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[bioontology-support] Feedback

Woodbridge, Mark R m.woodbridge at imperial.ac.uk
Thu Apr 15 10:38:42 PDT 2010


Thanks Natasha. The search service will also be useful to us. It doesn't look like those responses contain term definitions either, but I guess I can make supplemental requests to the concept service (one per term, though this might be a bit slow) to get the definitions required for disambiguation if the term appears in more than one ontology.

________________________________________
From: Natasha Noy [noy at stanford.edu]
Sent: 15 April 2010 18:11
To: Woodbridge, Mark R
Cc: Trish Whetzel; bioontology-support at mailman.stanford.edu
Subject: Re: [bioontology-support] Feedback

Mark,

Then it seems that what you want is the Search service, not annotator.
You can set it to do exact match. But it is a different service, so
the results are in different form. I don't know if this is helpful to
you.

Check out http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services

Service call:
http://rest.bioontology.org/bioportal/search/river bank/?
ontologyids=1069&isexactmatch=1

Note that you need to use the ontology id (1069), not the version id
for the search service. But then of course you don't need to change
the service arguments when a new version appears -- it will always use
the latest version.

Natasha


On Apr 15, 2010, at 8:54 AM, Woodbridge, Mark R wrote:

> 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]
>> 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
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> whetzel at stanford.edu
> http://www.bioontology.org
>
>
>
>


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