Question: How Do I Deal Programmatically With Retired Ensembl Ids?
0
gravatar for Ryan Thompson
6.6 years ago by
Ryan Thompson3.4k
TSRI, La Jolla, CA
Ryan Thompson3.4k wrote:

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?

ensembl • 2.1k views
ADD COMMENTlink written 6.6 years ago by Ryan Thompson3.4k
1
gravatar for JC
6.6 years ago by
JC7.7k
Mexico
JC7.7k wrote:

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.

ADD COMMENTlink written 6.6 years ago by JC7.7k
0
gravatar for Ryan Thompson
6.5 years ago by
Ryan Thompson3.4k
TSRI, La Jolla, CA
Ryan Thompson3.4k wrote:

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.

ADD COMMENTlink written 6.5 years ago by Ryan Thompson3.4k
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