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restructing the directory hierarchy for optional modules and mappings

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sjm222 2010-12-09 21:30:13 +00:00
parent cab7ae870d
commit 4912d62841
4 changed files with 302 additions and 89 deletions
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234
productMods/WEB-INF/ontologies/optional/mapping/scirr-ero-mapping-1.2.owl Normal file
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@ -0,0 +1,234 @@
<?xml version="1.0"?>
<!DOCTYPE rdf:RDF [
<!ENTITY foaf "http://xmlns.com/foaf/0.1/" >
<!ENTITY bibo "http://purl.org/ontology/bibo/" >
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
<!ENTITY obo "http://purl.obolibrary.org/obo/" >
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
<!ENTITY core "http://vivoweb.org/ontology/core#" >
<!ENTITY snap "http://www.ifomis.org/bfo/1.1/snap#" >
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
<!ENTITY research "http://purl.org/net/OCRe/research.owl#" >
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
<!ENTITY scirr "http://vivoweb.org/ontology/scientific-research-resource#" >
]>
<rdf:RDF
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
xmlns:scirr="http://vivoweb.org/ontology/scientific-research-resource#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:core="http://vivoweb.org/ontology/core#"
xmlns:research="http://purl.org/net/OCRe/research.owl#">
<owl:Ontology rdf:about="http://vivoweb.org/ontology/scientific-research-resource/mapping/ero">
</owl:Ontology>
<!-- http://purl.obolibrary.org/obo/ERO_0000031 -->
<owl:ObjectProperty rdf:about="&obo;ERO_0000031">
<owl:equivalentProperty rdf:resource="&scirr;usesProtocolOrSoftware"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/ERO_0000033 -->
<owl:ObjectProperty rdf:about="&obo;ERO_0000033">
<owl:equivalentProperty rdf:resource="&scirr;knowsTechnique"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/ERO_0000034 -->
<owl:ObjectProperty rdf:about="&obo;ERO_0000034">
<owl:equivalentProperty rdf:resource="&scirr;hasManufacturer"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/ERO_0000234 -->
<owl:ObjectProperty rdf:about="&obo;ERO_0000234">
<owl:equivalentProperty rdf:resource="&scirr;hasOrganismProcessOrDiseaseFocus"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/ERO_0000397 -->
<owl:ObjectProperty rdf:about="&obo;ERO_0000397">
<owl:equivalentProperty rdf:resource="&scirr;performsTechniqueOrService"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000306 -->
<owl:ObjectProperty rdf:about="&obo;OBI_0000306">
<owl:equivalentProperty rdf:resource="&scirr;hasFunction"/>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/ERO_0000001 -->
<owl:Class rdf:about="&obo;ERO_0000001">
<owl:equivalentClass rdf:resource="&core;Laboratory"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000002 -->
<owl:Class rdf:about="&obo;ERO_0000002">
<owl:equivalentClass rdf:resource="&core;CoreLaboratory"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000004 -->
<owl:Class rdf:about="&obo;ERO_0000004">
<owl:equivalentClass rdf:resource="&scirr;Instrument"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000006 -->
<owl:Class rdf:about="&obo;ERO_0000006">
<owl:equivalentClass rdf:resource="&scirr;Reagent"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000007 -->
<owl:Class rdf:about="&obo;ERO_0000007">
<owl:equivalentClass rdf:resource="&scirr;Technique"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000014 -->
<owl:Class rdf:about="&obo;ERO_0000014">
<owl:equivalentClass rdf:resource="&scirr;ResearchProject"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000015 -->
<owl:Class rdf:about="&obo;ERO_0000015">
<owl:equivalentClass rdf:resource="&scirr;HumanStudy"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000016 -->
<owl:Class rdf:about="&obo;ERO_0000016">
