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[bioontology-support] searching for synonyms (was: How to handle imported ontologies on bioportal)

Michael Dorf mdorf at stanford.edu
Thu Apr 7 16:35:36 PDT 2016


Hi Sridevi,

I believe this issue is now resolved. Please see the examples below:

http://bioportal.bioontology.org/search?q=common%20chimpanzee&ontologies=NMOSP&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories=

http://bioportal.bioontology.org/search?q=chimpanzee&ontologies=NMOSP&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories=

http://data.bioontology.org/search?q=common%20chimpanzee&ontologies=NMOSP&exact_match=true

Please let me know if you run into any further issues.

Thanks,

Michael



On Feb 10, 2016, at 15:28, 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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