[BioC] connect to HapMart with biomaRt

[Steffen Durinck]

Hi Richard,

No unfortunately the status of the HapMap BioMart has not changed since.  All available BioMarts are displayed by listMarts()

Cheers,
Steffen

----- Original Message -----
From: Richard Pearson <richard.pearson at postgrad.manchester.ac.uk>
Date: Saturday, May 17, 2008 5:40 am
Subject: Re: [BioC] connect to HapMart with biomaRt
To: Steffen Durinck <durincks at mail.nih.gov>
Cc: bioconductor at stat.math.ethz.ch

> Hi Steffen
> 
> 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?
> Best wishes
> 
> Richard.
> 
> 
> 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.
> > 
> > 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
> >>
> > 
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> 
> -- 
> Richard D. Pearson             
> richard.pearson at postgrad.manchester.ac.ukSchool 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
> 
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