{"id":42755975,"url":"https://github.com/bio2bel/bio2bel","last_synced_at":"2026-01-29T20:13:54.443Z","repository":{"id":54196528,"uuid":"99800349","full_name":"bio2bel/bio2bel","owner":"bio2bel","description":"A Python framework for integrating biological databases and structured data sources in Biological Expression Language (BEL)","archived":false,"fork":false,"pushed_at":"2021-11-03T19:14:38.000Z","size":427,"stargazers_count":21,"open_issues_count":22,"forks_count":5,"subscribers_count":2,"default_branch":"master","last_synced_at":"2026-01-03T13:38:39.308Z","etag":null,"topics":["biological-expression-language","data-integration","ontologies"],"latest_commit_sha":null,"homepage":"http://bio2bel.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":"CHANGELOG.rst","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":"2017-08-09T11:21:36.000Z","updated_at":"2024-06-16T15:25:48.000Z","dependencies_parsed_at":"2022-08-13T09:00:22.722Z","dependency_job_id":null,"html_url":"https://github.com/bio2bel/bio2bel","commit_stats":null,"previous_names":[],"tags_count":30,"template":false,"template_full_name":null,"purl":"pkg:github/bio2bel/bio2bel","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Fbio2bel","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Fbio2bel/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Fbio2bel/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Fbio2bel/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bio2bel","download_url":"https://codeload.github.com/bio2bel/bio2bel/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio2bel%2Fbio2bel/sbom","scorecard":{"id":239062,"data":{"date":"2025-08-11","repo":{"name":"github.com/bio2bel/bio2bel","commit":"3604e406ffd93121c24b831cea245ea7490182f0"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":3.1,"checks":[{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Code-Review","score":0,"reason":"Found 2/30 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/tests.yml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yml:13: update your workflow using https://app.stepsecurity.io/secureworkflow/bio2bel/bio2bel/tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yml:15: update your workflow using https://app.stepsecurity.io/secureworkflow/bio2bel/bio2bel/tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yml:35: update your workflow using https://app.stepsecurity.io/secureworkflow/bio2bel/bio2bel/tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yml:37: update your workflow using https://app.stepsecurity.io/secureworkflow/bio2bel/bio2bel/tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yml:57: update your workflow using https://app.stepsecurity.io/secureworkflow/bio2bel/bio2bel/tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yml:59: update your workflow using https://app.stepsecurity.io/secureworkflow/bio2bel/bio2bel/tests.yml/master?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/tests.yml:20","Warn: pipCommand not pinned by hash: .github/workflows/tests.yml:42","Warn: pipCommand not pinned by hash: .github/workflows/tests.yml:64","Info:   0 out of   6 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   3 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: MIT License: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Signed-Releases","score":0,"reason":"Project has not signed or included provenance with any releases.","details":["Warn: release artifact v0.3.8 not signed: https://api.github.com/repos/bio2bel/bio2bel/releases/27336015","Warn: release artifact v0.3.7 not signed: https://api.github.com/repos/bio2bel/bio2bel/releases/26592975","Warn: release artifact v0.3.6 not signed: https://api.github.com/repos/bio2bel/bio2bel/releases/25093198","Warn: release artifact v0.3.8 does not have provenance: https://api.github.com/repos/bio2bel/bio2bel/releases/27336015","Warn: release artifact v0.3.7 does not have provenance: https://api.github.com/repos/bio2bel/bio2bel/releases/26592975","Warn: release artifact v0.3.6 does not have provenance: https://api.github.com/repos/bio2bel/bio2bel/releases/25093198"],"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 4 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}}]},"last_synced_at":"2025-08-17T06:18:50.929Z","repository_id":54196528,"created_at":"2025-08-17T06:18:50.929Z","updated_at":"2025-08-17T06:18:50.929Z"},"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","data-integration","ontologies"],"created_at":"2026-01-29T20:13:53.615Z","updated_at":"2026-01-29T20:13:54.427Z","avatar_url":"https://github.com/bio2bel.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Bio2BEL |build| |coverage| |docs| |zenodo|\n==========================================\nBio2BEL is a project aimed at bringing biological databases and other structured knowledge sources in a wide variety\nof schemata into the unified framework of the\n`Biological Expression Language \u003chttps://biological-expression-language.github.io/\u003e`_ [1]_.\n\nTwo important places to look:\n\n- `How to make a Bio2BEL Repository \u003chttp://bio2bel.readthedocs.io/en/latest/tutorial.html\u003e`_\n- `How to use the CLI \u003chttp://bio2bel.readthedocs.io/en/latest/cli.html\u003e`_\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\nDownload the latest stable code from `PyPI \u003chttps://pypi.org/project/bio2bel\u003e`_ with:\n\n.. code-block:: sh\n\n   $ python -m pip install bio2bel\n\nor get the latest from GitHub with:\n\n.. code-block:: sh\n\n   $ git clone https://github.com/bio2bel/bio2bel.git\n   $ cd bio2bel\n   $ python -m pip install -e .\n\nor check the `installation instructions \u003chttp://bio2bel.readthedocs.io/en/latest/#installation\u003e`_.\n\nCitation\n--------\nIf you find Bio2BEL useful for your work, please consider citing:\n\n.. [1] Hoyt, C. T., *et al.* (2019). `Integration of Structured Biological Data Sources using Biological Expression Language\n       \u003chttps://doi.org/10.1101/631812\u003e`_. *bioRxiv*, 631812.\n\n.. |build| image:: https://travis-ci.com/bio2bel/bio2bel.svg?branch=master\n    :target: https://travis-ci.com/bio2bel/bio2bel\n    :alt: Build Status\n\n.. |coverage| image:: https://codecov.io/gh/bio2bel/bio2bel/coverage.svg?branch=master\n    :target: https://codecov.io/gh/bio2bel/bio2bel?branch=master\n    :alt: Coverage Status\n\n.. |docs| image:: http://readthedocs.org/projects/bio2bel/badge/?version=latest\n    :target: http://bio2bel.readthedocs.io/en/latest/?badge=latest\n    :alt: Documentation Status\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel.svg\n    :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel.svg\n    :alt: Current version on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel.svg\n    :alt: MIT License\n\n.. |zenodo| image:: https://zenodo.org/badge/99800349.svg\n    :target: https://zenodo.org/badge/latestdoi/99800349\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio2bel%2Fbio2bel","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbio2bel%2Fbio2bel","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio2bel%2Fbio2bel/lists"}