<owl:equivalentClass rdf:resource="&scirr;ClinicalTrial"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000020 -->
<owl:Class rdf:about="&obo;ERO_0000020">
<owl:equivalentClass rdf:resource="&scirr;BiologicalSpecimen"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000071 -->
<owl:Class rdf:about="&obo;ERO_0000071">
<owl:equivalentClass rdf:resource="&core;Software"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000391 -->
<owl:Class rdf:about="&obo;ERO_0000391">
<owl:equivalentClass rdf:resource="&scirr;AccessService"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000392 -->
<owl:Class rdf:about="&obo;ERO_0000392">
<owl:equivalentClass rdf:resource="&scirr;StorageService"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000393 -->
<owl:Class rdf:about="&obo;ERO_0000393">
<owl:equivalentClass rdf:resource="&scirr;TrainingService"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/ERO_0000394 -->
<owl:Class rdf:about="&obo;ERO_0000394">
<owl:equivalentClass rdf:resource="&scirr;ProductionService"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000011 -->
<owl:Class rdf:about="&obo;OBI_0000011">
<owl:equivalentClass rdf:resource="&core;Process"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000272 -->
<owl:Class rdf:about="&obo;OBI_0000272">
<owl:equivalentClass rdf:resource="&scirr;Protocol"/>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0100026 -->
<owl:Class rdf:about="&obo;OBI_0100026">
<owl:equivalentClass rdf:resource="&scirr;Organism"/>
</owl:Class>
<!-- http://purl.org/net/OCRe/research.owl#Interventional_study -->
<owl:Class rdf:about="&research;Interventional_study">
<owl:equivalentClass rdf:resource="&scirr;InterventionalStudy"/>
</owl:Class>
<!-- http://purl.org/net/OCRe/research.owl#Observational_study -->
<owl:Class rdf:about="&research;Observational_study">
<owl:equivalentClass rdf:resource="&scirr;ObservationalStudy"/>
</owl:Class>
<!-- http://purl.org/net/OCRe/research.owl#Quantitative_human_study -->
<owl:Class rdf:about="&research;Quantitative_human_study">
<owl:equivalentClass rdf:resource="&scirr;QuantitativeHumanStudy"/>
</owl:Class>
<!-- Generated by the OWL API (version 3.1.0.1602) http://owlapi.sourceforge.net -->

0
productMods/WEB-INF/ontologies/optional-module/bfo/bfo-1.1.owl → productMods/WEB-INF/ontologies/optional/module/bfo-extension/bfo-1.1.owl
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67
productMods/WEB-INF/ontologies/optional/module/bfo-extension/scirr-bfo-1.2.owl Normal file
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@ -0,0 +1,67 @@
<?xml version="1.0"?>
<!DOCTYPE rdf:RDF [
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
<!ENTITY snap "http://www.ifomis.org/bfo/1.1/snap#" >
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
<!ENTITY scientific-research-resource "http://vivoweb.org/ontology/scientific-research-resource#" >
]>
<rdf:RDF xmlns="http://vivoweb.org/ontology/scientific-research-resource/bfo#"
xml:base="http://vivoweb.org/ontology/scientific-research-resource/bfo"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:scientific-research-resource="http://vivoweb.org/ontology/scientific-research-resource#"
xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<owl:Ontology rdf:about="http://vivoweb.org/ontology/scientific-research-resource/bfo-extension">
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://vivoweb.org/ontology/scientific-research-resource#Function -->
<owl:Class rdf:about="&scientific-research-resource;Function">
<rdfs:subClassOf rdf:resource="&snap;RealizableEntity"/>
</owl:Class>
<!-- http://vivoweb.org/ontology/scientific-research-resource#Organism -->
<owl:Class rdf:about="&scientific-research-resource;Organism">
<rdfs:subClassOf rdf:resource="&snap;Object"/>
</owl:Class>
<!-- http://vivoweb.org/ontology/scientific-research-resource#Reagent -->
