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[bioontology-support] Return UMLS codes from Web Annotator

Trish Whetzel whetzel at stanford.edu
Wed Sep 8 08:12:50 PDT 2010


Hi Ying,

The Annotator output is fairly minimal in order to keep the returned  
payload reduced. To find additional details about a term, such as the  
CUI, you can use the Term Services ( http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Term_services 
  ).

For example, the value of the <localConceptId> from the Annotator  
output is the value needed for the {ontology version id}/{concept id}  
for the "Get term" web service, which yields the URL below:
http://rest.bioontology.org/bioportal/concepts/42789/276239002?email=example@example.org
 From here, the CUI can be extracted.

Best regards,
Trish


On Sep 2, 2010, at 8:48 AM, Ying Li wrote:

> Trish
>
> Hello, may I get umls code directly from xml format of mgrep output?  
> I saw there is a <fullId> tag which returns a website, then we could  
> parse this website to get umls cui. However, it makes things  
> complicated. So do you have any suggestions to return umls cuis  
> simply? By the way, I use Python language. Thank you very much.
>
> Best Regards,
> Ying




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