Marc Carlson gave a great presentation about this issue at BioC2011
developers day, I think the slides are online?

If not, the general consensus seemed to be that Pathway Commons and
reactome.db etc. were the way forward

I too am sad that KEGG could not be funded in the public interest but I
guess that is the fallout from a recession.


On Mon, Jan 16, 2012 at 12:58 AM, Asta Laiho <asta.laiho@btk.fi> wrote:

> Hi,
>
> I just saw the following information regarding the continuation of the
> KEGG.db Bioconductor package:
>
> KEGG.db contains mappings based on older data because the original
>  resource was removed from the the public domain before the most
>  recent update was produced. This package should now be considered
>  deprecated and future versions of Bioconductor may not have it
>  available.  One possible alternative to consider is to look at the
>  reactome.db package
>
> I am very sad to hear about the news as KEGG has become an important
> resource for the researchers and using it through Bioconductor has been
> very valuable for many people. I'm not sure what the original reason for
> removing the database content form the public domain is, officially I found
> the following information:
>
> Plea to support KEGG
> http://www.kegg.jp/kegg/docs/plea.html
> and the comment in the Editorial of the NAR DB issue
> (Nucl. Acids Res. 2012 40 D1: D1-D8).
> http://nar.oxfordjournals.org/content/40/D1/D1.full
>
> If someone has further information for clarifying the situation it would
> be great to share it on the emailing list.
>
> - Asta
>
>
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>
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-- 
If people do not believe that mathematics is simple,
it is only because they do not realize how complicated life is. John von
Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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