Link Between Ensembl And Omim

Question

[Mdeng]

Hello everyone,

does anyone of you know, if there is a link between the EnsemblDB and the OMIM-DB? In special a link between the EnsemblIDs (ENST, ENSP, ENSG) and a OMIM-ID would be nice. At the this point I would use the gene symbols. But I am a bit afraid if they are congruent in both databases. Like e.g. "NKX3-1", "NKX3.1" etc.

Maybe you've an idea or a hint.

Cheers.

Answer 1

[Michael Kuhn]

𝄆 If you want to get mappings from a database like Ensembl , look at BioMart 𝄇

On the Attributes / External References you find: MIM Morbid Accession, MIM Morbid Description, MIM Gene Accession, MIM Gene Description

[Mdeng]

Perfect, did not recordnis that it's just called MIM instead of OMIM.

Answer 2

[tiagoantao]

Go to the HUGO consortium and download their list of genes. It provides a link between old and new gene names

http://www.genenames.org/cgi-bin/hgnc_stats.pl

Example:

HGNC:7838       NKX3-1  NK3 homeobox 1  Approved        NKX3A   NKX3.1, BAPX2   8p21.2

[Mdeng]

This is kinda temporary solution. I am looking for an explicit link between those DBs. This would also blow up my SQL queries.