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[bioontology-support] omeprazole

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon May 23 10:58:07 PDT 2016


I forgot to mention a tip in my last reply.  You can have the annotator exclude synonyms if so desired, e.g., this REST call won’t return “omeprazole”:

http://data.bioontology.org/annotator?text=result&ontologies=CHEBI&exclude_synonyms=true

Jennifer



On May 23, 2016, at 10:49 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Alexander,


On May 23, 2016, at 9:42 AM, Alexander Garcia Castro <alexgarciac at gmail.com<mailto:alexgarciac at gmail.com>> wrote:

I am annotating documents with the ncbo annotation service. I am using chebi; as incredible as it may sound omeprazole is a synonym of result.

this is so absurd that I cant get my head around it. it means that if the annotator finds result, it take result and label it as omeprazole absurd!!!!


I looked at the OBO file for the CHEBI ontology that was uploaded to BioPortal (version 139).  The term “Result” is encoded as a synonym of “omeprazole”.  Excerpt below, beginning from line 1,113,927:


[Term]
id: CHEBI:7772
name: omeprazole
def: "A racemate comprising equimolar amounts of (R)- and (S)-omeprazole." []
…
synonym: "Result" RELATED [HMDB:]
...


The BioPortal annotator does exact string comparison between text and ontology term names, synonyms, and IDs.  As far as I can tell, our software is functioning as advertised.

Is your chief complaint that these two terms should not be synonyms?  If so, I suggest you contact the ontology authors.



and this is not the only issue. things like this happen with many ontologies.


If you’re seeing issues with “many ontologies”, you’ll need to be more specific.  We can’t help you with BioPortal issues unless you provide us with a reasonable amount of detail.

Jennifer

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