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[bioontology-support] issues with ontology visualization

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Feb 17 12:24:25 PST 2016


Hello Sridevi,

We had some issues with instability this morning, but the site should be back to normal now.  Apologies for the inconvenience.

Jennifer


On Feb 17, 2016, at 10:30 AM, sridevi polavaram <spolavar at gmail.com<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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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