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[bioontology-support] xrefs with REST

Tomasz Adamusiak tomasz at ebi.ac.uk
Fri Jul 31 07:02:44 PDT 2009


Hi Natasha,

The mappings service is really neat! Could the xrefs be made accessible 
through REST on the side anyway? I could especially use the GeneRIFs, 
UMLS and SNOMED xrefs from DO.

Although the original terms in DO have no xrefs:
http://rest.bioontology.org/bioportal/virtual/1009/DOID:9778/

their cross-products in cell line ontology have some already:
http://rest.bioontology.org/bioportal/virtual/1245/DOID:9778/

Cheers
Tomasz


Natasha Noy wrote, On 2009-07-30 06:53:
> Tomazs,
>
> We have some of the xrefs there as mappings, but definitely not all.
> It's simple an issue of resources on our side at the moment. Is someone
> (hint...) were to give us a table with all these mappings, we'll happily
> upload it to BioPortal. We'll get to it on our side at some point,
> undoubtedly, but maybe not soon enough.
>
> On the service, we will be announcing a mapping service tomorrow. It is
> a temporary service that will get replaced with a more detailed set of
> services eventually, but here it is:
>
> http://bioportal.bioontology.org/mappings/service/(ontology_id)/(concept_id)
>
>
> concept id is optional. It returns all mappings to and from one ontology
> (or one concept).
>
> This is probably not at the level of detail that you might need, but
> that's what we just made available. Do you have specific requirements
> for a mapping service? We might try to get you something sooner.
>
> Natasha
>
>
> On Jul 26, 2009, at 6:24 AM, Tomasz Adamusiak wrote:
>
>> Hi,
>>
>> Could the obo xrefs be exposed through REST services? They're not
>> visible through web interface as far as I can tell either. I guess
>> that's what the mappings are for. Is there a way to access them with
>> REST?
>>
>> Example for http://bioportal.bioontology.org/visualize/40350/DOID:14617
>> id: DOID:14617
>> name: prostate Cancer metastatic
>> synonym: "metastatic prostate Carcinoma" EXACT [NCI2004_11_17:C8946]
>> xref: GeneRIF:11912162
>> xref: GeneRIF:14602722
>>
>> Cheers
>> Tomasz
>>
>> --
>> Tomasz Adamusiak, MD, PhD
>> European Bioinformatics Institute
>> +44 (0) 1223 492 562
>> tomasz.adamusiak at ebi.ac.uk
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



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