From 4912d628416f044b19ff2b86f222162715b5fa79 Mon Sep 17 00:00:00 2001
From: sjm222 <sjm222@43c2fc9b-1942-4403-87b2-35b4218f7473>
Date: Thu, 9 Dec 2010 21:30:13 +0000
Subject: [PATCH] restructing the directory hierarchy for optional modules and
 mappings

---
 .../mapping/scirr-ero-mapping-1.2.owl         | 234 ++++++++++++++++++
 .../module/bfo-extension}/bfo-1.1.owl         |   0
 .../module/bfo-extension/scirr-bfo-1.2.owl    |  67 +++++
 .../module/bfo-extension/vivo-bfo-1.2.owl}    |  90 +------
 4 files changed, 302 insertions(+), 89 deletions(-)
 create mode 100644 productMods/WEB-INF/ontologies/optional/mapping/scirr-ero-mapping-1.2.owl
 rename productMods/WEB-INF/ontologies/{optional-module/bfo => optional/module/bfo-extension}/bfo-1.1.owl (100%)
 create mode 100644 productMods/WEB-INF/ontologies/optional/module/bfo-extension/scirr-bfo-1.2.owl
 rename productMods/WEB-INF/ontologies/{optional-module/bfo/bfo-vivo-1.2.owl => optional/module/bfo-extension/vivo-bfo-1.2.owl} (81%)

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
new file mode 100644
index 00000000..9992ae8c
--- /dev/null
+++ b/productMods/WEB-INF/ontologies/optional/mapping/scirr-ero-mapping-1.2.owl
@@ -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 -->
+
diff --git a/productMods/WEB-INF/ontologies/optional-module/bfo/bfo-1.1.owl b/productMods/WEB-INF/ontologies/optional/module/bfo-extension/bfo-1.1.owl
similarity index 100%
rename from productMods/WEB-INF/ontologies/optional-module/bfo/bfo-1.1.owl
rename to productMods/WEB-INF/ontologies/optional/module/bfo-extension/bfo-1.1.owl
diff --git a/productMods/WEB-INF/ontologies/optional/module/bfo-extension/scirr-bfo-1.2.owl b/productMods/WEB-INF/ontologies/optional/module/bfo-extension/scirr-bfo-1.2.owl
new file mode 100644
index 00000000..8ffcfecf
--- /dev/null
+++ b/productMods/WEB-INF/ontologies/optional/module/bfo-extension/scirr-bfo-1.2.owl
@@ -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 -->
+
diff --git a/productMods/WEB-INF/ontologies/optional-module/bfo/bfo-vivo-1.2.owl b/productMods/WEB-INF/ontologies/optional/module/bfo-extension/vivo-bfo-1.2.owl
similarity index 81%
rename from productMods/WEB-INF/ontologies/optional-module/bfo/bfo-vivo-1.2.owl
rename to productMods/WEB-INF/ontologies/optional/module/bfo-extension/vivo-bfo-1.2.owl
index 8e721fe0..337d1879 100644
--- a/productMods/WEB-INF/ontologies/optional-module/bfo/bfo-vivo-1.2.owl
+++ b/productMods/WEB-INF/ontologies/optional/module/bfo-extension/vivo-bfo-1.2.owl
@@ -27,8 +27,7 @@
      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/bfo#">
-          <owl:imports rdf:resource="http://www.ifomis.org/bfo/1.1"/>
+    <owl:Ontology rdf:about="http://vivoweb.org/ontology/core/bfo-extension">
     </owl:Ontology>
     
 
@@ -42,16 +41,12 @@
      -->
 
     
-
-
     <!-- 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">
@@ -59,7 +54,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#AcademicDegree -->
 
     <owl:Class rdf:about="&core;AcademicDegree">
@@ -67,7 +61,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#Address -->
 
     <owl:Class rdf:about="&core;Address">
@@ -75,7 +68,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#Agreement -->
 
     <owl:Class rdf:about="&core;Agreement">
@@ -83,7 +75,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#AwardOrHonor -->
 
     <owl:Class rdf:about="&core;AwardOrHonor">
@@ -91,7 +82,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#AwardOrHonorReceipt -->
 
     <owl:Class rdf:about="&core;AwardOrHonorReceipt">
@@ -99,7 +89,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#DateTimeInterval -->
 
     <owl:Class rdf:about="&core;DateTimeInterval">
@@ -107,7 +96,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#DateTimeValue -->
 
     <owl:Class rdf:about="&core;DateTimeValue">
@@ -115,7 +103,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#DateTimeValuePrecision -->
 
     <owl:Class rdf:about="&core;DateTimeValuePrecision">
@@ -123,7 +110,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#EducationalTraining -->
 
     <owl:Class rdf:about="&core;EducationalTraining">
@@ -131,7 +117,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#Equipment -->
 
     <owl:Class rdf:about="&core;Equipment">
@@ -139,7 +124,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#EventSeries -->
 
     <owl:Class rdf:about="&core;EventSeries">
@@ -147,15 +131,12 @@
     </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">
@@ -163,7 +144,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#Position -->
 
     <owl:Class rdf:about="&core;Position">
@@ -171,7 +151,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#Process -->
 
     <owl:Class rdf:about="&core;Process">
@@ -179,7 +158,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#Relationship -->
 
     <owl:Class rdf:about="&core;Relationship">
@@ -187,7 +165,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#Role -->
 
     <owl:Class rdf:about="&core;Role">
@@ -195,7 +172,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#Service -->
 
     <owl:Class rdf:about="&core;Service">
@@ -203,7 +179,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#SubjectArea -->
 
     <owl:Class rdf:about="&core;SubjectArea">
@@ -211,7 +186,6 @@
     </owl:Class>
     
 
-
     <!-- http://vivoweb.org/ontology/core#URLLink -->
 
     <owl:Class rdf:about="&core;URLLink">
@@ -219,73 +193,11 @@
     </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 -->
 
     <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 -->
 
     <owl:Class rdf:about="&foaf;Agent">