<owl:Class rdf:about="&scientific-research-resource;Reagent">
<rdfs:subClassOf rdf:resource="&snap;MaterialEntity"/>
</owl:Class>
<!-- http://vivoweb.org/ontology/scientific-research-resource#Specimen -->
<owl:Class rdf:about="&scientific-research-resource;Specimen">
<rdfs:subClassOf rdf:resource="&snap;MaterialEntity"/>
</owl:Class>
</rdf:RDF>
<!-- Generated by the OWL API (version 3.1.0.1602) http://owlapi.sourceforge.net -->

90
productMods/WEB-INF/ontologies/optional-module/bfo/bfo-vivo-1.2.owl → productMods/WEB-INF/ontologies/optional/module/bfo-extension/vivo-bfo-1.2.owl
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@ -27,8 +27,7 @@
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:core="http://vivoweb.org/ontology/core#" xmlns:core="http://vivoweb.org/ontology/core#"
xmlns:span="http://www.ifomis.org/bfo/1.1/span#"> xmlns:span="http://www.ifomis.org/bfo/1.1/span#">
<owl:Ontology rdf:about="http://vivoweb.org/ontology/bfo#"> <owl:Ontology rdf:about="http://vivoweb.org/ontology/core/bfo-extension">
<owl:imports rdf:resource="http://www.ifomis.org/bfo/1.1"/>
</owl:Ontology> </owl:Ontology>
@ -42,16 +41,12 @@
--> -->
<!-- http://purl.org/NET/c4dm/event.owl#Event --> <!-- http://purl.org/NET/c4dm/event.owl#Event -->
<owl:Class rdf:about="&event;Event"> <owl:Class rdf:about="&event;Event">
<rdfs:subClassOf rdf:resource="&span;Process"/> <rdfs:subClassOf rdf:resource="&span;Process"/>
</owl:Class> </owl:Class>
<!-- http://purl.org/ontology/bibo/DocumentStatus --> <!-- http://purl.org/ontology/bibo/DocumentStatus -->
<owl:Class rdf:about="&bibo;DocumentStatus"> <owl:Class rdf:about="&bibo;DocumentStatus">
@ -59,7 +54,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#AcademicDegree --> <!-- http://vivoweb.org/ontology/core#AcademicDegree -->
<owl:Class rdf:about="&core;AcademicDegree"> <owl:Class rdf:about="&core;AcademicDegree">
@ -67,7 +61,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#Address --> <!-- http://vivoweb.org/ontology/core#Address -->
<owl:Class rdf:about="&core;Address"> <owl:Class rdf:about="&core;Address">
@ -75,7 +68,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#Agreement --> <!-- http://vivoweb.org/ontology/core#Agreement -->
<owl:Class rdf:about="&core;Agreement"> <owl:Class rdf:about="&core;Agreement">
@ -83,7 +75,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#AwardOrHonor --> <!-- http://vivoweb.org/ontology/core#AwardOrHonor -->
<owl:Class rdf:about="&core;AwardOrHonor"> <owl:Class rdf:about="&core;AwardOrHonor">
@ -91,7 +82,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#AwardOrHonorReceipt --> <!-- http://vivoweb.org/ontology/core#AwardOrHonorReceipt -->
<owl:Class rdf:about="&core;AwardOrHonorReceipt"> <owl:Class rdf:about="&core;AwardOrHonorReceipt">
@ -99,7 +89,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#DateTimeInterval --> <!-- http://vivoweb.org/ontology/core#DateTimeInterval -->
<owl:Class rdf:about="&core;DateTimeInterval"> <owl:Class rdf:about="&core;DateTimeInterval">
@ -107,7 +96,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#DateTimeValue --> <!-- http://vivoweb.org/ontology/core#DateTimeValue -->
<owl:Class rdf:about="&core;DateTimeValue"> <owl:Class rdf:about="&core;DateTimeValue">
@ -115,7 +103,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#DateTimeValuePrecision --> <!-- http://vivoweb.org/ontology/core#DateTimeValuePrecision -->
<owl:Class rdf:about="&core;DateTimeValuePrecision"> <owl:Class rdf:about="&core;DateTimeValuePrecision">
@ -123,7 +110,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#EducationalTraining --> <!-- http://vivoweb.org/ontology/core#EducationalTraining -->
<owl:Class rdf:about="&core;EducationalTraining"> <owl:Class rdf:about="&core;EducationalTraining">
@ -131,7 +117,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#Equipment --> <!-- http://vivoweb.org/ontology/core#Equipment -->
