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[bioontology-support] Annotator Question

Trish Whetzel whetzel at stanford.edu
Wed Apr 20 18:16:30 PDT 2011


Hi Guy,

All of the web service calls below return results when I enter them into a browser to make the call. 

Trish 


On Apr 20, 2011, at 1:33 PM, Guy Haskin Fernald wrote:

> 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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