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[bioontology-support] issues with ontology visualization

sridevi polavaram spolavar at gmail.com
Wed Feb 17 10:32:35 PST 2016


@1:31pm EST it is working again!

On Wed, Feb 17, 2016 at 1:30 PM, sridevi polavaram <spolavar at gmail.com>
wrote:

> 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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