.dataset = dataset;
 	}
 	
-private Set<String> constructPersonGrantsQueryTemplate(String constructProperty, String roleTypeProperty) {
+private Set<String> constructPersonGrantsQueryTemplate(String constructProperty, String roleType) {
 		
 		Set<String> differentPerspectiveQueries = new HashSet<String>();
 		
 		String justGrantsQuery = ""
 			+ " CONSTRUCT {  "
-			+ "     ?person vivosocnet:lastCachedAt ?now . "
+			+ "     ?Person vivosocnet:lastCachedAt ?now . "
-			+ "     ?person vivosocnet:" + constructProperty + " ?Grant . "
+			+ "     ?Person vivosocnet:" + constructProperty + " ?Grant . "
 			+ "      "
 			+ "     ?Grant rdf:type core:Grant . "
 			+ "     ?Grant rdfs:label ?grantLabel . "
 			+ "      "
 			+ " } "
 			+ " WHERE { "
-			+ "     ?person core:" + roleTypeProperty + " ?Role .  "
+    		+ "     ?Person <http://purl.obolibrary.org/obo/RO_0000053> ?Role .  "
-			+ "     ?Role core:roleContributesTo ?Grant . "
+    	    + "     ?Role rdf:type core:" + roleType + " . "
+			+ "     ?Role core:relatedBy ?Grant . "
+			+ "     ?Grant rdf:type core:Grant . "
 			+ "     ?Grant rdfs:label ?grantLabel . "
 			+ "      "
 			+ "     LET(?now := afn:now()) "
@@ -60,14 +62,16 @@ private Set<String> constructPersonGrantsQueryTemplate(String constructProperty,
 
 		String justDateTimeOnGrantsQuery = ""
 			+ " CONSTRUCT {  "
-			+ "     ?person vivosocnet:lastCachedAt ?now . "
+			+ "     ?Person vivosocnet:lastCachedAt ?now . "
 			+ "     ?Grant vivosocnet:startDateTimeOnGrant ?startDateTimeValueForGrant . "
 //			+ "     ?Grant vivosocnet:endDateTimeOnGrant ?endDateTimeValueForGrant . "
 			+ "      "
 			+ " } "
 			+ " WHERE { "
-			+ "     ?person core:" + roleTypeProperty + " ?Role .  "
+    		+ "     ?Person <http://purl.obolibrary.org/obo/RO_0000053> ?Role .  "
-			+ "     ?Role core:roleContributesTo ?Grant . "
+    	    + "     ?Role rdf:type core:" + roleType + " . "
+			+ "     ?Role core:relatedBy ?Grant . "
+			+ "     ?Grant rdf:type core:Grant . "
 			+ "      "
 			+ "         ?Grant core:dateTimeInterval ?dateTimeIntervalValueForGrant .          "
 //			+ "         OPTIONAL { "
@@ -84,13 +88,15 @@ private Set<String> constructPersonGrantsQueryTemplate(String constructProperty,
 		
 		String justDateTimeOnRolesQuery = ""
 			+ " CONSTRUCT {  "
-			+ "     ?person vivosocnet:lastCachedAt ?now . "
+			+ "     ?Person vivosocnet:lastCachedAt ?now . "
 			+ "     ?Grant vivosocnet:startDateTimeOnRole ?startDateTimeValue . "
 //			+ "     ?Grant vivosocnet:endDateTimeOnRole ?endDateTimeValue . "
 			+ " } "
 			+ " WHERE { "
-			+ "     ?person core:" + roleTypeProperty + " ?Role .  "
+    		+ "     ?Person <http://purl.obolibrary.org/obo/RO_0000053> ?Role .  "
-			+ "     ?Role core:roleContributesTo ?Grant . "
+    	    + "     ?Role rdf:type core:" + roleType + " . "
+			+ "     ?Role core:relatedBy ?Grant . "
+			+ "     ?Grant rdf:type core:Grant . "
 			+ "      "
 			+ "         ?Role core:dateTimeInterval ?dateTimeIntervalValue . "
 //			+ "         OPTIONAL { "
@@ -117,9 +123,9 @@ private Set<String> constructPersonGrantsQueryTemplate(String constructProperty,
 
