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[Bioc-devel] interest in wikipathway annotation packages

2 messages · Robert M. Flight, Marc Carlson

Original
Robert M. Flight
# 
Hi All,

As a means to providing alternatives to KEGG pathways, I'm wondering
if there is any interest or previous work done on creating annotation
packages for WikiPathways or data from PathwayCommons. I have been
considering getting into this, but am wondering if there is interest
or support from the general community. From what I can tell,
generating at least gene / small-molecule memberships in pathways
should not be too difficult. If anyone knows different, I would
appreciate feedback.

Cheers,

-Robert

Robert M. Flight, Ph.D.
University of Louisville Bioinformatics Laboratory
University of Louisville
Louisville, KY

PH 502-852-1809 (HSC)
PH 502-852-0467 (Belknap)
EM robert.flight at louisville.edu
EM rflight79 at gmail.com

Williams and Holland's Law:
? ? ?? If enough data is collected, anything may be proven by
statistical methods.
1 day later
Marc Carlson
# 
Hi Robert,

There have not been any packages made based on either of those two 
resources.  (There is a reactome.db package that has been contributed 
though.)  At this point, I think that anything decent that can be used 
in lieu of KEGG should at least be considered.  And we are exploring our 
options now for alternatives.  Any additional information you have about 
what is out there will of course be appreciated.

My main fear with the loss of KEGG is that there will be plenty of nice 
alternate ontologies to choose from, but very few annotations that match 
those ontologies to genes.  And obviously, the former is not useful 
without the latter.


   Marc
On 05/26/2011 11:27 AM, Robert M. Flight wrote: