From b8608ee92974d8ec2f8fca1789c0740a69912f2e Mon Sep 17 00:00:00 2001
From: sjm222 <sjm222@43c2fc9b-1942-4403-87b2-35b4218f7473>
Date: Tue, 8 Feb 2011 14:55:36 +0000
Subject: [PATCH] Deleting these incomplete files for now so we don't risk
 shipping them with the release in the current state. I will check them back
 in when updated.

---
 .../optional/mapping/scirr-bfo-1.2.owl        |  67 -----
 .../mapping/scirr-ero-mapping-1.2.owl         | 234 ------------------
 .../optional/mapping/vivo-bfo-1.2.owl         | 211 ----------------
 3 files changed, 512 deletions(-)
 delete mode 100644 productMods/WEB-INF/ontologies/optional/mapping/scirr-bfo-1.2.owl
 delete mode 100644 productMods/WEB-INF/ontologies/optional/mapping/scirr-ero-mapping-1.2.owl
 delete mode 100644 productMods/WEB-INF/ontologies/optional/mapping/vivo-bfo-1.2.owl

diff --git a/productMods/WEB-INF/ontologies/optional/mapping/scirr-bfo-1.2.owl b/productMods/WEB-INF/ontologies/optional/mapping/scirr-bfo-1.2.owl
deleted file mode 100644
index 8ffcfecf..00000000
--- a/productMods/WEB-INF/ontologies/optional/mapping/scirr-bfo-1.2.owl
+++ /dev/null
@@ -1,67 +0,0 @@
-<?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 -->
-
diff --git a/productMods/WEB-INF/ontologies/optional/mapping/scirr-ero-mapping-1.2.owl b/productMods/WEB-INF/ontologies/optional/mapping/scirr-ero-mapping-1.2.owl
deleted file mode 100644
index 9992ae8c..00000000
--- a/productMods/WEB-INF/ontologies/optional/mapping/scirr-ero-mapping-1.2.owl
+++ /dev/null
@@ -1,234 +0,0 @@
-<?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 -->
-
diff --git a/productMods/WEB-INF/ontologies/optional/mapping/vivo-bfo-1.2.owl b/productMods/WEB-INF/ontologies/optional/mapping/vivo-bfo-1.2.owl
deleted file mode 100644
index 337d1879..00000000
--- a/productMods/WEB-INF/ontologies/optional/mapping/vivo-bfo-1.2.owl
+++ /dev/null
@@ -1,211 +0,0 @@
-<?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 xsd "http://www.w3.org/2001/XMLSchema#" >
-    <!ENTITY core "http://vivoweb.org/ontology/core#" >
-    <!ENTITY event "http://purl.org/NET/c4dm/event.owl#" >
-    <!ENTITY snap "http://www.ifomis.org/bfo/1.1/snap#" >
-    <!ENTITY span "http://www.ifomis.org/bfo/1.1/span#" >
-    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
-    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
-]>
-
-
-<rdf:RDF xmlns="http://vivoweb.org/ontology/bfo#"
-     xml:base="http://vivoweb.org/ontology/bfo"
-     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-     xmlns:foaf="http://xmlns.com/foaf/0.1/"
-     xmlns:event="http://purl.org/NET/c4dm/event.owl#"
-     xmlns:bibo="http://purl.org/ontology/bibo/"
-     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#"
-     xmlns:core="http://vivoweb.org/ontology/core#"
-     xmlns:span="http://www.ifomis.org/bfo/1.1/span#">
-    <owl:Ontology rdf:about="http://vivoweb.org/ontology/core/bfo-extension">
-    </owl:Ontology>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Classes
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-    <!-- http://purl.org/NET/c4dm/event.owl#Event -->
-
-    <owl:Class rdf:about="&event;Event">
-        <rdfs:subClassOf rdf:resource="&span;Process"/>
-    </owl:Class>
-    
-    <!-- http://purl.org/ontology/bibo/DocumentStatus -->
-
-    <owl:Class rdf:about="&bibo;DocumentStatus">
-        <rdfs:subClassOf rdf:resource="&snap;SpecificallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#AcademicDegree -->
-
-    <owl:Class rdf:about="&core;AcademicDegree">
-        <rdfs:subClassOf rdf:resource="&snap;SpecificallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#Address -->
-
-    <owl:Class rdf:about="&core;Address">
