[ensembl-dev] level of curation of NHGRI-EBI GWAS-catalog risk alleles?

andrew126 at mac.com andrew126 at mac.com
Fri Dec 2 08:31:23 GMT 2016


I’m writing to inquire about the level of curation for the NHGRI-EBI GWAS-catalog risk alleles.

I’m using Ensembl API 86, but I don’t think this question is particularly specific to the API or version.

When recovering phenotype features which have a $pf->source_name of “NHGRI-EBI GWAS catalog”, occasionally I find no annotated risk allele and other times I find annotated risk alleles ($pf->risk_allele) which appear to be reverse complemented relative to the forward strand of the genome.  I can provide examples of each, if that would be useful.

Should I assume that the risk_allele field is freeform text and is not curated for allele validity etc. against the rest of the genome, db, etc.?

Thanks very much for any guidance.



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