<owl:Class rdf:about="&core;Equipment"> <owl:Class rdf:about="&core;Equipment">
@ -139,7 +124,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#EventSeries --> <!-- http://vivoweb.org/ontology/core#EventSeries -->
<owl:Class rdf:about="&core;EventSeries"> <owl:Class rdf:about="&core;EventSeries">
@ -147,15 +131,12 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#InformationResource --> <!-- http://vivoweb.org/ontology/core#InformationResource -->
<owl:Class rdf:about="&core;InformationResource"> <owl:Class rdf:about="&core;InformationResource">
<rdfs:subClassOf rdf:resource="&snap;GenericallyDependentContinuant"/> <rdfs:subClassOf rdf:resource="&snap;GenericallyDependentContinuant"/>
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#Location --> <!-- http://vivoweb.org/ontology/core#Location -->
<owl:Class rdf:about="&core;Location"> <owl:Class rdf:about="&core;Location">
@ -163,7 +144,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#Position --> <!-- http://vivoweb.org/ontology/core#Position -->
<owl:Class rdf:about="&core;Position"> <owl:Class rdf:about="&core;Position">
@ -171,7 +151,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#Process --> <!-- http://vivoweb.org/ontology/core#Process -->
<owl:Class rdf:about="&core;Process"> <owl:Class rdf:about="&core;Process">
@ -179,7 +158,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#Relationship --> <!-- http://vivoweb.org/ontology/core#Relationship -->
<owl:Class rdf:about="&core;Relationship"> <owl:Class rdf:about="&core;Relationship">
@ -187,7 +165,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#Role --> <!-- http://vivoweb.org/ontology/core#Role -->
<owl:Class rdf:about="&core;Role"> <owl:Class rdf:about="&core;Role">
@ -195,7 +172,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#Service --> <!-- http://vivoweb.org/ontology/core#Service -->
<owl:Class rdf:about="&core;Service"> <owl:Class rdf:about="&core;Service">
@ -203,7 +179,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#SubjectArea --> <!-- http://vivoweb.org/ontology/core#SubjectArea -->
<owl:Class rdf:about="&core;SubjectArea"> <owl:Class rdf:about="&core;SubjectArea">
@ -211,7 +186,6 @@
</owl:Class> </owl:Class>
<!-- http://vivoweb.org/ontology/core#URLLink --> <!-- http://vivoweb.org/ontology/core#URLLink -->
<owl:Class rdf:about="&core;URLLink"> <owl:Class rdf:about="&core;URLLink">
@ -219,73 +193,11 @@
</owl:Class> </owl:Class>
<!-- http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant -->
<owl:Class rdf:about="&snap;GenericallyDependentContinuant"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant -->
<owl:Class rdf:about="&snap;IndependentContinuant"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#MaterialEntity -->
<owl:Class rdf:about="&snap;MaterialEntity"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#Object -->
<owl:Class rdf:about="&snap;Object"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#Quality --> <!-- http://www.ifomis.org/bfo/1.1/snap#Quality -->
<owl:Class rdf:about="&snap;Quality"/> <owl:Class rdf:about="&snap;Quality"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#Role -->
<owl:Class rdf:about="&snap;Role"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant -->
<owl:Class rdf:about="&snap;SpecificallyDependentContinuant"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#ThreeDimensionalRegion -->
<owl:Class rdf:about="&snap;ThreeDimensionalRegion"/>
<!-- http://www.ifomis.org/bfo/1.1/span#Process -->
<owl:Class rdf:about="&span;Process"/>
<!-- http://www.ifomis.org/bfo/1.1/span#TemporalInstant -->
<owl:Class rdf:about="&span;TemporalInstant"/>
<!-- http://www.ifomis.org/bfo/1.1/span#TemporalInterval -->
<owl:Class rdf:about="&span;TemporalInterval"/>
<!-- http://xmlns.com/foaf/0.1/Agent --> <!-- http://xmlns.com/foaf/0.1/Agent -->
<owl:Class rdf:about="&foaf;Agent"> <owl:Class rdf:about="&foaf;Agent">