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latest ontology and migration code

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This commit is contained in:
stellamit 2011-10-31 17:30:46 +00:00
parent 4484f6ff40
commit 89b65a6c0e
10 changed files with 2652 additions and 2549 deletions
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10
productMods/WEB-INF/filegraph/tbox/scires-1.4.owl
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@ -64,6 +64,11 @@
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
<vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">In Phase 2 trials, an experimental study drug or treatment is given to a larger group of people (100-300) to see if it is effective and to further evaluate its safety.</vitro:descriptionAnnot>
</rdf:Description>
<rdf:Description rdf:nodeID="A0">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ERO_0000460"/>
<owl:allValuesFrom rdf:resource="http://purl.org/ontology/bibo/Document"/>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000392">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
<vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A service in which a service consumer provides some material or data as input which a service provider stores and returns as output.</vitro:descriptionAnnot>
@ -130,11 +135,6 @@ NOTE that we are not addressing for now the issue of whether a foaf:Person is a
<vitro:descriptionAnnot 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.
</vitro:descriptionAnnot>
</rdf:Description>
<rdf:Description rdf:nodeID="A0">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ERO_0000460"/>
<owl:allValuesFrom rdf:resource="http://purl.org/ontology/bibo/Document"/>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000004">
<rdfs:subClassOf rdf:nodeID="A0"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>

2526
productMods/WEB-INF/filegraph/tbox/vivo-core-1.4.owl
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2540
productMods/WEB-INF/ontologies/public/vivo-core-public-1.4.owl
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2
productMods/WEB-INF/ontologies/update/diff.tab.txt
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@ -1,8 +1,6 @@
http://vivoweb.org/ontology/core#SubjectArea No Delete Delete
http://vivoweb.org/ontology/core#hasSubjectArea No Delete Delete
http://vivoweb.org/ontology/core#hasResearchArea No Delete Delete
http://vivoweb.org/ontology/core#subjectAreaFor No Delete Delete
http://vivoweb.org/ontology/core#researchAreaOf No Delete Delete
http://vivoweb.org/ontology/core#roleIn No Delete Delete
http://vivoweb.org/ontology/core#relatedRole No Delete Delete
http://vivoweb.org/ontology/core#VocabularySourceReference No Delete Delete

5
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/ExternalConcept.sparql
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@ -17,10 +17,7 @@ Construct {
?something vivo:hasAssociatedConcept ?uri .
?uri vivo:conceptAssociatedWith ?something
} where {
{?something vivo:hasSubjectArea ?concept}
union
{?something vivo:hasResearchArea ?concept}
?something vivo:hasSubjectArea ?concept .
?concept rdf:type vivo:SubjectArea .
?concept vivo:sourceVocabularyReference ?urllink .
?urllink vivo:linkURI ?uri

24
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/ExternalResearchArea.sparql Normal file
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@ -0,0 +1,24 @@
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX swrl: <http://www.w3.org/2003/11/swrl#>
PREFIX swrlb: <http://www.w3.org/2003/11/swrlb#>
PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>
PREFIX vivo: <http://vivo.library.cornell.edu/ns/0.1#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX event: <http://purl.org/NET/c4dm/event.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
Construct {
?person vivo:hasResearchArea ?uri .
?uri vivo:researchAreaOf ?person
} where {
?person vivo:hasResearchArea ?concept .
?concept rdf:type vivo:SubjectArea .
?concept vivo:sourceVocabularyReference ?urllink .
?urllink vivo:linkURI ?uri
}

10
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/InternalConcept.sparql
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@ -19,15 +19,9 @@ Construct {
_:concept rdf:type skos:Concept .
_:concept rdfs:label ?label
} where {
{?something vivo:hasSubjectArea ?concept}
union
{?something vivo:hasResearchArea ?concept}
?something vivo:hasSubjectArea ?concept .
?concept rdf:type vivo:SubjectArea .
optional {?concept rdfs:label ?label}
optional {?concept vivo:vocabularySourceReference ?urllink}
optional {?concept vivo:sourceVocabularyReference ?urllink}
filter (!bound(?urllink))
}

