[ensembl-dev] mapping phenotypes to pheno ids

[Laurent Gil]

Dear Nicole,

Sorry for the late reply.
Unfortunately we don't have this information available for most of the 
data: for some PhenotypeFeature objects, the "external_id" attribute 
represents e.g. the OMIM ID, but this is not always true. Furthermore, 
you can retrieve some OMIM Gene ID through the variation Study object 
(by using the method "study->external_reference" in the PhenotypeFeature 
object).

Best regards,

Laurent

On 19/08/2013 17:30, Nicole Washington wrote:
> Hi,
>
> I'm starting to use the variation API to fetch variations associated with phenotypes.
>
> I don't see an obvious way of mapping the variations to, for example, the OMIM id (or other external ids) of the phenotype itself, other than doing string matching of the phenotype description.  Do you have any xrefs to the external phenotype ids available via the API?
>
> Thanks for your time,
>
> Nicole
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