 		Set<String> differentInvestigatorTypeQueries = new HashSet<String>();
 		
-		Set<String> investigatorRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsAnInvestigator", "hasInvestigatorRole");
+		Set<String> investigatorRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsAnInvestigator", "InvestigatorRole");
-		Set<String> piRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsPI", "hasPrincipalInvestigatorRole");
+		Set<String> piRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsPI", "PrincipalInvestigatorRole");
-		Set<String> coPIRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsCoPI", "hasCo-PrincipalInvestigatorRole");
+		Set<String> coPIRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsCoPI", "CoPrincipalInvestigatorRole");
 
 		differentInvestigatorTypeQueries.addAll(investigatorRoleQuery);
 		differentInvestigatorTypeQueries.addAll(piRoleQuery);

src/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/PeopleToPublicationsModelConstructor.java

@@ -48,8 +48,11 @@ public class PeopleToPublicationsModelConstructor implements ModelConstructor {
 		+ "     ?journal rdfs:label ?journalLabel .  "
 		+ " } "
 		+ " WHERE {  "
-		+ "         ?person core:authorInAuthorship ?Resource .  "
+		+ "         ?person core:relatedBy ?Resource .  "
-		+ "         ?Resource core:linkedInformationResource ?Document .  "
+		+ "         ?person rdf:type foaf:Person .  "
+		+ "         ?Resource rdf:type core:Authorship .  "
+		+ "         ?Resource core:relates ?Document .  "
+		+ "         ?Document rdf:type bibo:Document . "
 		+ "         ?Document rdfs:label ?DocumentLabel . "
 		+ "          "
 		+ "         OPTIONAL { "

src/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/PersonToGrantsModelConstructor.java

@@ -40,7 +40,7 @@ public class PersonToGrantsModelConstructor implements ModelConstructor {
 		this.dataset = dataset;
 	}
 	
-private Set<String> constructPersonGrantsQueryTemplate(String constructProperty, String roleTypeProperty) {
+private Set<String> constructPersonGrantsQueryTemplate(String constructProperty, String roleType) {
 		
 		Set<String> differentPerspectiveQueries = new HashSet<String>();
 		
@@ -54,8 +54,10 @@ private Set<String> constructPersonGrantsQueryTemplate(String constructProperty,
 			+ "      "
 			+ " } "
 			+ " WHERE { "
-			+ "     <" + personURI + "> core:" + roleTypeProperty + " ?Role .  "
+			+ "     <" + personURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
-			+ "     ?Role core:roleContributesTo ?Grant . "
+		    + "     ?Role rdf:type core:" + roleType + " . "
+    		+ "     ?Role core:relatedBy ?Grant . "
+    		+ "     ?Grant rdf:type core:Grant . "
 			+ "     ?Grant rdfs:label ?grantLabel . "
 			+ "      "
 			+ "     LET(?now := afn:now()) "
@@ -69,8 +71,10 @@ private Set<String> constructPersonGrantsQueryTemplate(String constructProperty,
 			+ "      "
 			+ " } "
 			+ " WHERE { "
-			+ "     <" + personURI + "> core:" + roleTypeProperty + " ?Role .  "
+			+ "     <" + personURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
-			+ "     ?Role core:roleContributesTo ?Grant . "
+		    + "     ?Role rdf:type core:" + roleType + " . "
+    		+ "     ?Role core:relatedBy ?Grant . "
+    		+ "     ?Grant rdf:type core:Grant . "
 			+ "      "
 			+ "         ?Grant core:dateTimeInterval ?dateTimeIntervalValueForGrant .          "
 //			+ "         OPTIONAL { "
@@ -92,8 +96,10 @@ private Set<String> constructPersonGrantsQueryTemplate(String constructProperty,
 //			+ "     ?Grant vivosocnet:endDateTimeOnRole ?endDateTimeValue . "
 			+ " } "
 			+ " WHERE { "
-			+ "     <" + personURI + "> core:" + roleTypeProperty + " ?Role .  "
+			+ "     <" + personURI + "> <http://purl.obolibrary.org/obo/RO_0000053> ?Role . "
-			+ "     ?Role core:roleContributesTo ?Grant . "
+		    + "     ?Role rdf:type core:" + roleType + " . "
+    		+ "     ?Role core:relatedBy ?Grant . "
+    		+ "     ?Grant rdf:type core:Grant . "
 			+ "      "
 			+ "         ?Role core:dateTimeInterval ?dateTimeIntervalValue . "
 //			+ "         OPTIONAL { "
@@ -120,9 +126,9 @@ private Set<String> constructPersonGrantsQueryTemplate(String constructProperty,
 
