[BioC] About the state of KEGG-related packages

[Calin Voichita]

Enrico,

The ROntoTools package uses the KEGGREST to download and parse the KEGG data into graph objects. In addition it performs  both an over-representation analysis and a more advanced impact analysis on the given set of pathways.

If you want just to use the pathway data (as downloaded and parsed by this package), by using the function keggPathwayGraphs("hsa") or keggPathwayGraphs("hsa", updateCache = TRUE) to re-download the data you can obtain a list of graph objects representing the pathways in KEGG.

Regards,
Calin

On Jul 29, 2013, at 4:31 PM, Enrico Ferrero <enricoferrero86 at gmail.com> wrote:

> Hi Marc,
> 
> Thanks for your answer.
> So, apparently, the only two packages relying on KEGGREST are PAPi and
> ROntoTools, an unfortunately limited selection.
> May I ask, given the current situation, what is the most advisable way
> to perform pathway enrichment analysis using Bioconductor?
> 
> Thank you.
> Best,
> 
> 
> On 29 July 2013 19:37, Marc Carlson <mcarlson at fhcrc.org> wrote:
>> 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 The KEGG.db and KEGGSOAP packages are no longer updated and any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 package that relies on them is also outdated.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,
>>> 
>> 
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> 
> 
> 
> -- 
> Enrico Ferrero
> PhD Student
> Steve Russell Lab - Department of Genetics
> FlyChip - Cambridge Systems Biology Centre
> University of Cambridge
> 
> e.ferrero at gen.cam.ac.uk
> http://flypress.gen.cam.ac.uk/
> 
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-- 
Calin Voichita
Ph.D. Candidate
Intelligent Systems and Bioinformatics Laboratory (ISBL)
Department of Computer Science - Wayne State University
Phone: +1(313)577-5070                   Fax: +1(313)577-6868
Detroit, MI 48202, USA
http://vortex.cs.wayne.edu