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Alexander Garcia Castro
alexgarciac at gmail.com
Mon May 23 10:57:13 PDT 2016
Hi Jennifer, I am not complaining about the ncbo annotator, it works. I am
complaining about the ontologies. the ncbo works as advertised, the
ontologies are the ones making it hard. thanks for the email, and sorry if
I gave the impression that I was complaining about the annotator, it does
work as advertised.
On Mon, May 23, 2016 at 7:49 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:
> Hello Alexander,
> On May 23, 2016, at 9:42 AM, Alexander Garcia Castro <
> 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
> 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:
> 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
> 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.
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