[BioC] problem of cMAP package

Robert Gentleman rgentlem at fhcrc.org
Thu May 7 20:15:07 CEST 2009

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

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]]
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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
rgentlem at fhcrc.org

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