[BioC] Continuation of the KEGG.db package

[January Weiner]

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

Is there a way to directly access the Pathway Commons data from R? For
example, to do enrichment analysis? Reactome.db has its own package, I
think.

j.


>
> 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 at 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
>>
>>
>>        [[alternative HTML version deleted]]
>>
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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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>
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-- 
-------- Dr. January Weiner 3 --------------------------------------
Max Planck Institute for Infection Biology
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