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

[Mohammad Goodarzi]

Hello,

Thank you for your reply.
Is it possible to guide me how to use one of your archive with Biomart or
any other programming language ?
When it comes to 3000 genes , it is very difficult to do them one by one .

Thanks
Mohammad

On Mon, 22 Jan 2018 at 04:21, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:

> Hi Mohammad.
>
> It looks like most of your IDs are now retired. If we take your first
> example:
>
> http://www.ensembl.org/Homo_sapiens/Gene/Idhistory?g=ENSG00000122718
>
> 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.
>
>
> Regards,
>
> Kieron
>
> [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
> >
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