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[bioontology-support] Classes Subtree Search endpoint

Ray Fergerson ray.fergerson at stanford.edu
Tue Apr 1 16:22:52 PDT 2014


You should be able to get the information you want on the annotation call. 
Just list the properties you want on the 'include' parameter. (e.g. 
include=prefLabel,synonyms)

Ray

-----Original Message-----
From: bioontology-support 
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of 
foerdsch
Sent: Tuesday, April 1, 2014 3:01 PM
To: bioontology-support at lists.stanford.edu
Subject: [bioontology-support] Classes Subtree Search endpoint

Dear NCBO Support Team,

I am facing some difficulties using the new API. I am writing a script which 
should lookup if words of a given sentence occur in a number of ontologies 
and if they do, extract the id, prefLabel, synonyms the word found and the 
position in the sentence.

So what I did is following:

First I use the Annotator endpoint to identify word occurences of a given 
ontology, e.g. SNOMEDCT:
http://data.bioontology.org/annotator?apikey=XXXXXXXX&format=xml&ontologies=SNOMEDCT&text=An%20example%20text

Then I extracted the found <text> (here “text”), the class <id> (here 
“http://purl.bioontology.org/ontology/SNOMEDCT/900000000000466004”), and the 
ontology acronym (here “SNOMEDCT”).
With those parameters I invoke the Classes Subtree Search endpoint to get 
<prefLabel> and the <synonyms>:

http://data.bioontology.org/search?q=TEXT&ontology=SNOMEDCT&subtree_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F900000000000466004&apikey=XXXXXXXX&exact_match=true&format=xml

This works like a charm with the SNOMEDCT ontology. However with other ones, 
e.g. FMA it fails.
http://data.bioontology.org/search?q=ORGAN&ontology=FMA&subtree_id=http%3A%2F%2Fsig.uw.edu%2Ffma%23Organ&apikey=XXXXXXXX
Gives me a 502 Bad Gateway.

Could you please comment on this? Am I missing sth?
TIA,
Ferdinand




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