 		Set<String> differentInvestigatorTypeQueries = new HashSet<String>();
 		
-		Set<String> investigatorRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsAnInvestigator", "hasInvestigatorRole");
+		Set<String> investigatorRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsAnInvestigator", "InvestigatorRole");
-		Set<String> piRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsPI", "hasPrincipalInvestigatorRole");
+		Set<String> piRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsPI", "PrincipalInvestigatorRole");
-		Set<String> coPIRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsCoPI", "hasCo-PrincipalInvestigatorRole");
+		Set<String> coPIRoleQuery = constructPersonGrantsQueryTemplate("hasGrantAsCoPI", "CoPrincipalInvestigatorRole");
 
 		differentInvestigatorTypeQueries.addAll(investigatorRoleQuery);
 		differentInvestigatorTypeQueries.addAll(piRoleQuery);

src/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/PersonToPublicationsModelConstructor.java

@@ -51,8 +51,10 @@ public class PersonToPublicationsModelConstructor implements ModelConstructor {
 		+ "     ?journal rdfs:label ?journalLabel .  "
 		+ " } "
 		+ " WHERE {  "
-		+ "         <" + personURI + "> core:authorInAuthorship ?Resource .  "
+		+ "         <" + personURI + "> core:relatedBy ?Resource .  "
-		+ "         ?Resource core:linkedInformationResource ?Document .  "
+		+ "         ?Resource rdf:type core:Authorship .  "
+		+ "         ?Resource core:relates ?Document .  "
+		+ "         ?Document rdf:type bibo:Document . "
 		+ "         ?Document rdfs:label ?DocumentLabel . "
 		+ "          "
 		+ "         OPTIONAL { "

src/edu/cornell/mannlib/vitro/webapp/visualization/modelconstructor/SubOrganizationWithinModelConstructor.java

@@ -50,7 +50,8 @@ public class SubOrganizationWithinModelConstructor implements ModelConstructor {
 		+ " CONSTRUCT { "
 		+ "     ?organization rdf:type foaf:Organization . "
 		+ "     ?organization rdfs:label ?organizationLabel . "
-		+ "     ?organization core:subOrganizationWithin ?parentOrganization . "
+		+ "     ?organization <http://purl.obolibrary.org/obo/BFO_0000050> ?parentOrganization . "
+	    + "     ?parentOrganization rdf:type foaf:Organization .     "
 		+ "     ?parentOrganization rdfs:label ?parentOrganizationLabel .     "
 		+ " }  "
 		+ " WHERE { "
@@ -58,7 +59,8 @@ public class SubOrganizationWithinModelConstructor implements ModelConstructor {
 		+ "     ?organization rdfs:label ?organizationLabel . "
 		+ "      "
 		+ "     OPTIONAL { "
-		+ "         ?organization core:subOrganizationWithin ?parentOrganization . "
+		+ "         ?organization <http://purl.obolibrary.org/obo/BFO_0000050> ?parentOrganization . "
+	    + "         ?parentOrganization rdf:type foaf:Organization .     "
 		+ "         ?parentOrganization rdfs:label ?parentOrganizationLabel . "
 		+ "     }     "
 		+ " } ";

