How Do I Deal Programmatically With Retired Ensembl Ids?

Question

[Ryan Thompson]

I have dataset with some apparently retired Ensemble peptide IDs, such as ENSP00000400710. Presumably the dataset was processed with an older version of the Ensembl database. I want to translate these into gene IDs, and in many cases, the peptide ID is retired but the gene ID is not. Is there a way to get all non-retired gene IDs from a set of retired peptide IDs programmatically?

Answer 1

[JC]

you can use the Perl API to check out old releases or use the ID history converter, but the ENSP00000400710 is actually accesible in the browser.

Answer 2

[Ryan Thompson]

I figured out which version of Ensembl the annotation used, and I found the historical biomart server for that version, and everything went nicely from then on.