[biomart-users] Re: BioMart portal

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[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


a.










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

listMarts(host="www.ensembl.org")
               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
Oxford
OX3 9DS

Tel. <a href="tel:%2B44%20%280%291865%20222477" value="+441865222477" target="_blank">+44 (0)1865 222477
www.imm.ox.ac.uk/alison-simmons-2



 


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