[BioC] connect to HapMart with biomaRt
richard.pearson at postgrad.manchester.ac.uk
Sat May 17 14:35:22 CEST 2008
Just wondering - has there been any change on this since your post in early 2007 - i.e. do HapMap now have webservice or public MySQL capabilities?
Steffen Durinck wrote:
> 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.
>> -------- 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).
>> Wei ZOU, PhD
>> Clinical Data, Inc.®
>> >From Targeted Science to Better Healthcare
>> Five Science Park
>> New Haven, CT 06511
>> Tel: 203.786.3513
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
Richard D. Pearson richard.pearson at postgrad.manchester.ac.uk
School of Computer Science, http://www.cs.man.ac.uk/~pearsonr
University of Manchester, Tel: +44 161 275 6178
Oxford Road, Mob: +44 7971 221181
Manchester M13 9PL, UK. Fax: +44 161 275 6204
More information about the Bioconductor