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[bioontology-support] issues with ontology visualization

sridevi polavaram spolavar at gmail.com
Wed Feb 17 10:30:04 PST 2016


It is 1:23pm EST and once again i get the error page saying 'We're sorry
but something has gone wrong. We have been notified of this error.'

when i try to browse NMOBR
http://bioportal.bioontology.org/ontologies/NMOBR/?p=classes

whatever that is causing this issue is practically making this link
unusable. I hope you can reproduce it at your end!

Thank you.
Sridevi



On Tue, Feb 16, 2016 at 9:32 PM, sridevi polavaram <spolavar at gmail.com>
wrote:

> 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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