<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Guy,</div><div><br></div><div>All of the web service calls below return results when I enter them into a browser to make the call. </div><div><br></div><div>Trish </div><div><br></div><br><div><div>On Apr 20, 2011, at 1:33 PM, Guy Haskin Fernald wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks,<div><br></div><div>Trish -- what would the correct search call be?  These do not work (although the UMLS code is in the <a href="http://purl/">http://purl</a>.... page).</div><div><br></div><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><a href="http://rest.bioontology.org/bioportal/search/10012594">http://rest.bioontology.org/bioportal/search/10012594</a></div><div><a href="http://rest.bioontology.org/bioportal/search/10012594/?ontologies=44777">http://rest.bioontology.org/bioportal/search/10012594/?ontologies=44777</a></div><div><a href="http://rest.bioontology.org/bioportal/search/10012594/?ontologies=44777&isexactmatch=1">http://rest.bioontology.org/bioportal/search/10012594/?ontologies=44777&isexactmatch=1</a></div></blockquote><div><br></div><div>I looked over the documentation, but I am missing something.</div><div><br></div><div>Thanks,</div><div><br></div><div>Guy</div><div><br></div><div><br><div><div>On Apr 19, 2011, at 9:32 PM, Nigam Shah wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Guy,<div><br></div><div>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.</div>
<div><br></div><div>Trish Whetzel, cc'ed can help further as well.</div><div><br></div><div>Regards,</div><div>Nigam.<br><br><div class="gmail_quote">On Tue, Apr 19, 2011 at 9:16 PM, Guy Haskin Fernald <span dir="ltr"><<a href="mailto:guyhf@stanford.edu">guyhf@stanford.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; position: static; z-index: auto; "><div style="word-wrap:break-word">Nigam,<div><br></div><div>Thanks for your quick help in the hall today at MSOB.  I have another question.</div>
<div><br></div><div>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:</div>
<div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><a href="http://bioportal.bioontology.org/visualize/42280/?conceptid=10012594" target="_blank">http://bioportal.bioontology.org/visualize/42280/?conceptid=10012594</a></div>
</blockquote><div><br></div><div>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?</div><div><br></div>
<div>Here is what my POST looks like:</div><div><br></div><div><div>Path: /obs/annotator</div><div>Form data:</div><div><span style="white-space:pre-wrap">   </span>ontologiesToKeepInResult=42280</div><div><span style="white-space:pre-wrap">   </span>format=xml</div>
<div><span style="white-space:pre-wrap">  </span>semanticTypes=T047</div><div><span style="white-space:pre-wrap">       </span>textToAnnotate=Diabetes</div><div><span style="white-space:pre-wrap">  </span>longestOnly=false</div><div>
<span style="white-space:pre-wrap">     </span>ontologiesToExpand=42280</div></div><div><br></div><div>And here is the resulting XML -- the UMLS identifier is not there:</div><div><br></div><div><div><?xml version="1.0" encoding="UTF-8"?></div>
<div><success></div><div>  <accessedResource>/obs/annotator</accessedResource></div><div>  <accessDate>2011-04-19 21:13:06.254 PDT</accessDate></div><div>  <data></div><div>    <annotatorResultBean></div>
<div>      <resultID>OBA_RESULT_9bd6</resultID></div><div>      <statistics></div><div>        <statisticsBean></div><div>          <contextName>MGREP</contextName></div><div>          <nbAnnotation>1</nbAnnotation></div>
<div>        </statisticsBean></div><div>        <statisticsBean></div><div>          <contextName>MAPPING</contextName></div><div>          <nbAnnotation>0</nbAnnotation></div><div>        </statisticsBean></div>
<div>        <statisticsBean></div><div>          <contextName>CLOSURE</contextName></div><div>          <nbAnnotation>0</nbAnnotation></div><div>        </statisticsBean></div><div>      </statistics></div>
<div>      <parameters></div><div>        <longestOnly>false</longestOnly></div><div>        <wholeWordOnly>true</wholeWordOnly></div><div>        <filterNumber>true</filterNumber></div>
<div>        <withDefaultStopWords>false</withDefaultStopWords></div><div>        <isStopWordsCaseSenstive>false</isStopWordsCaseSenstive></div><div>        <withSynonyms>true</withSynonyms></div>
<div>        <minTermSize>3</minTermSize></div><div>        <withContext>true</withContext></div><div>        <semanticTypes></div><div>          <string>T047</string></div><div>        </semanticTypes></div>
<div>        <stopWords/></div><div>        <ontologiesToExpand></div><div>          <string>42280</string></div><div>        </ontologiesToExpand></div><div>        <ontologiesToKeepInResult></div>
<div>          <string>42280</string></div><div>        </ontologiesToKeepInResult></div><div>        <isVirtualOntologyId>false</isVirtualOntologyId></div><div>        <levelMax>0</levelMax></div>
<div>        <mappingTypes/></div><div>        <textToAnnotate>Diabetes</textToAnnotate></div><div>        <outputFormat>xml</outputFormat></div><div>      </parameters></div><div>      <annotations></div>
<div>        <annotationBean></div><div>          <score>10</score></div><div>          <concept></div><div>            <id>15955631</id></div><div>            <localConceptId>42280/10012594</localConceptId></div>
<div>            <localOntologyId>42280</localOntologyId></div><div>            <isTopLevel>1</isTopLevel></div><div>            <fullId><a href="http://purl.bioontology.org/ontology/MDR/10012594" target="_blank">http://purl.bioontology.org/ontology/MDR/10012594</a></fullId></div>
<div>            <preferredName>Diabetes</preferredName></div><div>            <synonyms/></div><div>            <definitions/></div><div>            <semanticTypes></div><div>              <semanticTypeBean></div>
<div>                <id>19428230</id></div><div>                <semanticType>T047</semanticType></div><div>                <description>Disease or Syndrome</description></div><div>              </semanticTypeBean></div>
<div>            </semanticTypes></div><div>          </concept></div><div>          <context class="mgrepContextBean"></div><div>            <contextName>MGREP</contextName></div><div>
            <isDirect>true</isDirect></div><div>            <from>1</from></div><div>            <to>8</to></div><div>            <term></div><div>              <name>Diabetes</name></div>
<div>              <localConceptId>42280/10012594</localConceptId></div><div>              <isPreferred>1</isPreferred></div><div>            </term></div><div>          </context></div>
<div>        </annotationBean></div><div>      </annotations></div><div>      <ontologies></div><div>        <ontologyUsedBean></div><div>          <localOntologyId>42280</localOntologyId></div>
<div>          <name>MedDRA</name></div><div>          <version>12.0</version></div><div>          <virtualOntologyId>1422</virtualOntologyId></div><div>          <nbAnnotation>1</nbAnnotation></div>
<div>          <score>10</score></div><div>        </ontologyUsedBean></div><div>      </ontologies></div><div>    </annotatorResultBean></div><div>  </data></div><div></success></div>
</div><div><br></div><div>Thanks,</div><div><br></div><font color="#888888"><div>Guy</div></font></div></blockquote></div><br></div>
</blockquote></div><br></div></div></blockquote></div><br></body></html>