Replace MSigDB Pathways with Reactome and PID

Reactome and PID are retrieved via Pathway Commons.

MSigDB was removed due to potential licensing issues. See
https://doi.org/10.15363/thinklab.d108

README.md

@@ -1,9 +1,15 @@
 # A compilation of pathway gene sets
 
-[![DOI 10.5281/zenodo.45588](https://zenodo.org/badge/doi/10.5281/zenodo.45588.svg)](https://doi.org/10.5281/zenodo.45588)
+[![DOI](https://zenodo.org/badge/14475/dhimmel/pathways.svg)](https://zenodo.org/badge/latestdoi/14475/dhimmel/pathways)
 
-This repository compiles pathway gene sets from [WikiPathways](http://www.wikipathways.org/index.php/WikiPathways) and [MSigDB](http://www.broadinstitute.org/gsea/msigdb/collection_details.jsp) into an easy-to-parse tsv ([`data/pathways.tsv`](data/pathways.tsv)).
+This repository compiles pathway gene sets for inclusion into the Rephetio hetnet. Pathways are compiled from [WikiPathways](http://www.wikipathways.org/index.php/WikiPathways) and [Pathway Commons](http://www.pathwaycommons.org/pc2/) into a user-friendly TSV ([`data/pathways.tsv`](data/pathways.tsv)). The resources extracted from Pathway Commons are the [Pathway Interaction Database](https://pid.nci.nih.gov/) (PID) and [Reactome](http://www.reactome.org/).
 
-Only protein-coding human genes (Entrez GeneIDs) are included. See the corresponding [Thinklab discussion](https://doi.org/10.15363/thinklab.d72) for more information.
+Only protein-coding human genes (as Entrez Gene IDs) are included. See the corresponding [Thinklab discussion](https://doi.org/10.15363/thinklab.d72) for more information.
 
 Execute the [`merge-resources.ipynb`](merge-resources.ipynb) python notebook to rebuild the dataset.
+
+## License
+
+All original content in this repository is released as [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/) (public domain). WikiPathways data is [licensed](http://www.wikipathways.org/index.php/WikiPathways:License_Terms) as [CC BY 3.0](http://creativecommons.org/licenses/by/3.0/). Reactome data is licensed as [CC BY 4.0](http://creativecommons.org/licenses/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.