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[bioontology-support] searching for synonyms (was: How to handle imported ontologies on bioportal)

sridevi polavaram spolavar at gmail.com
Thu Apr 7 17:21:23 PDT 2016


Awesome! it is indeed working now! I will be testing both NMOSP and NMOBR
thoroughly in next two weeks. Hopefully i don't have to bug you anymore :)

Thank you,
Sridevi

On Thu, Apr 7, 2016 at 7:35 PM, Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Sridevi,
>
> I believe this issue is now resolved. Please see the examples below:
>
>
> http://bioportal.bioontology.org/search?q=common%20chimpanzee&ontologies=NMOSP&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories=
>
>
> http://bioportal.bioontology.org/search?q=chimpanzee&ontologies=NMOSP&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories=
>
>
> http://data.bioontology.org/search?q=common%20chimpanzee&ontologies=NMOSP&exact_match=true
>
> Please let me know if you run into any further issues.
>
> Thanks,
>
> Michael
>
>
>
> On Feb 10, 2016, at 15:28, sridevi polavaram <spolavar at gmail.com> wrote:
>
> Any updates on issue NCBO-1605 - can't search NMOSP by synonym?
>
> Thank you
> Sridevi
>
>
> On Tue, Jan 19, 2016 at 11:47 PM, sridevi polavaram <spolavar at gmail.com>
> wrote:
>
>> Thank you, Mike. see inline below.
>>
>>
>>> 2. The issue with NMOSP still stands. It is tracked internally as
>>> NCBO-1605 - can't search NMOSP by synonym. Even after having deployed the
>>> patch and re-parsing/re-indexing the ontology, I am unable to get any hits
>>> on "chimpanzee" or "common chimpanzee". This means that even after
>>> re-indexing, these values did not get picked up as "synonyms" of the
>>> concept "Pan troglodytes":
>>>
>>>
>>> http://data.bioontology.org/search?q=Pan%20troglodytes&ontologies=NMOSP&exact_match=true
>>>
>>>
>>> http://data.bioontology.org/search?q=common%20chimpanzee&ontologies=NMOSP&exact_match=true
>>>
>>>
>>> We will continue looking into the issue and update you as more details
>>> become available.
>>>
>>>
>> For now, I will be using only two properties for synonyms in my owl
>> ontologies:
>> http://www.geneontology.org/formats/oboInOWL#hasExactSynonym
>> http://www.geneontology.org/formats/oboInOWL#hasRelatedSynonym
>>
>> It is really strange that the synonym defined as these two properties
>> were working fine with NMOSP before! I will keep my fingers crossed.
>>
>> Thank you
>> Sridevi
>>
>
>
>
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