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[bioontology-support] Annotator Question

Guy Haskin Fernald guyhf at stanford.edu
Wed Apr 20 13:33:07 PDT 2011


Thanks,

Trish -- what would the correct search call be?  These do not work (although the UMLS code is in the http://purl.... page).

http://rest.bioontology.org/bioportal/search/10012594
http://rest.bioontology.org/bioportal/search/10012594/?ontologies=44777
http://rest.bioontology.org/bioportal/search/10012594/?ontologies=44777&isexactmatch=1

I looked over the documentation, but I am missing something.

Thanks,

Guy


On Apr 19, 2011, at 9:32 PM, Nigam Shah wrote:

> Hi Guy,
> 
> The Annotator Web service does not provide the UMLS CUI (we know, its kind of odd, and hopefully fixed soon). Meanwhile, you can use the term ID, make a call to the "search" web service, and look up the CUI, using the term id that the Annotator gives you.
> 
> Trish Whetzel, cc'ed can help further as well.
> 
> Regards,
> Nigam.
> 
> On Tue, Apr 19, 2011 at 9:16 PM, Guy Haskin Fernald <guyhf at stanford.edu> wrote:
> Nigam,
> 
> Thanks for your quick help in the hall today at MSOB.  I have another question.
> 
> I am trying to go from the term "Diabetes" to the UMLS identifier "C0011849".  If I search all ontologies with the text "Diabetes" I get several results, e.g. from MedRA:
> 
> http://bioportal.bioontology.org/visualize/42280/?conceptid=10012594
> 
> That page lists "C0011849" but the XML result from the annotator service does not.  How can I get the the annotator web service to return the UMLS concept ID?
> 
> Here is what my POST looks like:
> 
> Path: /obs/annotator
> Form data:
> 	ontologiesToKeepInResult=42280
> 	format=xml
> 	semanticTypes=T047
> 	textToAnnotate=Diabetes
> 	longestOnly=false
> 	ontologiesToExpand=42280
> 
> And here is the resulting XML -- the UMLS identifier is not there:
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <success>
>   <accessedResource>/obs/annotator</accessedResource>
>   <accessDate>2011-04-19 21:13:06.254 PDT</accessDate>
>   <data>
>     <annotatorResultBean>
>       <resultID>OBA_RESULT_9bd6</resultID>
>       <statistics>
>         <statisticsBean>
>           <contextName>MGREP</contextName>
>           <nbAnnotation>1</nbAnnotation>
>         </statisticsBean>
>         <statisticsBean>
>           <contextName>MAPPING</contextName>
>           <nbAnnotation>0</nbAnnotation>
>         </statisticsBean>
>         <statisticsBean>
>           <contextName>CLOSURE</contextName>
>           <nbAnnotation>0</nbAnnotation>
>         </statisticsBean>
>       </statistics>
>       <parameters>
>         <longestOnly>false</longestOnly>
>         <wholeWordOnly>true</wholeWordOnly>
>         <filterNumber>true</filterNumber>
>         <withDefaultStopWords>false</withDefaultStopWords>
>         <isStopWordsCaseSenstive>false</isStopWordsCaseSenstive>
>         <withSynonyms>true</withSynonyms>
>         <minTermSize>3</minTermSize>
>         <withContext>true</withContext>
>         <semanticTypes>
>           <string>T047</string>
>         </semanticTypes>
>         <stopWords/>
>         <ontologiesToExpand>
>           <string>42280</string>
>         </ontologiesToExpand>
>         <ontologiesToKeepInResult>
>           <string>42280</string>
>         </ontologiesToKeepInResult>
>         <isVirtualOntologyId>false</isVirtualOntologyId>
>         <levelMax>0</levelMax>
>         <mappingTypes/>
>         <textToAnnotate>Diabetes</textToAnnotate>
>         <outputFormat>xml</outputFormat>
>       </parameters>
>       <annotations>
>         <annotationBean>
>           <score>10</score>
>           <concept>
>             <id>15955631</id>
>             <localConceptId>42280/10012594</localConceptId>
>             <localOntologyId>42280</localOntologyId>
>             <isTopLevel>1</isTopLevel>
>             <fullId>http://purl.bioontology.org/ontology/MDR/10012594</fullId>
>             <preferredName>Diabetes</preferredName>
>             <synonyms/>
>             <definitions/>
>             <semanticTypes>
>               <semanticTypeBean>
>                 <id>19428230</id>
>                 <semanticType>T047</semanticType>
>                 <description>Disease or Syndrome</description>
>               </semanticTypeBean>
>             </semanticTypes>
>           </concept>
>           <context class="mgrepContextBean">
>             <contextName>MGREP</contextName>
>             <isDirect>true</isDirect>
>             <from>1</from>
>             <to>8</to>
>             <term>
>               <name>Diabetes</name>
>               <localConceptId>42280/10012594</localConceptId>
>               <isPreferred>1</isPreferred>
>             </term>
>           </context>
>         </annotationBean>
>       </annotations>
>       <ontologies>
>         <ontologyUsedBean>
>           <localOntologyId>42280</localOntologyId>
>           <name>MedDRA</name>
>           <version>12.0</version>
>           <virtualOntologyId>1422</virtualOntologyId>
>           <nbAnnotation>1</nbAnnotation>
>           <score>10</score>
>         </ontologyUsedBean>
>       </ontologies>
>     </annotatorResultBean>
>   </data>
> </success>
> 
> Thanks,
> 
> Guy
> 

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