[biomart-users] Re: BioMart portal

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

[biomart-users] Re: BioMart portal

Arek Kasprzyk
Hi Daniele,

Yes, that's definitely possible. There are detailed instructions on the following page:

I hope you don't mind that I will cc your email to our users list in case other users are having similar difficulties


On 9 November 2015 at 10:40, Daniele Muraro <[hidden email]> wrote:
To whom it may concern,

I am a user of biomaRt and I have been applying the software to annotate human ensembl gene ids.
Today, I tried to connect to the portal using

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

but the connection was rejected.
I noticed from your website (http://www.biomart.org/notice.html) that the BioMart community portal is temporarily unavailable and it is suggested to change the host from 'www.biomart.org' to 'www.ensembl.org’.
So, I tried with

ensembl = useMart(“ensembl", dataset = "hsapiens_gene_ensembl", host=“www.ensembl.org”)

and received the error

Error in useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org") :
  Incorrect BioMart name, use the listMarts function to see which BioMart databases are available

by running listMarts I received

               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 82
2     ENSEMBL_MART_SNP  Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4    ENSEMBL_MART_VEGA               Vega 62
5                pride        PRIDE (EBI UK)

I would like to be able to reproduce the same annotation that I obtained using as host 'www.biomart.org' with the command

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

Is this possible?

Thank you for your attention.

All the best,

Daniele Muraro

Daniele Muraro
Postdoctoral Researcher
MRC Human Immunology Unit
University of Oxford
Weatherall Institute of Molecular Medicine
Headley Way

Tel. <a href="tel:%2B44%20%280%291865%20222477" value="+441865222477" target="_blank">+44 (0)1865 222477


You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at http://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.