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[bioontology-support] Annotator Question

Nigam Shah nigam at stanford.edu
Tue Apr 19 21:32:18 PDT 2011


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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