Dear bioconductor fellows, I tried to map genes to biocarta pathways using cMAP package, but I found that the molecule identifiers provided by cMAP functions are quite different from that given in the biocarta pathway website or cMAP pathway interaction database website. I noticed that there was a similar complaint about this problem in the mailing list about two years ago. I'm wondering when it will be fixed. Thank you for your attention. Ahrim [[alternative HTML version deleted]]

Hi Ahrim, I don't think it will get "fixed", or changed much, unless someone who is using it wants to do that. It looked very promising two or three years ago, but it seems to have slowed down as a project and it is not obvious how to download the data in any reasonable format. Also, Biocarta terms of use seem to be quite restrictive, so I doubt that any real use of the data in a manner consistent with the creation of a Bioconductor packages are possible. If you have new information, it would be good to know more. I think for pathways, we only really have KEGG. For basic interactions there is RIntact and similar packages that let you download interaction data from different sites. best wishes Robert Youn, Ahrim (NIH/NCI) [F] wrote: > Dear bioconductor fellows, > > > > I tried to map genes to biocarta pathways using cMAP package, but I > found that the molecule identifiers provided by cMAP functions are quite > different from that given in the biocarta pathway website or cMAP > pathway interaction database website. I noticed that there was a similar > complaint about this problem in the mailing list about two years ago. > I'm wondering when it will be fixed. > > Thank you for your attention. > > > > Ahrim > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

>From the cMAP package reference page Mappings were based on data provided by: cMAP: http://cmap.nci.nih.gov/PW/Download. Build: Unavailable. Downloaded:Tue Sep 12 16:52:56 2006 Package built: Tue Sep 12 16:52:56 2006 I think cMAP is not being maintained per se by NCBI. We described it extensively in the 2005 Springer monograph, ch 7.6.2 PERHAPS our cMAP package should be dropped. users/those with use cases should comment. On Thu, May 7, 2009 at 1:57 PM, Youn, Ahrim (NIH/NCI) [F] < youna2@mail.nih.gov> wrote: > Dear bioconductor fellows, > > > > I tried to map genes to biocarta pathways using cMAP package, but I > found that the molecule identifiers provided by cMAP functions are quite > different from that given in the biocarta pathway website or cMAP > pathway interaction database website. I noticed that there was a similar > complaint about this problem in the mailing list about two years ago. > I'm wondering when it will be fixed. > > Thank you for your attention. > > > > Ahrim > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Vincent Carey, PhD Biostatistics, Channing Lab 617 525 2265 [[alternative HTML version deleted]]