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whetzel at stanford.edu
Thu Apr 15 08:52:13 PDT 2010
We'll check into why the definition field is empty. As for returning
only the term 'river bank', that is possible by setting the parameter
'longestOnly' to true. More details on all parameters for the
Annotator are described here: http://www.bioontology.org/wiki/index.php/Annotator_User_Guide
On Apr 15, 2010, at 6:56 AM, Woodbridge, Mark R wrote:
> 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 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
> Thank you for your feedback!
> On Apr 14, 2010, at 4:08 AM, admin at bioontology.org wrote:
>> Name : Mark Woodbridge
>> Email : m.woodbridge at imperial.ac.uk
>> 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
>> -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.
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
Trish Whetzel, PhD
The National Center for Biomedical Ontology
whetzel at stanford.edu
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