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[bioontology-support] Annotator returns no hits for sequence ontology terms - can you help?

Trish Whetzel whetzel at stanford.edu
Thu May 27 10:55:20 PDT 2010


Hi Helen,

I'll be talking with Clement a bit later today and will discuss this  
issue.

Trish


On May 27, 2010, at 10:19 AM, Nigam Shah wrote:

> Hi Helen
>
> I am traveling on the interview trail and can't troubleshoot right  
> now. I am ccing Clement and Trish who might be able to help. I can  
> look into this next week.
>
> Nigam.
>
> On May 27, 2010, at 9:27 AM, Helen Johnson  
> <helen.linguist at gmail.com> wrote:
>
>> Hi Nigam,
>>
>> I am trying to use the NCBO Annotator to recognize
>> Sequence Ontology (localOntologyID=36782, virtualOntologyID=1045)
>> terms in text.
>>
>> When i ran my experiment on a full text document in our local
>> application, i found that the Annotator had returned no results.
>>
>> I next tried using the web interface
>> (there are now two urls to the Annotator? i tried both:
>> http://rest.bioontology.org/test_oba.html
>> http://bioportal.bioontology.org/annotator#
>> ), inputting a simple sentence with the terms "allele" (SO:
>> SO:0001023) and "diplotype" (SO:0001028).
>> Params: all default, except in "ontologiesToKeepInResults" i input
>> 36782, and chose "false" for isVirtualOntologyID.
>> i also tried
>> Params, all default, except in "ontologiesToKeepInResults" i input
>> 1045, and chose "true" for isVirtualOntologyID.
>>
>> In both these attempts the Annotator returned no hits.
>>
>> However, doing an online test with a sentence that contains the  
>> word "cell",
>> using 42165 for the ontologiesToKeepInResults in one run, and using
>> the virtualOntologyID 1006 in another run,
>> both runs return hits to Cell Type Ontology terms.
>> (both websites were successful, too).
>>
>> Do you know:
>> am i doing something wrong?
>> or is there something that needs be fixed on the Annotator end?
>>
>> not relevant to my current issues, but what's the difference between
>> the two websites?
>>
>> Thanks for helping me out with this.
>> -helen
>>
>>
>> --
>> Helen L. Johnson
>> Sr. Professional Research Assistant
>> Center for Computational Pharmacology,
>> University of Colorado Denver, Health Sciences Center
>> email:   helen.linguist at gmail.com




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