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Merge branch 'maint-rel-1.6' into develop

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j2blake 2013-11-05 17:53:10 -05:00
commit bea4c9dd96
7 changed files with 81 additions and 82 deletions
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39
doc/install.html
View file

@ -339,6 +339,25 @@ issuing SPARQL queries that read data, and its URI for issuing SPARQL UPDATE com
es_MX
</td>
</tr>
<tr>
<td colspan="2">
These values are used when deploying VIVO as an OpenSocial container
and integrating with OpenSocial gadgets
(see <a href="#opensocial">Step 13</a>, below). If you are creating
a VIVO installation that does not use OpenSocial gadgets, these values are omitted.
</td>
</tr>
<tr class="odd_row">
<td>
OpenSocial.shindigURL<br>
OpenSocial.tokenService<br>
OpenSocial.tokenKeyFile<br>
OpenSocial.sandbox
</td>
<td>
&nbsp;
</td>
</tr>
</tbody>
</table>
@ -938,26 +957,6 @@ issuing SPARQL queries that read data, and its URI for issuing SPARQL UPDATE com
</td>
</tr>
<tr>
<td colspan="2">
These values are used when deploying VIVO as an OpenSocial container
and integrating with OpenSocial gadgets
(see <a href="#opensocial">Step 13</a>, below). If you are creating
a VIVO installation that does not use OpenSocial gadgets, these values are omitted.
</td>
</tr>
<tr class="odd_row">
<td>
OpenSocial.shindigURL<br>
OpenSocial.tokenService<br>
OpenSocial.tokenKeyFile<br>
OpenSocial.sandbox
</td>
<td>
&nbsp;
</td>
</tr>
</tbody>
</table>

16
doc/setting_up_orng.html
View file

@ -188,7 +188,7 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle
<h3 id="vivo_settings">I.iv Configure VIVO</h3>
<p>
In the VIVO home directory, the file called <em>runtime.properties</em>
In the VIVO distribution directory, the file called <em>build.properties</em>
contains configuration options for the VIVO application.
You must set some additional parameters so VIVO will be able to communicate with Shindig-ORNG.
</p>
@ -333,7 +333,7 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle
<ul>
<li>
VIVO was not re-deployed with <tt>ant deploy</tt> after the OpenSocial
values were set in <em>runtime.properties</em>
values were set in <em>build.properties</em>
</li>
</ul>
</td>
@ -405,7 +405,7 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle
<td>
<ul>
<li>
<em>OpenSocial.tokenKeyFile</em> is not set in <em>runtime.properties</em>,
<em>OpenSocial.tokenKeyFile</em> is not set in <em>build.properties</em>,
or the file does not exist at the specified location.
</li>
</ul>
@ -449,7 +449,7 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle
<td>
<ul>
<li>
In <em>runtime.properties</em>, <em>OpenSocial.tokenService</em> is not set correctly.
In <em>build.properties</em>, <em>OpenSocial.tokenService</em> is not set correctly.
</li>
</ul>
</td>
@ -692,11 +692,11 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle
<h3 id="redeploying">III.i. Re-running the deployment script</h2>
<p>
The OpenSocial framework relies on several of the settings in the <em>runtime.properties</em> file,
The OpenSocial framework relies on several of the settings in the <em>build.properties</em> and <em>runtime.properties</em> files,
in addition to the ones that are explicitly linked to it.
</p>
<p>
Each time you change the settings in <em>runtime.properties</em>, you should re-deploy
Each time you change the settings in <em>build.properties</em> or <em>runtime.properties</em>, you should re-deploy
the framework with
<pre> ant orng</pre>
</p>
@ -750,12 +750,12 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle
Disabling the gadgets, as above, will remove essentially all of the OpenSocial processing
within VIVO. To remove the remainder of it, you can disable the connection between
VIVO and the OpenSocial service. Do this by removing or commenting
the <em>OpenSocial</em> properties in <em>runtime.properties</em>
the <em>OpenSocial</em> properties in <em>build.properties</em>
(see <a href="#vivo_settings">section I.iv. Configure VIVO</a>).
</p>
<p>
Restart Tomcat to make this change take effect.
To make this change take effect, re-deploy VIVO and restart Tomcat.
</p>
<h4>Remove the OpenSocial webapp from Tomcat</h4>

3
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql
View file

@ -8,7 +8,8 @@ CONSTRUCT {
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s vivo:middleName ?middleName
?s vivo:middleName ?middleName .
?s a foaf:Person
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard
}

1
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard2d.sparql
View file

@ -8,6 +8,7 @@ CONSTRUCT {
?name vivo:middleName ?middleName .
} WHERE {
?s vivo:middleName ?middleName .
?s a foaf:Person .
?s arg:ARG_2000028 ?vcard .
?vcard v:hasName ?name
}

80
rdf/tbox/filegraph/object-properties.owl
View file

@ -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>
@ -561,25 +558,6 @@
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">related technique</obo:IAO_0000111>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/ERO_0000007"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<rdfs:domain>
<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_0000009"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000071"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000161"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000162"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000285"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/ERO_0000630"/>
<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>
</rdfs:domain>
</owl:ObjectProperty>
@ -593,8 +571,6 @@
<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 +890,7 @@ 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 +1640,8 @@ 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 +1649,21 @@ 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 +1671,16 @@ 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 +1697,6 @@ 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 +1709,6 @@ 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"/>

13
rdf/tbox/filegraph/research-resource.owl
View file

@ -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>

11
rdf/tbox/firsttime/initialTBoxAnnotations.n3
View file

@ -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 .
@ -5980,7 +5983,11 @@ vcard:Name
rdfs:label "Name"@en-US .
obo:BFO_0000055
rdfs:label "realizes"@en-US .
rdfs:label "realizes"@en-US ;
vitro:hiddenFromDisplayBelowRoleLevelAnnot
<http://vitro.mannlib.cornell.edu/ns/vitro/role#nobody> ;
vitro:prohibitedFromUpdateBelowRoleLevelAnnot
<http://vitro.mannlib.cornell.edu/ns/vitro/role#nobody> .
geo:nationalityAR
rdfs:label "nationalityAR"@en-US ;
@ -6173,6 +6180,8 @@ 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