[ensembl-dev] snps linked to omim
Andrea Edwards
edwardsa at cs.man.ac.uk
Thu Feb 17 18:09:23 GMT 2011
hello
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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