[BioC] Pathway Interaction Database with BioC?

[Li.Long at isb-sib.ch]

Hi, Tony,

A while ago, I prepared the package "pathRender" to render pathway info
from cMAP database.  For a long while, cMAP (cmap.nci.nih.gov) download
provides inconsistant/incomplete data, compared to online query.  As a
result,
the data you get from bioC package "cMAP" is different from those you see
online.

The PID database indicates some data are from BioCarta (which is part of
cMAP as well), probably it's time to take another look at these packages
and do something about it.

Best,

Li

> Is anyone working on tools to integrate the Pathway Interaction Database
> http://pid.nci.nih.gov/PID/index.shtml with BioC?  (basically, XML
> conversion to a graph object to query intersections, relationships,
> and associations)?
>
> best,
> -tony
>
> blindglobe at gmail.com
> Muttenz, Switzerland.
> "Commit early,commit often, and commit in a repository from which we can
> easily
> roll-back your mistakes" (AJR, 4Jan05).
>
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