{"id":42755932,"url":"https://github.com/bio2bel/reactome","last_synced_at":"2026-01-29T20:13:48.846Z","repository":{"id":56248903,"uuid":"103138323","full_name":"bio2bel/reactome","owner":"bio2bel","description":"Integration of pathway-related information from Reactome in BEL","archived":false,"fork":false,"pushed_at":"2020-11-18T17:13:55.000Z","size":1274,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2026-01-03T13:43:56.625Z","etag":null,"topics":["biological-expression-language","networks-biology","pathways","reactome","system-biology"],"latest_commit_sha":null,"homepage":"http://bio2bel-reactome.rtfd.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bio2bel.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-09-11T13:19:33.000Z","updated_at":"2023-03-05T06:44:33.000Z","dependencies_parsed_at":"2022-08-15T15:21:01.980Z","dependency_job_id":null,"html_url":"https://github.com/bio2bel/reactome","commit_stats":null,"previous_names":[],"tags_count":10,"template":false,"template_full_name":null,"purl":"pkg:github/bio2bel/reactome","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Freactome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Freactome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Freactome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Freactome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bio2bel","download_url":"https://codeload.github.com/bio2bel/reactome/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Freactome/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28884284,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-29T19:55:09.949Z","status":"ssl_error","status_checked_at":"2026-01-29T19:55:08.490Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["biological-expression-language","networks-biology","pathways","reactome","system-biology"],"created_at":"2026-01-29T20:13:48.256Z","updated_at":"2026-01-29T20:13:48.839Z","avatar_url":"https://github.com/bio2bel.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Bio2BEL Reactome |build| |coverage| |documentation| |zenodo|\n============================================================\nThis package handles the nomenclature and membership of chemicals/proteins in Reactome pathways.\nIt is integrated with the `ComPath environment \u003chttps://github.com/ComPath\u003e`_ for pathway database\ncomparison.\n\nIf you find this package useful, please consider citing [domingofernandez2018]_:\n\n.. [domingofernandez2018] Domingo-Fernandez, D., *et al* (2018). `ComPath: an ecosystem for exploring, analyzing,\n   and curating mappings across pathway databases \u003chttps://doi.org/10.1038/s41540-018-0078-8\u003e`_.\n   *Npj Systems Biology and Applications*, __5__(1), 3.\n\n**Warning** This package creates ``partOf`` relationships in BEL, but does not convert Reactome mechanistic\nrelationships to BEL. That functionality is implemented in the\n`PathMe project \u003chttps://github.com/pathwaymerger/pathme\u003e`_.\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\n``bio2bel_reactome`` can be installed easily from `PyPI \u003chttps://pypi.python.org/pypi/bio2bel_reactome\u003e`_ with the\nfollowing code in your favorite terminal:\n\n.. code-block:: sh\n\n    $ pip install bio2bel_reactome\n\nor from the latest code on `GitHub \u003chttps://github.com/bio2bel/reactome\u003e`_ in development mode with:\n\n.. code-block:: sh\n\n    $ git clone https://github.com/bio2bel/reactome.git\n    $ cd reactome\n    $ pip install -e .\n\nSetup\n-----\nReactome can be downloaded and populated from either the Python REPL or the automatically installed command line\nutility.\n\nPython REPL\n~~~~~~~~~~~\n.. code-block:: python\n\n    \u003e\u003e\u003e import bio2bel_reactome\n    \u003e\u003e\u003e reactome_manager = bio2bel_reactome.Manager()\n    \u003e\u003e\u003e reactome_manager.populate()\n\nCommand Line Utility\n~~~~~~~~~~~~~~~~~~~~\n.. code-block:: bash\n\n    bio2bel_reactome populate\n\nOther Command Line Utilities\n----------------------------\n- Run an admin site for simple querying and exploration :code:`bio2bel_reactome web` (http://localhost:5000/admin/)\n- Export gene sets for programmatic use :code:`bio2bel_reactome export`\n\nCitation\n--------\n- Fabregat, Antonio et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 44.Database issue (2016):\n  D481–D487. PMC. Web. 6 Oct. 2017.\n- Croft, David et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 42.Database issue (2014): D472–D477.\n  PMC. Web. 6 Oct. 2017.\n\n.. |build| image:: https://travis-ci.com/bio2bel/reactome.svg?branch=master\n    :target: https://travis-ci.com/bio2bel/reactome\n    :alt: Build Status\n\n.. |coverage| image:: https://codecov.io/gh/bio2bel/reactome/coverage.svg?branch=master\n    :target: https://codecov.io/gh/bio2bel/reactome?branch=master\n    :alt: Coverage Status\n\n.. |documentation| image:: http://readthedocs.org/projects/bio2bel-interpro/badge/?version=latest\n    :target: http://bio2bel.readthedocs.io/projects/reactome/en/latest/?badge=latest\n    :alt: Documentation Status\n\n.. |climate| image:: https://codeclimate.com/github/bio2bel/reactome/badges/gpa.svg\n    :target: https://codeclimate.com/github/bio2bel/reactome\n    :alt: Code Climate\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_reactome.svg\n    :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_reactome.svg\n    :alt: Current version on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_reactome.svg\n    :alt: MIT License\n\n.. |zenodo| image:: https://zenodo.org/badge/103138323.svg\n    :target: https://zenodo.org/badge/latestdoi/103138323\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio2bel%2Freactome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbio2bel%2Freactome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio2bel%2Freactome/lists"}