websites/dennogumi.org-archive
Archived
1
0
Fork 0
Code Releases Activity
This repository has been archived on 2021-01-06. You can view files and clone it, but cannot push or open issues or pull requests.
dennogumi.org-archive/_posts/2007-11-15-gene-identifiers.markdown

1.1 KiB
Raw Permalink Blame History

author comments date layout slug title wordpress_id categories header tags
einar true 2007-11-15 19:57:16+00:00 page gene-identifiers Gene identifiers 336
Science
image_fullwidth
banner_other.jpg
annotation
bioinformatics
microarray
python

While working today on an annotation class in Python I stumbled on a problem. Normally I work with lists of genes that are consistent, i.e. all Entrez Gene IDs (or RefSeq IDs, or Genome Browser IDs...), but today I had a list of mixed identifiers.

The subsequent idea was "let's implement auto-detection of common identifiers in the class". The problem is... is there any actual documentation on how identifiers are made? So far, using regular expressions, I've tracked down a few:

  • RefSeq

  • GenBank

  • Entrez Gene

  • UCSC Genome Browser

  • Ensembl

However, I have no idea if I have implemented all types of these IDs. Does anyone know a place where to look these information up?

(On a related note: my thesis defense will be on January 14th, 2008, so I have to get the printing going)