[ensembl-dev] OMIM numbers for genes

[Paul Flicek]

As a clarification, the GRCh37 site is based on Ensembl release 75 with selected data updates and regular updates to the API and website. 

From the GRCh37 site:

"This archive is based on Ensembl Release 75 data, and gives continuing access to human assembly GRCh37, as well as all our other release 75 species (data freeze March 2014) for comparative purposes. Human variation and regulation data has since been updated in March 2015.

The API and website will be updated in tandem with the release of the main Ensembl website, and we will also periodically update this site with new human data, which will be announced in this panel."


I hope this helps. 

Paul


> On 11 Oct 2016, at 15:31, Matthew Laird <lairdm at ebi.ac.uk> wrote:
> 
> Hi Wolf,
> 
> If I'm understanding what you're describing, I'm assuming you're looking at GRCh37 Biomart for this inconsistency. While we maintain GRCh37 archives, we no longer actively update xrefs for that assembly, they're all frozen as of Ensembl release 37. Looking up HYDIN in Ensembl 86, GRCh38 I see only 610812 is returned for this HGNC symbol, so whatever mis-mapping was occurring seems to be corrected.
> 
> If I'm misunderstanding the issue you're raising, please let us know. Thanks.
> 
>> On 11/10/16 12:11, Wolf Beat wrote:
>> Hi,
>> 
>> i had an interesting issue with the OMIM number for a certain gene, HYDIN.
>> 
>> When querying biomart, i get two OMIM numbers back for this gene:
>> 
>> HYDROCEPHALUS-INDUCING, MOUSE, HOMOLOG OF, 2; HYDIN2    610813
>> and
>> HYDROCEPHALUS-INDUCING, MOUSE, HOMOLOG OF; HYDIN    610812
>> 
>> The Problem, the first one is wrong. The first one is for the HYDIN2 gene, which is located on chromosome 1. HYDIN is on chromosome 16.
>> Looking at the OMIM pages linked this is confirmed:
>> HYDIN: http://omim.org/entry/610812
>> HYDIN2: http://omim.org/entry/610813
>> 
>> And here the ensembl pages:
>> HYDIN:  http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000157423;r=16:70807378-71230722
>> HYDIN2: http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000239475;r=1:146310555-146349531
>> 
>> So my question is, is this an error on the part of ensembl (wrong annotation), some misunderstanding of my part and can i fix/detect this problem on my side?
>> 
>> Thank you very much.
>> 
>> Kind regards
>> 
>> Beat Wolf
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> 
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