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?
2 answers
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.
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.
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