[BioC] Are bioconductor packages designed for enrichment analysis affected by KEGG privatization ?

Marc Carlson mcarlson at fhcrc.org
Wed Aug 3 21:17:46 CEST 2011

Hi Radhouane,

The loss of KEGG is a real bummer for the community, but there are other 
resources on the horizon and some that are already available.  You can 
for example check out the reactome.db package (contributed by Willem 
Ligtenberg) and note that it has a lot of the same kinds of information 
as the KEGG.db package has traditionally had.  And software packages 
like GOstats can just be enhanced to work with new  resources as they 
come online, and in the meantime they will still work with older 
packages based on the older snapshots from when KEGG was still freely 

So in short, life goes on.  With or without KEGG, there will continue to 
be many great ways to do pathway analysis for the simple reason that 
there is still a community of bright people like yourself who are 
interested in those questions.


On 08/03/2011 10:42 AM, Radhouane Aniba wrote:
> Hi,
> Some bioconductor packages like GSEA or GOStats that additionally to GO are
> designed to measure gene set enrichment using KEGG pathways, still work and
> give results even after the new paid license and subscription like we all
> know the story.
> My question can be discussed in two different ways, I am wondering how
> people developing these packages are doing ? Does thes packages call KEGG
> directly or an image of it, if this is the second case how a user can be
> sure about the KEGG version used ?
> The second part of my question concerns the development of other packages
> for gene set enrichment, do you expect this kind of packages decreasing in
> the coming few years due to KEGG privatization ? if now, how can we ( for
> late people like me) download an image of KEGG database corresponding to a
> version existing before privatization, as it was in public domain it is not
> going against the new license rules to distribute it.
> Regards
> Radhouane

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