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[bioontology-support] Feedback

Woodbridge, Mark R m.woodbridge at imperial.ac.uk
Thu Apr 15 08:54:25 PDT 2010


Hi Trish,

longestOnly isn't quite what I want - I would like a response only if there is an exact match e.g. 'river bank' should return a match but 'river bark' should return no matches. Using longestOnly in this case would return 'river' as a match. However, as I explained, I can get the functionality I need by looking at the indexes given in the response. I just thought it might be useful to provide such a parameter for users who want to check if a provided term is present in an ontology.

Thanks for looking into the definition field. It would be very useful to allow our users to interactively disambiguate multiple matches by looking at the definitions.

Mark.

________________________________
From: Trish Whetzel [whetzel at stanford.edu]
Sent: 15 April 2010 16:52
To: Woodbridge, Mark R
Cc: Natasha Noy; bioontology-support at mailman.stanford.edu
Subject: Re: [bioontology-support] Feedback

Hi Mark,

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.

Trish


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

--
Mark Woodbridge
CISBIC Data Management
Imperial College London

________________________________________
From: Natasha Noy [noy at stanford.edu<mailto:noy at stanford.edu>]
Sent: 15 April 2010 00:02
To: admin at bioontology.org<mailto:admin at bioontology.org>
Cc: bioontology-support at mailman.stanford.edu<mailto: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<mailto:admin at bioontology.org> wrote:

Name : Mark Woodbridge

Email : m.woodbridge at imperial.ac.uk<mailto: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.
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu<mailto:whetzel at stanford.edu>
http://www.bioontology.org



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