WikiPathways integration

[Tristan Figueroa-Reid]

In some of your earlier database updates, there was an indication that WikiPathways was a data source for BioPAX files, though it doesn't appear to exist anymore.

Is this due to a data format transition on WikiPathways's side, or is there another reason?

[Gary Bader]

Hi Tristan,
I seem to remember that the wikipathways biopax files were not complete enough, especially regarding the number of interactions. You can still find the old data containing wikipathways on our download site e.g. https://download.baderlab.org/PathwayCommons/PC2/v9/

Best,
Gary

On 7 Jan 2026, at 10:56, Tristan Figueroa-Reid wrote:

In some of your earlier database updates, there was an indication that WikiPathways was a data source for BioPAX files, though it doesn't appear to exist anymore.

Is this due to a data format transition on WikiPathways's side, or is there another reason? --
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