28
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/InternalResearchArea.sparql Normal file
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@ -0,0 +1,28 @@
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX swrl: <http://www.w3.org/2003/11/swrl#>
PREFIX swrlb: <http://www.w3.org/2003/11/swrlb#>
PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>
PREFIX vivo: <http://vivo.library.cornell.edu/ns/0.1#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX event: <http://purl.org/NET/c4dm/event.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
Construct {
?person vivo:hasResearchArea _:concept .
_:concept vivo:researchAreaOf ?person .
_:concept rdf:type skos:Concept .
_:concept rdfs:label ?label
} where {
?person vivo:hasResearchArea ?concept .
?concept rdf:type vivo:SubjectArea .
optional {?concept rdfs:label ?label}
optional {?concept vivo:sourceVocabularyReference ?urllink}
filter (!bound(?urllink))
}

22
productMods/WEB-INF/ontologies/update/sparqlConstructs/deletions/ResearchArea.sparql Normal file
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@ -0,0 +1,22 @@
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX swrl: <http://www.w3.org/2003/11/swrl#>
PREFIX swrlb: <http://www.w3.org/2003/11/swrlb#>
PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>
PREFIX vivo: <http://vivo.library.cornell.edu/ns/0.1#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX event: <http://purl.org/NET/c4dm/event.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
Construct {
?person vivo:hasResearchArea ?concept .
?concept vivo:researchAreaOf ?person
} where {
?person vivo:hasResearchArea ?concept .
?concept rdf:type vivo:SubjectArea .
}

34
productMods/WEB-INF/ontologies/user/tbox/vivo-core-1.4-annotations.rdf
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@ -745,6 +745,15 @@
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#nobody"/>
</rdf:Description>
<rdf:Description rdf:about="http://vivoweb.org/ontology/core#researchAreaOf">
<vitro:inPropertyGroupAnnot rdf:resource="http://vivoweb.org/ontology#vitroPropertyGroupoverview"/>
<vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">10</vitro:displayRankAnnot>
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<rdfs:label xml:lang="en-US">research area of</rdfs:label>
<vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</vitro:displayLimitAnnot>
<vitro:selectFromExistingAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</vitro:selectFromExistingAnnot>
</rdf:Description>
<rdf:Description rdf:about="http://aims.fao.org/aos/geopolitical.owl#populationTotal">
<vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#nobody"/>
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
@ -1921,13 +1930,6 @@
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<rdfs:label xml:lang="en-US">GDPYear</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://vivoweb.org/ontology/core#PostdocOrFellowAdvisingRelationship">
<vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayLimitAnnot>
<vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayRankAnnot>
<rdfs:label xml:lang="en-US">Postdoc or Fellow Advising Relationship</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://vivoweb.org/ontology/core#NonAcademic">
<vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
@ -1936,6 +1938,13 @@
<vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">-1</vitro:displayRankAnnot>
<rdfs:label xml:lang="en-US">Non-Academic</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://vivoweb.org/ontology/core#PostdocOrFellowAdvisingRelationship">
<vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayLimitAnnot>
<vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</vitro:displayRankAnnot>
<rdfs:label xml:lang="en-US">Postdoc or Fellow Advising Relationship</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://vivoweb.org/ontology/core#governingAuthorityFor">
<vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</vitro:displayLimitAnnot>
<vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">8</vitro:displayRankAnnot>
@ -1981,8 +1990,8 @@
<rdfs:label xml:lang="en-US">reviewer role of</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://vivoweb.org/ontology/core#IssuedCredential">
<vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</vitro:displayLimitAnnot>
<vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</vitro:displayRankAnnot>
<vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">2</vitro:displayLimitAnnot>
<vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<rdfs:label xml:lang="en-US">Issued Credential</rdfs:label>
<vitro:inClassGroup rdf:resource="http://vivoweb.org/ontology#vitroClassGroupactivities"/>
@ -3873,6 +3882,15 @@
<rdfs:label xml:lang="en-US">outreach provider role of</rdfs:label>
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
</rdf:Description>
<rdf:Description rdf:about="http://vivoweb.org/ontology/core#hasResearchArea">
<vitro:selectFromExistingAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</vitro:selectFromExistingAnnot>
<vitro:hiddenFromDisplayBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">5</vitro:displayLimitAnnot>
<vitro:inPropertyGroupAnnot rdf:resource="http://vivoweb.org/ontology#vitroPropertyGroupoverview"/>
<vitro:displayRankAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">10</vitro:displayRankAnnot>
<rdfs:label xml:lang="en-US">has research area</rdfs:label>
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
</rdf:Description>
<rdf:Description rdf:about="http://vivoweb.org/ontology/core#Department">
<vitro:prohibitedFromUpdateBelowRoleLevelAnnot rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/role#public"/>
<vitro:displayLimitAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#int">-1</vitro:displayLimitAnnot>