Gene identifiers

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)

Dialogue & Discussion