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[bioontology-support] issues with ontology visualization

Michael Dorf mdorf at stanford.edu
Tue Feb 16 15:10:52 PST 2016


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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