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[bioontology-support] Feedback

Natasha Noy noy at stanford.edu
Thu Apr 15 10:50:47 PDT 2010


Yes, no definitions there either. However, you probably won't get that  
many search hits on exact match, so calling concept service to  
disambiguate for a handful of terms shouldn't slow you down too much.

We are reluctant to return more information than we absolutely need in  
the search service since for some non-exact matches, those services  
can return lots of results.

Natasha


On Apr 15, 2010, at 10:38 AM, Woodbridge, Mark R wrote:

> 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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