-        <rdfs:subClassOf rdf:resource="&snap;GenericallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#Agreement -->
-
-    <owl:Class rdf:about="&core;Agreement">
-        <rdfs:subClassOf rdf:resource="&snap;SpecificallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#AwardOrHonor -->
-
-    <owl:Class rdf:about="&core;AwardOrHonor">
-        <rdfs:subClassOf rdf:resource="&snap;GenericallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#AwardOrHonorReceipt -->
-
-    <owl:Class rdf:about="&core;AwardOrHonorReceipt">
-        <rdfs:subClassOf rdf:resource="&snap;SpecificallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#DateTimeInterval -->
-
-    <owl:Class rdf:about="&core;DateTimeInterval">
-        <rdfs:subClassOf rdf:resource="&span;TemporalInterval"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#DateTimeValue -->
-
-    <owl:Class rdf:about="&core;DateTimeValue">
-        <rdfs:subClassOf rdf:resource="&span;TemporalInstant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#DateTimeValuePrecision -->
-
-    <owl:Class rdf:about="&core;DateTimeValuePrecision">
-        <rdfs:subClassOf rdf:resource="&snap;GenericallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#EducationalTraining -->
-
-    <owl:Class rdf:about="&core;EducationalTraining">
-        <rdfs:subClassOf rdf:resource="&snap;SpecificallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#Equipment -->
-
-    <owl:Class rdf:about="&core;Equipment">
-        <rdfs:subClassOf rdf:resource="&snap;Object"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#EventSeries -->
-
-    <owl:Class rdf:about="&core;EventSeries">
-        <rdfs:subClassOf rdf:resource="&span;Process"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#InformationResource -->
-
-    <owl:Class rdf:about="&core;InformationResource">
-        <rdfs:subClassOf rdf:resource="&snap;GenericallyDependentContinuant"/>
-    </owl:Class>
-    
-    <!-- http://vivoweb.org/ontology/core#Location -->
-
-    <owl:Class rdf:about="&core;Location">
-        <rdfs:subClassOf rdf:resource="&snap;ThreeDimensionalRegion"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#Position -->
-
-    <owl:Class rdf:about="&core;Position">
-        <rdfs:subClassOf rdf:resource="&snap;Quality"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#Process -->
-
-    <owl:Class rdf:about="&core;Process">
-        <rdfs:subClassOf rdf:resource="&span;Process"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#Relationship -->
-
-    <owl:Class rdf:about="&core;Relationship">
-        <rdfs:subClassOf rdf:resource="&snap;SpecificallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#Role -->
-
-    <owl:Class rdf:about="&core;Role">
-        <rdfs:subClassOf rdf:resource="&snap;Role"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#Service -->
-
-    <owl:Class rdf:about="&core;Service">
-        <rdfs:subClassOf rdf:resource="&snap;GenericallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#SubjectArea -->
-
-    <owl:Class rdf:about="&core;SubjectArea">
-        <rdfs:subClassOf rdf:resource="&snap;IndependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://vivoweb.org/ontology/core#URLLink -->
-
-    <owl:Class rdf:about="&core;URLLink">
-        <rdfs:subClassOf rdf:resource="&snap;SpecificallyDependentContinuant"/>
-    </owl:Class>
-    
-
-    <!-- http://www.ifomis.org/bfo/1.1/snap#Quality -->
-
-    <owl:Class rdf:about="&snap;Quality"/>
-    
-
-    <!-- http://xmlns.com/foaf/0.1/Agent -->
-
-    <owl:Class rdf:about="&foaf;Agent">
-        <rdfs:subClassOf rdf:resource="&snap;MaterialEntity"/>
-    </owl:Class>
-</rdf:RDF>
-
-
-
-<!-- Generated by the OWL API (version 3.1.0.1602) http://owlapi.sourceforge.net -->
-