Download data from OMIM

Question

[Biojl]

Hi,

I want to download all the gene identifiers related with a biolgoical function and/or disease. I can search it in the OMIM database but I can't find a button to download all the information as a table.

I also tried to register for the FTP download, download the whole genemap and then parse the results myself looking for what I need but apparently the FTP server is saturated.

Anyone has an alternative?

Thanks!

PD: GO terms is not good enough, since some of the genes are only related through disease.

[gauravdube007]

Hello Biojl can you please help me with this post?

Thanks in advance.

Answer 1

[Giovanni M Dall'Olio]

Get the file gene_info.gz in the NCBI FTP ( ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ ). Check the lines starting with the code "9606" (which is the ID for Homo sapiens). You will find the OMIM info in the sixth column, defined as MIM:<omim id="">.

Note that this is the ID of the gene in OMIM, not the id of the disease. You still have to intersect it with the files downloaded in the OMIM FTP.