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[bioontology-support] How to handle imported ontologies on bioportal

Michael Dorf mdorf at stanford.edu
Mon Nov 23 17:23:19 PST 2015


Hi Sridevi,

We have an active tracker open on this issue.  An engineer is working on the problem, but as Ray had mentioned, this turned out to be a tricky issue to address. We'll keep you posted when we've deployed the fix.

Meanwhile, I am wondering whether setting the "SYNONYM PROPERTY" for the latest submission to:

http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

would help this particular issue. We'll need to re-parse/re-index the ontology for this change to take effect.

Thanks,

Michael



On Nov 22, 2015, at 07:18, sridevi polavaram <spolavar at gmail.com<mailto:spolavar at gmail.com>> wrote:

Hi Mike,
 The problem i was referring to is when i search for synonyms i am getting inconsistent results. The NMOSP ontology right now seems to be working fine, as it is able to fetch the term when i search for "zebra fish". The REST service is also working fine in this regard.

However, when i search in NMOBR for a synonym e.g., "isocortex", it fails, i won't get the term 'neocortex'. The difference between the two ontologies is the format, NMOBR is in owl and uses oboInOWL:has_exact_synonym for the synonyms.

Do you see the problem now? If this bug gets fixed, I will be able to use both formats seamlessly.

Thank you
Sridevi

On Fri, Nov 20, 2015 at 8:29 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Sridevi,

Just FYI, Ray Fergerson is no longer at Stanford. I tried the search you mentioned (Cerebellum in NMOBR ontology) and I get a result within seconds. I've also tried the REST service directly (which is used by BioPortal UI), and it too returned results (single result) without a hitch:

http://data.bioontology.org/search?q=Cerebellum&ontologies=NMOBR

You'll need to append "&apikey=<your API key> to this query for it to work.

The difficult part here is that if I am unable to reproduce the problem on my end, it would be hard for me to troubleshoot it. Do you see issues with other search queries as well?

Thanks!

Michael Dorf


On Nov 20, 2015, at 11:05, sridevi polavaram <spolavar at gmail.com<mailto:spolavar at gmail.com>> wrote:

Cerebellum



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