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[bioontology-support] Feedback

Woodbridge, Mark R m.woodbridge at imperial.ac.uk
Thu Apr 15 06:56:49 PDT 2010


Hi Natasha,

Many thanks. It works perfectly now! There are a couple of extra features that would make the Annotator ideal for our usage scenario - I don't know if whether these are currently possible, or whether you have considered adding them:

- Optionally including term definitions in the response alongside the fullId and synonyms. I noticed that you do have a <definitions> element but it seems to be empty.

- Exact matches. In some cases I would like to submit a term (e.g. 'river bank') and only get a response if that terms exists in the specified ontology. (Though I can easily work round this by looking at the 'from' and 'to' indexes in the response and checking whether they span the whole input).

Many thanks for your help,

Mark

-- 
Mark Woodbridge
CISBIC Data Management
Imperial College London

________________________________________
From: Natasha Noy [noy at stanford.edu]
Sent: 15 April 2010 00:02
To: admin at bioontology.org
Cc: bioontology-support at mailman.stanford.edu; Woodbridge, Mark R
Subject: Re: [bioontology-support] Feedback

Thank you, Mark, for bringing this up to our attention. There were
some problems on our server that we have now fixed.

Please try it out and do not hesitate to let us know if you see more
problems!

Thank you for your feedback!

Natasha


On Apr 14, 2010, at 4:08 AM, admin at bioontology.org wrote:

> Name : Mark Woodbridge
>
> Email : m.woodbridge at imperial.ac.uk
>
> Comment:
> Hi,
>
> I'm trying to use the Annotator to identify ontology terms in free
> text. I'm not sure whether it is suitable for this use case, but I
> started with something simple:
>
> curl -d "textToAnnotate=river
> +
> bank
> &ontologiesToKeepInResult=42277&longestOnly=true&withSynonyms=false"
> -s "http://rest.bioontology.org/obs/annotator"
>
> i.e. I would like to search the Environment Ontology for "river
> bank" (ENVO:00000143). This seems to return "bar" (a synonym which I
> tried to exclude using the withSynonyms parameter) and "bank" but
> not "river bank".
>
> Am I doing something wrong? Any help would be greatly appreciated.
>
> Mark.
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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