[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
> http://lists.ensembl.org/mailman/listinfo/dev

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