[BioC] connect to HapMart with biomaRt

[Steffen Durinck]

Dear Wei,

In principle the biomaRt package can be used with any BioMart database. 
However the HapMap BioMart suite is an old version which has no 
webservice capabilities and the HapMap project has also not made a 
public MySQL access to their database available yet.  As soon as the 
HapMap project updates their BioMart suite to a more recent version or 
makes public access to their MySQL database available, you should be 
able to use the biomaRt package for queries. 
I've asked them already to do this but so far nothing has changed.  You 
could mail their helpdesk help at hapmap.org to request this, hopefully the 
more of us who ask for it the sooner we'll have this access.

regards,
Steffen


> -------- Original Message --------
> Subject: connect to HapMart with biomaRt
> Date: Mon, 12 Feb 2007 10:05:09 -0500
> From: Zou, Wei <wzou at pgxhealth.com>
> To: <huber at ebi.ac.uk>
>
> Dear Dr Huber:
>
>       As a user of biomaRt, I am wondering whether this package can (be
> tuned to) query HapMart (http://hapmart.hapmap.org/BioMart/martview).
>
>
> Thanks
>
>
> Wei ZOU, PhD 
> Biostatistician
> Clinical Data, Inc.®
> >From Targeted Science to Better Healthcare 
> Five Science Park
> New Haven, CT 06511
> Tel:    203.786.3513 
> www.clda.com
>