[BioC] connect to HapMart with biomaRt

[Richard Pearson]

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.uk
School of Computer Science,    http://www.cs.man.ac.uk/~pearsonr
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