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[bioontology-support] Bioportal annotator REST API not returning some types of SNOMED concepts?

Ray Fergerson ray.fergerson at stanford.edu
Fri Aug 16 16:41:28 PDT 2013


The difference is that your post prevents matches on synonyms. Just remove
the "withSynonyms=false" and it should work.

 

FYI, at the bottom of the Annotator results page, in gray, is a text
version of the parameters that we are passing in for that post.

 

Ray

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Pieter Sheth-Voss
Sent: Thursday, August 08, 2013 7:36 AM
To: support at bioontology.org
Subject: [bioontology-support] Bioportal annotator REST API not returning
some types of SNOMED concepts?

 

The Bioportal Annotator seems to not match some types of concepts in
SNOMED, specifically anatomy terms.   Might I be doing something wrong?

 

For instance, in the example web service
[http://bioportal.bioontology.org/annotator] if you type the following
text, searching SNOMEDCT, it matches all of the items correctly.

 

         "stomach knee larynx thyroid brain leg tibia femur pancreas
asthma"

 

But if I send the same post via the REST API, it seems to return only
terms for "asthma".  The trend I seem to see is it matches disorders,
signs, symptoms, etc. but not anatomical terms.

 

{ method: 'POST',

  uri: 'http://rest.bioontology.org/obs/annotator',

  headers: { 'Content-Type': 'text/plain' },

  body:
'format=xml&apikey=MY_API_KEY&ontologiesToKeepInResult=46896,49463&withSyn
onyms=false&textToAnnotate=stomach%20knee%20larynx%20thyroid%20brain%20leg
%20tibia%20femur%20pancreas%20asthma' 

}

 

Thanks!

Pieter

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