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

sridevi polavaram spolavar at gmail.com
Sun Nov 22 07:18:17 PST 2015


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> 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> wrote:
>
> Cerebellum
>
>
>
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