[Bioc-devel] interest in wikipathway annotation packages

Marc Carlson mcarlson at fhcrc.org
Sat May 28 02:20:55 CEST 2011

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.


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