Pathway Interaction Database with BioC?
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A.J. Rossini ▴ 210
@aj-rossini-973
Last seen 7.4 years ago
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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@lilongisb-sibch-1725
Last seen 7.4 years ago
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). > > _______________________________________________ > 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 >
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