Are Bioconductor Packages Designed For Enrichment Analysis Affected By Kegg Privatization ?

Question

[Radhouane Aniba]

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

[Ying W]

This question might be better for the bioconductor listserv since the maintainers of thoes packages might comment.

[Brad Chapman]

Bioconductor mailing list discussion: http://thread.gmane.org/gmane.science.biology.informatics.conductor/36093

[Radhouane Aniba]

Yes Brad I sent the question to bioconductor list as advised by Ying W

Answer 1

[Chris Evelo]

If you want to know how the packages do it you could check the vignettes. They should explain that. But most likely they use the KEGG webservices and these are still functional. So essentially nothing changed for that. The only thing that is behind a pa wall is the KEGG ftp service. I think no one, probably not even the people at KEGG itself knows what will happen in the future. For me that is one of the reasons to work with (and to help develop) guaranteed open data pathway resources with appropriate licenses.