edits as per the Toronto meeting and document at https://docs.google.…

…com/document/d/1970NY0lvKw2Geu0lYz75FfeigdT-pwmSyLFs8zNyXpg/edit#
EBISPOT · Sep 7, 2018 · 2d0fc40 · 2d0fc40
1 parent 88bf2aa
commit 2d0fc40
Showing 1 changed file with 33 additions and 16 deletions.
diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl
@@ -202,6 +202,7 @@
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">no restriction</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This consent code primary category indicates there is no restriction on use.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000004</oboInOwl:id>
+        <rdfs:comment>20180907, Meeting Moran Melanie: This is to be thought about more carefully - what is the intent when using &apos;no restriction&apos; as usually users still need to be researchers.</rdfs:comment>
         <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service</rdfs:comment>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">no restriction</rdfs:label>
     </owl:Class>
@@ -212,49 +213,50 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000005">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000002"/>
-        <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">general research use and clinical care</obo:DUO_0000041>
-        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This primary category consent code indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.</obo:IAO_0000115>
+        <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">general research use</obo:DUO_0000041>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This primary category consent code indicates that use is allowed for general research use for any research purpose.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000005</oboInOwl:id>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">general research use and clinical care</rdfs:label>
+        <rdfs:comment xml:lang="en">This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research.</rdfs:comment>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">general research use</rdfs:label>
     </owl:Class>
 
 
 
     <!-- http://purl.obolibrary.org/obo/DUO_0000006 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000006">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000002"/>
-        <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">health/medical/biomedical research and clinical care</obo:DUO_0000041>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000005"/>
+        <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">health/medical/biomedical research</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.</obo:IAO_0000115>
-        <obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">health medical biomedical research and clinical care</obo:IAO_0000232>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000006</oboInOwl:id>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">health or medical or biomedical research and clinical care</rdfs:label>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">health or medical or biomedical research</rdfs:label>
     </owl:Class>
 
 
 
     <!-- http://purl.obolibrary.org/obo/DUO_0000007 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000007">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000002"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000006"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/DUO_0000010"/>
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/DOID_4"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease-specific research and clinical care</obo:DUO_0000041>
+        <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease-specific research</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This primary category consent code indicates that use is allowed provided it is related to the specified disease.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000007</oboInOwl:id>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease specific research and clinical care</rdfs:label>
+        <rdfs:comment xml:lang="en">This term should be coupled with a term describing a disease from an ontology, such as the Disease Ontology, HPO, MonDO to specify the disease the restriction applies to.</rdfs:comment>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease specific research</rdfs:label>
     </owl:Class>
 
 
 
     <!-- http://purl.obolibrary.org/obo/DUO_0000011 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000011">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000002"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000005"/>
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">population origins or ancestry research</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry.</obo:IAO_0000115>
         <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">population origins/ancestry research</obo:IAO_0000118>
@@ -335,8 +337,10 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000018">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000017"/>
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">not-for-profit use only</obo:DUO_0000041>
-        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that use is limited to not-for-profit organizations.</obo:IAO_0000115>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.</obo:IAO_0000115>
+        <obo:IAO_0000118 xml:lang="en">non-commercial use</obo:IAO_0000118>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000018</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">NPU</oboInOwl:shorthand>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">not for profit use only</rdfs:label>
     </owl:Class>
 
@@ -349,6 +353,7 @@
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">publication required</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000019</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">PUB</oboInOwl:shorthand>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">publication required</rdfs:label>
     </owl:Class>
 
@@ -361,6 +366,8 @@
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">collaboration required</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s).</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000020</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">COL</oboInOwl:shorthand>
+        <rdfs:comment xml:lang="en">This could be coupled with a string describing the primary study investigator(s).</rdfs:comment>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">collaboration required</rdfs:label>
     </owl:Class>
 
@@ -373,6 +380,7 @@
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ethics approval required</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that the requestor must provide documentation of local IRB/ERB approval.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000021</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">IRB</oboInOwl:shorthand>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ethics approval required</rdfs:label>
     </owl:Class>
 
