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 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > 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

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@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 > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor> > > -- > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor