Useful genomic and genetic datasets and databases

Introduction

The purpose of this post is to list a few useful genomic and genetic datasets that might be useful to download when used frequently.

The advantage of having the data locally on one’s computer is that it can be queried rapidly without the need for repeated manual entry on websites.

The GeneReviews books are publicly available for download. For example, you can use wget on linux to download the books:

wget -r ftp://ftp.ncbi.nlm.nih.gov/pub/litarch/ca/84/

For a list of the files in the books, download the GeneReviews resources:

wget -r ftp://ftp.ncbi.nih.gov/pub/GeneReviews/

For more information and for retrictions regarding data use, consult the NCBI ftp and GeneReviews copyright description.

OMIM made the mim2gene.txt file publicly available, which contains the identifiers for OMIM, NCBI Gene, Ensembl Gene, and the HGNC gene symbols.

Additional useful datasets are available when submiting a download request. Consult the OMIM downloads for more information.

Orphanet is making part some of their datasets available for download at Orphadata.