[BioC] About the state of KEGG-related packages

[Marc Carlson]

Hi Enrico,

In general, I think you should assume that almost all KEGG resources are 
out of date since KEGG basically cut the world off with a pay wall some 
time ago.

The only exception I know of with any certainty is KEGGREST.  And that 
is only because KEGG has (at least for now) decided to allow continued 
access to their REST API.


   Marc




On 07/28/2013 02:42 PM, Enrico Ferrero wrote:
> Dear list,
>
> I will soon be doing some pathway enrichment analysis and would like
> to make the most of what Bioconductor has to offer, but I am a bit
> confused about the current state of packages relying upon KEGG, such
> as clusterProfiler, KEGGgraph, keggorthology, KEGGprofile, PathNet and
> pathview, just to name a few.
>
> As you probably know, KEGG has moved to a subscription-based model for
> accessing his FTP site in 2011 [1].
>
> The following is my understanding of how this has affected
> Bioconductor, but corrections and clarifications are welcome.
> The KEGG.db and KEGGSOAP packages are no longer updated and any
> package that relies on them is also outdated. On the other hand, since
> KEGG has continued to offer access through its REST API, the KEGGREST
> package is now the preferred way to pull up to date information out of
> KEGG.
> On top of this, some package maintainers may have used their own
> implementation to access KEGG, so there's no easy way to filter
> packages with updated or outdated information based on what they
> depend on.
>
> Provided this is broadly correct, my question is: how do I know which
> KEGG-related packages are reliable in terms of up-to-dateness and
> which not?
>
> Thank you.
>
> [1] http://www.kegg.jp/kegg/download/
>
> Best,
>