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[bioontology-support] xrefs with REST

Natasha Noy noy at stanford.edu
Wed Aug 5 11:13:27 PDT 2009


Hi Tomazs,

So, the problem is that these are not yet represented as mappings in  
BioPortal. So, we first need to get them in and then they will appear  
in the rest service results.

The xrefs-based mappings that we already have are the ones we got from  
Chris Mungall at some point but that was a while ago. If you could  
somehow extract the xrefs that you need from the ontologies you are  
interested in (we just don't have the cycles at the moment!) and give  
it to us in a simple spreadsheet, we will upload them as mappings and  
they will be available through rest service.

We will do it eventually ourselves of course, but if we can get some  
help from the community, it will speed up the process :)

Natasha


On Jul 31, 2009, at 7:02 AM, Tomasz Adamusiak wrote:

> 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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