src/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java

@@ -121,9 +121,10 @@ public class PersonPublicationCountQueryRunner implements QueryRunner<Set<Activi
 							+ "WHERE { \n"
 							+ "<" + queryURI + "> rdf:type foaf:Person ;\n" 
 							+ 					" rdfs:label ?authorLabel \n;" 
-							+ 					" core:authorInAuthorship ?authorshipNode .  \n" 
+							+ 					" core:relatedBy ?authorshipNode .  \n" 
 							+ "	?authorshipNode rdf:type core:Authorship ;" 
-							+ 					" core:linkedInformationResource ?document . \n"
+							+ 					" core:relates ?document . \n"
+							+ "	?document rdf:type bibo:Document . \n" 
 							+  SPARQL_QUERY_COMMON_WHERE_CLAUSE
 							+ "}\n";
 

src/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java

@@ -80,8 +80,10 @@ public class OrganizationUtilityFunctions {
 
 		String whereClause = "?organization rdf:type foaf:Organization ;" 
 						+ " rdfs:label ?organizationLabel . \n"
-				+ "OPTIONAL { ?organization core:hasSubOrganization ?subOrg } . \n"
+				+ "OPTIONAL { ?organization <http://purl.obolibrary.org/obo/BFO_0000051> ?subOrg . \n"
-				+ "OPTIONAL { ?organization core:subOrganizationWithin ?parent } . \n"
+			    + "           ?subOrg rdf:type foaf:Organization } . \n"
+				+ "OPTIONAL { ?organization <http://purl.obolibrary.org/obo/BFO_0000050> ?parent . \n"
+		    + "               ?parent rdf:type foaf:Organization } . \n"
 				+ "FILTER ( !bound(?parent) ). \n";
 
 		String groupOrderClause = "GROUP BY ?organization ?organizationLabel \n"

src/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java

@@ -123,9 +123,10 @@ public class UtilitiesRequestHandler implements VisualizationRequestHandler {
 			
 			String whereClause = 
 				"<" + individualURI + "> rdf:type foaf:Person ;" 
-					+ " core:authorInAuthorship ?authorshipNode . \n"
+					+ " core:relatedBy ?authorshipNode . \n"
 				+ "?authorshipNode rdf:type core:Authorship ;" 
-					+ " core:linkedInformationResource ?document .";
+					+ " core:relates ?document . \n"
+				+ "?document rdf:type bibo:Document .";
 
 			String groupOrderClause = "GROUP BY ?" + QueryFieldLabels.AUTHOR_URL + " \n"; 
 			
@@ -152,16 +153,22 @@ public class UtilitiesRequestHandler implements VisualizationRequestHandler {
 			ObjectProperty predicate = ModelUtils.getPropertyForRoleInClass(grantType, vitroRequest.getWebappDaoFactory());
 			String roleToGrantPredicate = "<" + predicate.getURI() + ">";
 			String whereClause = "{ <" + individualURI + "> rdf:type foaf:Person ;" 
-										+ " core:hasCo-PrincipalInvestigatorRole ?Role . \n"
+										+ " <http://purl.obolibrary.org/obo/RO_0000053> ?Role . \n"
+									+ "?Role rdf:type core:PrincipalInvestigatorRole . \n"
 									+ "?Role " + roleToGrantPredicate + " ?Grant . }"
 									+ "UNION \n"
 									+ "{ <" + individualURI + "> rdf:type foaf:Person ;" 
-										+ " core:hasPrincipalInvestigatorRole ?Role . \n"
+										+ " <http://purl.obolibrary.org/obo/RO_0000053> ?Role . \n"
+									+ "?Role rdf:type core:CoPrincipalInvestigatorRole . \n"
 									+ "?Role " + roleToGrantPredicate + " ?Grant . }"
 									+ "UNION \n"
 									+ "{ <" + individualURI + "> rdf:type foaf:Person ;" 
-										+ " core:hasInvestigatorRole ?Role . \n"
+										+ " <http://purl.obolibrary.org/obo/RO_0000053> ?Role . \n"
-									+ "?Role " + roleToGrantPredicate + " ?Grant . }";
+									+ "?Role rdf:type core:InvestigatorRole. \n"
+    								+ "?Role vitro:mostSpecificType ?subclass . \n"
+									+ "?Role " + roleToGrantPredicate + " ?Grant . \n" 
+									+ "FILTER (?subclass != core:PrincipalInvestigatorRole && "
+									+ "?subclass != core:CoPrincipalInvestigatorRole)}";
 
