[ensembl-dev] how to annotate many gene names from ensemble to gene name

Kieron Taylor ktaylor at ebi.ac.uk
Mon Jan 22 10:20:56 GMT 2018

Hi Mohammad.

It looks like most of your IDs are now retired. If we take your first example:


Our Gene page for this ID reports that it was retired in release 84. A revision of the sequence there, or validation of our genebuild has caused us to retire the ID as no longer meaning what we thought it did.

The BioMart service has no way to report data that is not current. Depending on your needs, you could use one of our archive servers to get the data surrounding your IDs, for example: [1]

The easiest thing might be to feed your list of failed IDs into our ID history tool [2]. This will tell you the last Ensembl release in which that ID was seen, and if possible report the ID that replaced it.

Another alternative is to cross-check your IDs to see which ones have been retired against our REST archive endpoint: [3]

Hopefully one of these methods will suit your needs.



[1] - http://mar2016.archive.ensembl.org/biomart/martview/3459e207de70960baa9be743908900d2
[2] - http://www.ensembl.org/Homo_sapiens/Tools/IDMapper?db=core
[3] - http://rest.ensembl.org/archive/id/ENSG00000122718?content-type=application/json

Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute

> On 21 Jan 2018, at 20:53, Mohammad Goodarzi <mohammad.godarzi at gmail.com> wrote:
> hello,
> I recently try to annotate a set of gene names. I have over 3000 genes that i cannot annotate using biomart for example.
> I have been searching a lot but I could not find a solution. can you please comment how would you do this ? I post a small set of them for the practice purpose and I am happy to get any opinion that help me to do this automatically.
> Please see below 
> Thanks
> ENSG00000122718
> ENSG00000130201
> ENSG00000150076
> ENSG00000150526
> ENSG00000155640
> ENSG00000166748
> ENSG00000168260
> ENSG00000168787
> ENSG00000170590
> ENSG00000170803
> ENSG00000171484
> ENSG00000172381
> ENSG00000172774
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

More information about the Dev mailing list