[ensembl-dev] Fwd: Re: Retrieving OMIM gene information
Andrea Edwards
edwardsa at cs.man.ac.uk
Mon Apr 18 15:14:49 BST 2011
-------- Original Message --------
Subject: Re: [ensembl-dev] Retrieving OMIM gene information
Date: Mon, 18 Apr 2011 14:54:51 +0100
From: Andrea Edwards <edwardsa at cs.man.ac.uk>
To: Duarte Molha <duartemolha at gmail.com>
Hi
Please find below some information i was given from ensembl regarding
this matter:
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
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).
2011/2/17 Andrea Edwards <edwardsa at cs.man.ac.uk
<mailto: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
On 18/04/11 09:33, Duarte Molha wrote:
>
> Dear all
>
> I am looking to retrieve the information of a gene is on OMIM database
> using the API.
>
> I’ve been looking though the api documentation and have not found what
> I was looking for.
>
> I apologise if it is really obvious.
>
> Could you point me in the right direction?
>
> Duarte Molha
>
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
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