https://github.com/dhimmel/pathways
A compilation of pathway gene sets
https://github.com/dhimmel/pathways
genes hetionet human pathway-commons pathway-interaction-database pathways reactome rephetio tsv wikipathways
Last synced: about 1 year ago
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A compilation of pathway gene sets
- Host: GitHub
- URL: https://github.com/dhimmel/pathways
- Owner: dhimmel
- Created: 2015-06-26T21:02:24.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2016-04-02T21:49:21.000Z (about 10 years ago)
- Last Synced: 2025-01-28T23:50:07.902Z (over 1 year ago)
- Topics: genes, hetionet, human, pathway-commons, pathway-interaction-database, pathways, reactome, rephetio, tsv, wikipathways
- Language: Jupyter Notebook
- Homepage: https://doi.org/10.15363/thinklab.d72
- Size: 2.38 MB
- Stars: 2
- Watchers: 3
- Forks: 3
- Open Issues: 1
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Metadata Files:
- Readme: README.md
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README
# A compilation of pathway gene sets
[](https://zenodo.org/badge/latestdoi/14475/dhimmel/pathways)
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 (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.