[ensembl-dev] snps linked to omim

[Pontus Larsson]

Hi Andrea,

The data we import from OMIM are annotations of phenotypes associated with
dbSNP variations and as such, they are stored in the variation_annotation
table (it is neither independent variations nor synonyms for existing
variations so we don't store it in the variation or variation_synonym
table).

There is some support in the API for working with these, you may want to
take a look at the VariationAnnotation and related modules.

As you have noticed, there is also a variation set for variations with OMIM
phenotype annotations (this variation set is a subset of the
'Phenotype-associated variations' set). For the task you want to do, the
best approach is probably what you already suggested: to get the variations
in this variation set and intersect it with your list of variations.

Best regards
/Pontus


2011/2/17 Andrea Edwards <edwardsa at cs.man.ac.uk>

> 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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