 			QueryRunner<ResultSet> numberOfGrantsQueryHandler = 
 			new GenericQueryRunner(fieldLabelToOutputFieldLabel,
@@ -302,8 +309,10 @@ public class UtilitiesRequestHandler implements VisualizationRequestHandler {
 			
 			String whereClause = "?organization rdf:type foaf:Organization ;" 
 								+ " rdfs:label ?organizationLabel . \n"  
-							+ "OPTIONAL { ?organization core:hasSubOrganization ?subOrg } . \n"
+							    + "OPTIONAL { ?organization core:http://purl.obolibrary.org/obo/BFO_0000051 ?subOrg  . \n"
-							+ "OPTIONAL { ?organization core:subOrganizationWithin ?parent } . \n"
+						        + "           ?subOrg rdf:type foaf:Organization } . \n"
+							    + "OPTIONAL { ?organization core:http://purl.obolibrary.org/obo/BFO_0000050 ?parent } . \n"
+				                + "           ?parent rdf:type foaf:Organization } . \n"
 							    + "FILTER ( !bound(?parent) ). \n";
 			
 			String groupOrderClause = "GROUP BY ?organization ?organizationLabel \n" 

src/edu/cornell/mannlib/vitro/webapp/visualization/visutils/AllPropertiesQueryRunner.java

@@ -3,7 +3,9 @@
 package edu.cornell.mannlib.vitro.webapp.visualization.visutils;
 
 import org.apache.commons.lang.StringUtils;
+
 import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.iri.IRI;
 import com.hp.hpl.jena.iri.IRIFactory;
@@ -38,7 +40,7 @@ public class AllPropertiesQueryRunner implements QueryRunner<GenericQueryMap> {
 	private String filterRule, individualURI;
 	private Dataset dataset;
 
-	private Log log;
+	private Log log = LogFactory.getLog(AllPropertiesQueryRunner.class.getName());
 
 	public AllPropertiesQueryRunner(String individualURI,
 							   String filterRule,
@@ -102,6 +104,8 @@ public class AllPropertiesQueryRunner implements QueryRunner<GenericQueryMap> {
 							+ filterClause
 							+ "}";
             	
+        log.debug("sparqlQuery = " + sparqlQuery.toString());
+        
 		return sparqlQuery;
 	}
 	

src/edu/cornell/mannlib/vitro/webapp/visualization/visutils/GenericQueryRunner.java

@@ -4,6 +4,8 @@ package edu.cornell.mannlib.vitro.webapp.visualization.visutils;
 
 import java.util.Map;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.query.Query;
@@ -33,6 +35,8 @@ public class GenericQueryRunner implements QueryRunner<ResultSet> {
 
 	private Map<String, String> fieldLabelToOutputFieldLabel;
 	
+	private Log log = LogFactory.getLog(GenericQueryRunner.class.getName());
+
 	private String groupOrderClause;
 
 	private String aggregationRules;
@@ -84,6 +88,8 @@ public class GenericQueryRunner implements QueryRunner<ResultSet> {
 		
 		sparqlQuery.append(this.groupOrderClause);
 		
