[BioC] biomaRt question

Steffen Durinck sdurinck at ebi.ac.uk
Thu Apr 7 08:20:47 CEST 2005

Hi Jo,

In the function martConnect you should write something like this (using 
the correct host,....)

mart <- new("Mart",
               ensembl = dbConnect(drv = driver,user = user, host = host 
, dbname = databases$ensembl, password = password),
               vega = dbConnect(drv = driver,user = user, host= host, 
dbname = databases$vega, password = password),
               sequence = dbConnect(drv = driver,user = user, host = 
host, dbname = databases$sequence, password = password),
               snp = dbConnect(drv = driver,user = user, host = host, 
dbname = databases$snp, password = password),
               arrayToSpecies = arrayToSpecies,
               arrayToEnsembl = arrayToEnsembl

You'll also need to change the host etc in the function listMarts

listMarts <- function(host = "ensembldb.ensembl.org", user = 
"anonymous", password = ""){

 driv <- dbDriver("MySQL", force.reload = FALSE);
 connection <- dbConnect(driv, user = user, host = host, password = 

If you can wait a few more hours I could  send you the latest release of 
biomaRt in which you don't have to make changes in the source code 
anymore but can change host from within your R session.  BioMart 
currently uses Ensembl_mart, snp_mart, vega_mart, and  sequence_mart.  
It will try to connect  to these marts all at  once.  We plan to include 
a way of selection so if you only use ensembl you don't have to install 
all other marts although these currently come together if you do a local 
ensembl install.


Dipl.-Ing. Johannes Rainer wrote:

> hi,
> as i am behind a http proxy and the biomart package tries to establish 
> a direct mysql connectioj to the ensembl database i had no chance to 
> test or use the biomaRt package.
> well, now i finally managed to install a local version of biomart 
> (after some problems i had with different versions of mysql (i 
> strongly recommend to use MySQL > 4.1 !)). my question is now, how and 
> where do i have to change biomaRt source to connect to my local 
> biomart database?
> another question: which mart database uses biomaRt, i assume the 
> ensemble_mart and not the uniprot and msd mart...
> cheers, jo
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