From da690ebf9d0bd63e799eceee54e4d9f0b09d8aac Mon Sep 17 00:00:00 2001
From: brianjlowe <bjl23@cornell.edu>
Date: Tue, 5 Nov 2013 15:25:27 -0500
Subject: [PATCH] VIVO-434 restoring "documentation for"

---
 rdf/tbox/filegraph/object-properties.owl     | 62 +++++++++-----------
 rdf/tbox/filegraph/research-resource.owl     | 13 ++++
 rdf/tbox/firsttime/initialTBoxAnnotations.n3 |  5 ++
 3 files changed, 46 insertions(+), 34 deletions(-)

diff --git a/rdf/tbox/filegraph/object-properties.owl b/rdf/tbox/filegraph/object-properties.owl
index 4c95312e..1f06a387 100644
--- a/rdf/tbox/filegraph/object-properties.owl
+++ b/rdf/tbox/filegraph/object-properties.owl
@@ -201,7 +201,6 @@
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000006"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000071"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0001716"/>
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
                 </owl:unionOf>
             </owl:Class>
         </rdfs:range>
@@ -317,7 +316,6 @@
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000006"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000007"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000071"/>
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
                 </owl:unionOf>
             </owl:Class>
         </rdfs:range>
@@ -497,7 +495,6 @@
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000071"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0001716"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000272"/>
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
                 </owl:unionOf>
             </owl:Class>
         </rdfs:domain>
@@ -575,7 +572,6 @@
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0001194"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0001200"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0001716"/>
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0400147"/>
                 </owl:unionOf>
             </owl:Class>
@@ -593,8 +589,6 @@
         <obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melissa Haendel</obo:IAO_0000119>
         <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melissa Haendel</obo:IAO_0000117>
         <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">used to study</obo:IAO_0000111>
-        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/ERO_0000985"/>
-        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
     </owl:ObjectProperty>
     
@@ -914,14 +908,7 @@ there is a measurement process p that has specified output m, a measurement datu
         <obo:IAO_0000112 xml:lang="en">http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)</obo:IAO_0000112>
         <obo:IAO_0000111 xml:lang="en">is_manufactured_by</obo:IAO_0000111>
         <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
-        <rdfs:range>
-            <owl:Class>
-                <owl:unionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
-                    <rdf:Description rdf:about="http://xmlns.com/foaf/0.1/Organization"/>
-                </owl:unionOf>
-            </owl:Class>
-        </rdfs:range>
+        <rdfs:range rdf:resource="http://xmlns.com/foaf/0.1/Organization"/>
     </owl:ObjectProperty>
     
 
@@ -1671,7 +1658,8 @@ there is a measurement process p that has specified output m, a measurement datu
     <!-- http://vivoweb.org/ontology/scientific-research#accessProvidedBy -->
 
     <owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/scientific-research#accessProvidedBy">
-
+        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/ERO_0000391"/>
+        <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000029"/>
     </owl:ObjectProperty>
     
 
@@ -1679,7 +1667,21 @@ there is a measurement process p that has specified output m, a measurement datu
     <!-- http://vivoweb.org/ontology/scientific-research#documentationFor -->
 
     <owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/scientific-research#documentationFor">
-
+         <rdfs:domain rdf:resource="http://purl.org/ontology/bibo/Document"/>
+        <rdfs:range>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000004"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000005"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000006"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000014"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000020"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000071"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0001716"/>
+                </owl:unionOf>
+            </owl:Class>
+        </rdfs:range>
+         <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000460"/>
     </owl:ObjectProperty>
     
 
@@ -1687,7 +1689,16 @@ there is a measurement process p that has specified output m, a measurement datu
     <!-- http://vivoweb.org/ontology/scientific-research#protocolRealizedBy -->
 
     <owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/scientific-research#protocolRealizedBy">
-
+     <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000481"/>
+        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000272"/>
+        <rdfs:range>
+            <owl:Class>
+                <owl:unionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000005"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000014"/>
+                </owl:unionOf>
+            </owl:Class>
+         </rdfs:range>
     </owl:ObjectProperty>
     
 
@@ -1704,7 +1715,6 @@ there is a measurement process p that has specified output m, a measurement datu
 
     <owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/efo/swo/SWO_0000741">
 
-        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000025"/>
         <rdfs:domain>
             <owl:Class>
                 <owl:unionOf rdf:parseType="Collection">
@@ -1717,22 +1727,6 @@ there is a measurement process p that has specified output m, a measurement datu
     
 
 
-    <!-- http://www.obofoundry.org/ro/ro.owl#has_agent -->
-
-    <owl:ObjectProperty rdf:about="http://www.obofoundry.org/ro/ro.owl#has_agent">
-
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://www.w3.org/2002/07/owl#DeprecatedProperty -->
-
-    <owl:ObjectProperty rdf:about="http://www.w3.org/2002/07/owl#DeprecatedProperty">
-
-    </owl:ObjectProperty>
-    
-
-
     <!-- http://www.w3.org/2002/07/owl#topObjectProperty -->
 
     <owl:ObjectProperty rdf:about="http://www.w3.org/2002/07/owl#topObjectProperty"/>
diff --git a/rdf/tbox/filegraph/research-resource.owl b/rdf/tbox/filegraph/research-resource.owl
index dccf8f43..795cdeb9 100644
--- a/rdf/tbox/filegraph/research-resource.owl
+++ b/rdf/tbox/filegraph/research-resource.owl
@@ -507,5 +507,18 @@
         <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
     </owl:Class>
 
+ <!-- http://purl.obolibrary.org/obo/OBI_0000272 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000272">
+        <rdfs:subClassOf rdf:resource="http://purl.org/ontology/bibo/Document"/>
+        <obo:IAO_0000119 xml:lang="en">OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)</obo:IAO_0000119>
+        <obo:IAO_0000112 xml:lang="en">PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice.</obo:IAO_0000112>
+        <obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
+        <obo:IAO_0000111 xml:lang="en">Protocol</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.</obo:IAO_0000115>
+        <obo:IAO_0000111 xml:lang="en">protocol</obo:IAO_0000111>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+    </owl:Class>
 
 </rdf:RDF>
diff --git a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 b/rdf/tbox/firsttime/initialTBoxAnnotations.n3
index cef6df9c..44a3d725 100644
--- a/rdf/tbox/firsttime/initialTBoxAnnotations.n3
+++ b/rdf/tbox/firsttime/initialTBoxAnnotations.n3
@@ -407,6 +407,9 @@ foaf:Person
 obo:OBI_0000643
       rdfs:label "has grain"@en-US .
 
+obo:OBI_0000272
+      rdfs:label "protocol"@en-US .
+
 vcard:Identification
       rdfs:label "Identification"@en-US .
 
@@ -6173,6 +6176,8 @@ obo:ERO_0001716
       vitro:prohibitedFromUpdateBelowRoleLevelAnnot
               <http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
       vitro:selectFromExistingAnnot
+              "true"^^xsd:boolean ;
+      vitro:offerCreateNewOptionAnnot
               "true"^^xsd:boolean .
 
 vcard:hasRelated