+		log.debug("sparqlQuery = " + sparqlQuery.toString());
+		
 		return sparqlQuery.toString();
 	}
 	

src/edu/cornell/mannlib/vitro/webapp/visualization/visutils/GenericQueryRunnerOnModel.java

@@ -4,6 +4,9 @@ package edu.cornell.mannlib.vitro.webapp.visualization.visutils;
 
 import java.util.Map;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
@@ -32,6 +35,8 @@ public class GenericQueryRunnerOnModel implements QueryRunner<ResultSet> {
 
 	private Map<String, String> fieldLabelToOutputFieldLabel;
 	
+	private Log log = LogFactory.getLog(GenericQueryRunnerOnModel.class.getName());
+
 	private String groupOrderClause;
 
 	private String aggregationRules;
@@ -83,6 +88,7 @@ public class GenericQueryRunnerOnModel implements QueryRunner<ResultSet> {
 		
 		sparqlQuery.append(this.groupOrderClause);
 		
+		log.debug("sparqlQuery = " + sparqlQuery.toString());
 		return sparqlQuery.toString();
 	}
 	

src/edu/cornell/mannlib/vitro/webapp/visualization/visutils/SelectOnModelUtilities.java

@@ -52,7 +52,8 @@ public class SelectOnModelUtilities {
 		
 		String whereClause = ""
 			+ " <" + subjectEntityURI + "> rdfs:label ?organizationLabel . "
-			+ " <" + subjectEntityURI + "> core:hasSubOrganization ?subOrganization . "
+			+ " <" + subjectEntityURI + "> <http://purl.obolibrary.org/obo/BFO_0000051> ?subOrganization . "
+            + " ?subOrganization rdf:type foaf:Organization .  "
 			+ " ?subOrganization rdfs:label ?subOrganizationLabel . "
 			+ " ?subOrganization rdf:type ?subOrgType . "
 			+ " ?subOrgType rdfs:label ?subOrganizationTypeLabel . ";
@@ -136,7 +137,8 @@ public class SelectOnModelUtilities {
 		
 		String whereClause = ""
 			+ " <" + subjectEntityURI + "> rdfs:label ?organizationLabel . "
-			+ " <" + subjectEntityURI + "> core:subOrganizationWithin ?parentOrganization . "
+			+ " <" + subjectEntityURI + "> <http://purl.obolibrary.org/obo/BFO_0000050> ?parentOrganization . "
+            + " ?parentOrganization rdf:type foaf:Organization .  "
 			+ " ?parentOrganization rdfs:label ?parentOrganizationLabel . ";
 		
 		QueryRunner<ResultSet> parentOrganizationsQuery = 

themes/wilma/i18n/all.properties

@@ -435,8 +435,8 @@ check_grants_to_exclude = Check those grants and projects you want to exclude fr
 manage_affiliated_people = Manage People Affiliated with
 check_people_to_exclude = Check those people you want to exclude from the profile page.
 
-manage_grants = Manage grants for
+manage_publications_for = Manage Publications for
-check_pubs_to_exclude = Check those grants you want to exclude from the profile page.
+check_pubs_to_exclude = Check those publications you want to exclude from the profile page.
 
 manage_web_pages = Manage Web Pages
 has_no_webpages = This individual currently has no web pages specified. Add a new web page by clicking on the button below.
@@ -840,3 +840,6 @@ full_name = Full name
 full_name_for = full name for
 first_name = First name
 last_name = Last name
+title_not_found = Title not found.
+speeches_capitalized = Speeches
+theses_capitalized = Theses 

themes/wilma/templates/individual--foaf-person.ftl

@@ -148,4 +148,3 @@ ${scripts.add('<script type="text/javascript" src="${urls.base}/js/individual/in
               '<script type="text/javascript" src="${urls.base}/js/individual/individualUriRdf.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/jquery-ui/js/jquery-ui-1.8.9.custom.min.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/imageUpload/imageUploadUtils.js"></script>')}
-