[ensembl-dev] snps linked to omim

Andrea Edwards edwardsa at cs.man.ac.uk
Thu Feb 17 18:09:23 GMT 2011


I am trying to find whether the human SNPs (60,000)  i have are listed 
in OMIM. I believe most SNPs in ensembl have a primary source of dbSNP. 
None of the human variations have a source id of 15 (OMIM) There is a 
table variation_synonym to hold data about multiple sources for a snp 
but I can't find any entries in this table which have a source_id = 15 
either. What am i doing wrong? There exists a variation_set called OMIM 
which has 11509 SNPs and I investigated some of these variations at 
random and I don't know how you have linked them to the OMIM variation set

I have seen there are methods get_all_synonyms and get 
_all_synonym_sources on the perl api for a variation. I presume i could 
call get_all_synonyms('OMIM') but I don't see how that can work when no 
variation synonyms have a source of 15/OMIM

Out of general curiosity, will the following 2 approaches give the same 
results: getting the OMIM variation set and seeing whether each of my 
60,000 snps is in that or getting the OMIM variation_synonyms for the 
60,000 snps and seeing which return an actual result? I'm presuming the 
second option will be far faster.

thanks a lot

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