[Bioc-devel] Bioc-devel Digest, Vol 86, Issue 14

[Tarca, Adi]

Hi Robert,

I think it woud be a good idea to have a wikipathways package that would include not only  gene / small-molecule memberships 
but aslo the types of relations between them that would enable packages such as SPIA and others to perform pathway analysis. I am not sure what would be the
best container for these pathways. Maye a graph type of object in which the additional properties of the edges (such as the type of relation, e.g. activation , and the 
mechanism type, e.g. phospohorilation) are included. Also to have some mechanisms to extract subgraphs based on certain types of relations only,  and support multiple organisms.
regards,
Adi Tarca
 


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Subject: Bioc-devel Digest, Vol 86, Issue 14

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Today's Topics:

   1. interest in wikipathway annotation packages (Robert M. Flight)


----------------------------------------------------------------------

Message: 1
Date: Thu, 26 May 2011 14:27:41 -0400
From: "Robert M. Flight" <rflight79 at gmail.com>
To: bioc-devel at r-project.org
Subject: [Bioc-devel] interest in wikipathway annotation packages
Message-ID: <BANLkTim1HmEd87v0Om_0H2Fw=hnzYc_rcA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

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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End of Bioc-devel Digest, Vol 86, Issue 14