Pathway databases for machine learning

Question

[melissachua90]

I want to perform CNN/ML-based pathway analysis on tumor multi-omics data. I'm looking for an ideal pathway database that's written in Python.

I've explored several pathway databases, including KEGG, Reactome, mygene, and WIKIPathways. I've also considered combining various sources but I don't know what's the best modus operandi.

Any thoughts?

[Ram]

Why did you delete this post, especially when it has an answer?

Answer 1

[BioInfoBeginner]

You might find this review by Nguyen et al. if you are unsure about various aspects of your own pathway analysis: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1790-4#change-history

Failing that, I think you could be more clear about what you are asking. There really is no 'best modus operandi', all of those pathway databases have strengths and weaknesses depending on their application.