@@ -391,6 +399,8 @@
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">geographical restriction</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that use is limited to within a specific geographic region.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000022</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">GS-[XX]</oboInOwl:shorthand>
+        <rdfs:comment xml:lang="en">This should be coupled with an ontology term describing the geographical location the restriction applies to.</rdfs:comment>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">geographical restriction</rdfs:label>
     </owl:Class>
 
@@ -404,6 +414,8 @@
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that requestor agrees not to publish results of studies until a specific date</obo:IAO_0000115>
         <obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">publication embargo</obo:IAO_0000118>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000024</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">MOR-[XX]</oboInOwl:shorthand>
+        <rdfs:comment xml:lang="en">This should be coupled with a date specified as ISO8601</rdfs:comment>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">publication moratorium</rdfs:label>
     </owl:Class>
 
@@ -416,6 +428,8 @@
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">time limit on use</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that use is approved for a specific number of months.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000025</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">TS-[XX]</oboInOwl:shorthand>
+        <rdfs:comment xml:lang="en">This should be coupled with an integer value indicating the number of months.</rdfs:comment>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">time limit on use</rdfs:label>
     </owl:Class>
 
@@ -428,6 +442,7 @@
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">user-specific restriction</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that use is limited to use by approved users.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000026</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">US</oboInOwl:shorthand>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">user specific restriction</rdfs:label>
     </owl:Class>
 
@@ -440,6 +455,7 @@
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">project-specific restriction</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that use is limited to use within an approved project.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000027</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">PS</oboInOwl:shorthand>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">project specific restriction</rdfs:label>
     </owl:Class>
 
@@ -452,6 +468,7 @@
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">institution-specific restriction</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This requirement indicates that use is limited to use within an approved institution.</obo:IAO_0000115>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000028</oboInOwl:id>
+        <oboInOwl:shorthand xml:lang="en">IS</oboInOwl:shorthand>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">institution specific restriction</rdfs:label>
     </owl:Class>
 
@@ -489,9 +506,9 @@
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000066"/>
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">population research</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An investigation concerning a specific population group.</obo:IAO_0000115>
-        <obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Should be paired with the an ontology term representing this population (e.g., xxx).</obo:IAO_0000232>
         <obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This definition is a placeholder as a result of meetings at ICBO2018.</obo:IAO_0000232>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO_0000032</oboInOwl:id>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Should be paired with the an ontology term representing this population (e.g., xxx).</rdfs:comment>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">population research</rdfs:label>
     </owl:Class>
 
@@ -516,9 +533,9 @@
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000066"/>
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">age category research</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An investigation concerning specific age categories.</obo:IAO_0000115>
-        <obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Should be paired with the an ontology term representing this population (e.g., xxx).</obo:IAO_0000232>
         <obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This definition is a placeholder as a result of meetings at ICBO2018.</obo:IAO_0000232>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO_0000034</oboInOwl:id>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Should be paired with the an ontology term representing this population (e.g., xxx).</rdfs:comment>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">age category research</rdfs:label>
     </owl:Class>
 
@@ -530,9 +547,9 @@
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000066"/>
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">gender category research</obo:DUO_0000041>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An investigation concerning specific gender categories.</obo:IAO_0000115>
-        <obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Should be paired with the an ontology term representing this population (e.g., xxx).</obo:IAO_0000232>
         <obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This definition is a placeholder as a result of meetings at ICBO2018.</obo:IAO_0000232>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO_0000035</oboInOwl:id>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Should be paired with the an ontology term representing this population (e.g., xxx).</rdfs:comment>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">gender category research</rdfs:label>
     </owl:Class>
 
@@ -595,7 +612,7 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000040">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000037"/>
         <obo:DUO_0000041 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease category research</obo:DUO_0000041>
-        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biomedical research concerning specific a disease or diseases.</obo:IAO_0000115>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biomedical research research concerning specific disease/s</obo:IAO_0000115>
         <obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This definition is a placeholder as a result of meetings at ICBO2018.</obo:IAO_0000232>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO_0000040</oboInOwl:id>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease category research</rdfs:label>