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[bioontology-support] issues with ontology visualization

sridevi polavaram spolavar at gmail.com
Tue Feb 16 18:32:18 PST 2016


Hi Michael,
 It was working spottily yesterday many times giving an error message, i
saw it working when i first uploaded it, but then it went down when i tried
to access it many times later. Now it seem to be working fine!

Thanks
Sridevi

On Tue, Feb 16, 2016 at 6:10 PM, Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Sridevi,
>
> I don't see any issues with NMOBR other than some of the terms repeat in
> the tree. Is this the issue you are referring to?
>
> Thanks!
>
> Misha
>
> On Feb 16, 2016, at 11:36, sridevi polavaram <spolavar at gmail.com> wrote:
>
> Hi John,
>  I have uploaded two new ontologies yesterday, the insect hierarchy and
> the vertebrate hierarchy. but only the insect hierarchy works (
> http://bioportal.bioontology.org/ontologies/INSECTH?p=classes), i am
> having issues with the second one (
> http://bioportal.bioontology.org/ontologies/NMOBR?p=classes). May i know
> what is the problem?
>
> Thank you,
> Sridevi
>
>
> On Wed, Feb 10, 2016 at 6:28 PM, 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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