[BioC] biomaRt

[Steve Lianoglou]

Hi Fraser,

On Tue, Jul 13, 2010 at 1:19 PM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> No, I am not talking about your internet connection, I am talking about the
> biomart web server at http://www.biomart.org/. The biomaRt package by
> default uses this web server, so if you cannot get the page to load in a
> browser, you will not be able to query using biomaRt either.

I think some people get confused and think the biomart service is
something owned/operated by the bioconductor folks: it's not.

As Jim points out, the web server is here:
http://biomart.org

The bioconductor package "biomaRt" is simply an R library that calls
out to the biomart.org service with well-formed URL's that are built
by the criteria constructed in your getBM (or whatever) function
calls.

If biomart.org is down, then your getBM calls will also fail, but
there's nothing that can be done about that on this list. Probably
your best bet is to contact the biomart.org people directly.

That having been said, it seems that biomart.org is back up now.

Hope that clears things up (if they needed clearing to begin with :-).

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact