Question: GOstats with Reactome database?
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gravatar for J.delasHeras@ed.ac.uk
8.3 years ago by
United Kingdom
J.delasHeras@ed.ac.uk1.9k wrote:
Dear all, with the demise of KEGG (well, at least without subscription), I was wondering whether there are any plans to get GOstats working with the Reactome database, or whether there is an "easy" way to persuade GOstats to work with it. Any ideas? Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507090 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
gostats • 642 views
ADD COMMENTlink modified 8.3 years ago by Martin Morgan ♦♦ 24k • written 8.3 years ago by J.delasHeras@ed.ac.uk1.9k
Answer: GOstats with Reactome database?
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gravatar for Martin Morgan
8.3 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
On 08/15/2011 05:48 AM, J.delasHeras at ed.ac.uk wrote: > Dear all, > > with the demise of KEGG (well, at least without subscription), I was > wondering whether there are any plans to get GOstats working with the > Reactome database, or whether there is an "easy" way to persuade GOstats > to work with it. Hi Jose -- Yes, we intend to revise the GOstats, GSEABase, and perhaps other packages to work more flexibly with Reactome & other data base packages. Whether this will be accomplished this release is not clear. Martin > Any ideas? > > Jose > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 8.3 years ago by Martin Morgan ♦♦ 24k
Quoting Martin Morgan <mtmorgan at="" fhcrc.org=""> on Mon, 15 Aug 2011 10:11:50 -0700: > On 08/15/2011 05:48 AM, J.delasHeras at ed.ac.uk wrote: >> Dear all, >> >> with the demise of KEGG (well, at least without subscription), I was >> wondering whether there are any plans to get GOstats working with the >> Reactome database, or whether there is an "easy" way to persuade GOstats >> to work with it. > > Hi Jose -- > > Yes, we intend to revise the GOstats, GSEABase, and perhaps other > packages to work more flexibly with Reactome & other data base > packages. Whether this will be accomplished this release is not clear. > > Martin > >> Any ideas? >> >> Jose Hi Martin, that's great news. I have become a bit of a fan of GOstats recently and would love to use a similar approach with other databases. Very grateful for all your work. Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507090 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
ADD REPLYlink written 8.3 years ago by J.delasHeras@ed.ac.uk1.9k
Dear Martin and Jose, We, at Reactome, would be encouraged by the development of Gostats to use our pathway data. If you would like to discuss this further, please let me know. Likewise, if there are any other BioConductor developers interested in using Reactome as a source of pathway data, drop me an email. In the meantime, we do provide a "Reactome Pathway Gene Set" and other annotation data at http://www.reactome.org/download/. Regards, Robin Robin Haw, PhD Scientific Associate and Outreach Coordinator (Reactome) Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 647-260-7985 Toll-free: 1-866-678-6427 http://www.oicr.on.ca http://www.reactome.org This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. On 11-08-15 1:21 PM, "J.delasHeras at ed.ac.uk" <j.delasheras at="" ed.ac.uk=""> wrote: >Quoting Martin Morgan <mtmorgan at="" fhcrc.org=""> on Mon, 15 Aug 2011 10:11:50 >-0700: > >> On 08/15/2011 05:48 AM, J.delasHeras at ed.ac.uk wrote: >>> Dear all, >>> >>> with the demise of KEGG (well, at least without subscription), I was >>> wondering whether there are any plans to get GOstats working with the >>> Reactome database, or whether there is an "easy" way to persuade >>>GOstats >>> to work with it. >> >> Hi Jose -- >> >> Yes, we intend to revise the GOstats, GSEABase, and perhaps other >> packages to work more flexibly with Reactome & other data base >> packages. Whether this will be accomplished this release is not clear. >> >> Martin >> >>> Any ideas? >>> >>> Jose > > >Hi Martin, > >that's great news. I have become a bit of a fan of GOstats recently >and would love to use a similar approach with other databases. > >Very grateful for all your work. > >Jose > >-- >Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk >The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507090 >Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 >Swann Building, Mayfield Road >University of Edinburgh >Edinburgh EH9 3JR >UK > > >-- >The University of Edinburgh is a charitable body, registered in >Scotland, with registration number SC005336. > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 8.3 years ago by Robin Haw50
Hi Robin, I am glad to hear that! We are definitely interested in getting reactome better exposure through Bioconductor. We may contact you to help facilitate this in the near future. Marc On 08/15/2011 02:37 PM, Robin Haw wrote: > Dear Martin and Jose, > > We, at Reactome, would be encouraged by the development of Gostats to use > our pathway data. If you would like to discuss this further, please let me > know. > > Likewise, if there are any other BioConductor developers interested in > using Reactome as a source of pathway data, drop me an email. In the > meantime, we do provide a "Reactome Pathway Gene Set" and other annotation > data at http://www.reactome.org/download/. > > Regards, > Robin > > Robin Haw, PhD > Scientific Associate and Outreach Coordinator (Reactome) > > Ontario Institute for Cancer Research > MaRS Centre, South Tower > 101 College Street, Suite 800 > Toronto, Ontario, Canada M5G 0A3 > > Tel: 647-260-7985 > Toll-free: 1-866-678-6427 > http://www.oicr.on.ca > http://www.reactome.org > > This message and any attachments may contain confidential and/or > privileged information for the sole use of the intended recipient. Any > review or distribution by anyone other than the person for whom it was > originally intended is strictly prohibited. If you have received this > message in error, please contact the sender and delete all copies. > Opinions, conclusions or other information contained in this message may > not be that of the organization. > > > > > On 11-08-15 1:21 PM, "J.delasHeras at ed.ac.uk"<j.delasheras at="" ed.ac.uk=""> wrote: > >> Quoting Martin Morgan<mtmorgan at="" fhcrc.org=""> on Mon, 15 Aug 2011 10:11:50 >> -0700: >> >>> On 08/15/2011 05:48 AM, J.delasHeras at ed.ac.uk wrote: >>>> Dear all, >>>> >>>> with the demise of KEGG (well, at least without subscription), I was >>>> wondering whether there are any plans to get GOstats working with the >>>> Reactome database, or whether there is an "easy" way to persuade >>>> GOstats >>>> to work with it. >>> Hi Jose -- >>> >>> Yes, we intend to revise the GOstats, GSEABase, and perhaps other >>> packages to work more flexibly with Reactome& other data base >>> packages. Whether this will be accomplished this release is not clear. >>> >>> Martin >>> >>>> Any ideas? >>>> >>>> Jose >> >> Hi Martin, >> >> that's great news. I have become a bit of a fan of GOstats recently >> and would love to use a similar approach with other databases. >> >> Very grateful for all your work. >> >> Jose >> >> -- >> Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk >> The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507090 >> Institute for Cell& Molecular Biology Fax: +44 (0)131 6507360 >> Swann Building, Mayfield Road >> University of Edinburgh >> Edinburgh EH9 3JR >> UK >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 8.3 years ago by Marc Carlson7.2k
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