{"id":17099072,"url":"https://github.com/dhimmel/pathways","last_synced_at":"2025-03-23T18:12:53.596Z","repository":{"id":82487707,"uuid":"38133593","full_name":"dhimmel/pathways","owner":"dhimmel","description":"A compilation of pathway gene sets","archived":false,"fork":false,"pushed_at":"2016-04-02T21:49:21.000Z","size":2492,"stargazers_count":2,"open_issues_count":1,"forks_count":3,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-28T23:50:07.902Z","etag":null,"topics":["genes","hetionet","human","pathway-commons","pathway-interaction-database","pathways","reactome","rephetio","tsv","wikipathways"],"latest_commit_sha":null,"homepage":"https://doi.org/10.15363/thinklab.d72","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dhimmel.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2015-06-26T21:02:24.000Z","updated_at":"2019-11-09T03:51:07.000Z","dependencies_parsed_at":null,"dependency_job_id":"be9f0e38-ff30-4cc4-a8ca-1b3b69458ea2","html_url":"https://github.com/dhimmel/pathways","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fpathways","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fpathways/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fpathways/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fpathways/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dhimmel","download_url":"https://codeload.github.com/dhimmel/pathways/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245144972,"owners_count":20568056,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["genes","hetionet","human","pathway-commons","pathway-interaction-database","pathways","reactome","rephetio","tsv","wikipathways"],"created_at":"2024-10-14T15:08:55.371Z","updated_at":"2025-03-23T18:12:53.567Z","avatar_url":"https://github.com/dhimmel.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# A compilation of pathway gene sets\n\n[![DOI](https://zenodo.org/badge/14475/dhimmel/pathways.svg)](https://zenodo.org/badge/latestdoi/14475/dhimmel/pathways)\n\nThis 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/).\n\nOnly 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.\n\nExecute the [`merge-resources.ipynb`](merge-resources.ipynb) python notebook to rebuild the dataset.\n\n## License\n\nAll 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.\n\nReuse 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fpathways","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdhimmel%2Fpathways","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fpathways/lists"}