The BioMart server appears to be unavailable. The website suggests that biomaRt can still be used by changing the host to 'www.ensembl.org'.

I have tried this:

library(biomaRt)
human<-useMart(host="www.ensembl.org", "ensembl", dataset="hsapiens_gene_ensembl")

But no luck. I am getting the errors below.

> library(biomaRt)
> human<-useMart(host="www.ensembl.org", "ensembl", dataset="hsapiens_gene_ensembl")
Error in useMart(host = "www.ensembl.org", "ensembl", dataset = "hsapiens_gene_ensembl") :
  Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
> list<-listMarts()
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

Any suggestions would be appreciated.

Thanks

scor

Dear scor,

using listMarts you'll see that the biomart name is now different:

> 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)

Thus, you have to use "ENSEMBL_MART_ENSEMBL" instead of "ensembl":

human <- useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")

cheers, jo

3 types have changed in use:

listMarts(host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host="www.ensembl.org")

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

useMart("ENSEMBL_MART_ENSEMBL",dataset="aplatyrhynchos_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="drerio_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="ggallus_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="oaries_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="rnorvegicus_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="sscrofa_gene_ensembl", host="www.ensembl.org")

listMarts(host="metazoa.ensembl.org")

useMart("metazoa_mart",dataset="bmori_eg_gene", host="metazoa.ensembl.org")

useMart("metazoa_mart",dataset="amellifera_eg_gene", host="metazoa.ensembl.org")

useMart("metazoa_mart",dataset="cgigas_eg_gene", host="metazoa.ensembl.org")

listMarts(host="plants.ensembl.org")

useMart("plants_mart",dataset="zmays_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="sbicolor_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="stuberosum_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="osativa_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="creinhardtii_eg_gene", host="plants.ensembl.org")

Hi,

I use rpy2, a python module which interrogates R, and I use "ENSEMBL_MART_ENSEMBL" instead of  "ensembl" but I have a error with getGene() function :

mart = ruseMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="www.ensembl.org")

Traceback (most recent call last):
  File "main_initiation.py", line 158, in <module>
    g = rgetGene(id=ensembl_gene_id, type="ensembl_gene_id", mart=mart)
  File "/usr/local/lib/python2.7/site-packages/rpy2-2.6.2-py2.7-linux-x86_64.egg/rpy2/robjects/functions.py", line 178, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/rpy2-2.6.2-py2.7-linux-x86_64.egg/rpy2/robjects/functions.py", line 106, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in martCheck(mart, "ensembl") :
  This function only works when used with the ensembl BioMart.

Any suggestions would be appreciated.

Thanks

Saraï

Thanks you!