This repository compiles pathway gene sets for inclusion into the Rephetio hetnet. Pathways are compiled from WikiPathways and Pathway Commons into a user-friendly TSV (data/pathways.tsv). The resources extracted from Pathway Commons are the Pathway Interaction Database (PID) and Reactome.

Only protein-coding human genes (as Entrez Gene IDs) are included. See the corresponding Thinklab discussion for more information.

Execute the merge-resources.ipynb python notebook to rebuild the dataset.

All original content in this repository is released as CC0 1.0 (public domain). WikiPathways data is licensed as CC BY 3.0. Reactome data is licensed as CC BY 4.0. PID data is in the public domain.

Reuse of the Pathway Commons download ([download/Pathway Commons.7.All.GSEA.hgnc.gmt](download/Pathway Commons.7.All.GSEA.hgnc.gmt)) is subject to the license terms of each contributing database.