Hi Everyone,
A colleague have started a project dealing with KEGG pathway enrichment analysis and as KEGG is going to be no more public (July 1st), I would like to know if there is a way to download an image of kegg to work with locally or if someone have already done this it will be grate to share it.
Thank you
Radhouane
Yes. If not mistaken, you can get a payed subscription allowing you to download the data. You can find information here.
This is more a comment than an answer, but it did not fit in the comment space.
Pathways, whether from KEGG or from anywhere else, are in the end not more than a construct that helps us to understand the relationships between a larger number of interactions. These individual interactions, and often their relationships should also be described in the literature (including online publications, blogs and published datasets, so it is more about previously published knowledge). If that is not the case an interaction should not be in a pathway.
I think that means that while pathways as a whole and (especially the format and the layout) can indeed be copyrighted the individual interactions can not, fall under that same copyright. Even is someone has a patent on an interaction (or a gene) that patent will normally not prevent you from using knowledge about it (although it might be wise to mention the patent).
Since many of us would prefer to have freely available pathways, not just to save the money, but also to be able to improve them with the strength of a community effort, I would strongly advocate to do just that. Initiatives like [?]WikiPathways[?] allow you to create new pathways or to extend existing ones and use those for for instance over representation analysis. If you find specific information that you think should be present in such freely available pathways and the basis of that information is available in published literature please add it. But please be careful before you copy larger chunks of formatted pathways. That might indeed be copyrighted or fall under licenses.
Disclosure: I am one of the authors of the papers about WikiPathways and [?]PathVisio[?] [[?]1[?], [?] 2[?], [?] 3[?]]. Those papers were written based on the same philosophy described here. But it means I do have an interest in WikiPathways being successful.
You don't blog? BTW, my full catch on the KEGG situation -> http://chem-bla-ics.blogspot.com/2011/07/kegg-subscription-model.html
The license is quite specific:
[?]
Whatever your opinion of KEGG's decision to change their data licensing model, I would strongly encourage you not to break the terms of their license.
I am not certain whether the new terms of use cover versions of KEGG from before the paywall came down. I do know the webservices & API are still free.
Like most of you I am not a lawyer, but from what I understood licenses only work after you add them. I understood that for open source that means that when you change a license that new license will only affect code you added after that time. I would expect that to mean that for content downloaded from KEGG before the change the new license does not have any effect. Unfortunately the old license was not very clear either.
Like most of you I am not a lawyer, but from what I understood licenses only work after you add them. I understood that for open source that means that when you change a license that new license will only affect code you added after that time. I would expect that to mean that for content downloaded from KEGG before the change the new license does not have any effect. Unfortunately the old license was not very clear.
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version 2.3.6
Thanks Egon, We will probably work on that for the coming months so it is not worth paying for a subscription (at least for now, may be we will do) Thanks
Egon wrote a nice blog about the KEGG developments and his ideas about likely future developments here: http://bit.ly/iWMUKi. He probably doesn't want to push it himself. So I thought I would just mention it.