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

sridevi polavaram spolavar at gmail.com
Wed Dec 23 13:39:55 PST 2015


Hi Michael,
 I just uploaded a newer version of NMOSp on the bioportal at:
https://bioportal.bioontology.org/ontologies/NMOSP?p=classes

but the synonyms are not searchable, e.g., "common chimpanzee" says no
match!

Do you have any idea when this can be fixed? I will be using this in my PhD
dissertation defense, which is scheduled in less than two months time. It
would be helpful to know the status so i can plan for it accordingly.

Wish you Happy holidays!

Thank you
Sridevi

On Mon, Nov 23, 2015 at 8:23 PM, Michael Dorf <mdorf at stanford.edu> wrote:

> 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> 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> 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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