{"id":25843072,"url":"https://github.com/incatools/ontology-term-usage","last_synced_at":"2026-05-10T21:54:59.278Z","repository":{"id":66914569,"uuid":"426788616","full_name":"INCATools/ontology-term-usage","owner":"INCATools","description":"determines how an ontology term has been used","archived":false,"fork":false,"pushed_at":"2021-12-07T21:15:21.000Z","size":23,"stargazers_count":4,"open_issues_count":2,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-01T06:39:18.349Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://v61vbincq3.execute-api.us-east-1.amazonaws.com/staging/docs","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc0-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/INCATools.png","metadata":{"files":{"readme":"README.md","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-11-10T21:52:40.000Z","updated_at":"2024-03-18T15:13:21.000Z","dependencies_parsed_at":"2023-05-20T10:15:16.787Z","dependency_job_id":null,"html_url":"https://github.com/INCATools/ontology-term-usage","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/INCATools/ontology-term-usage","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/INCATools%2Fontology-term-usage","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/INCATools%2Fontology-term-usage/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/INCATools%2Fontology-term-usage/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/INCATools%2Fontology-term-usage/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/INCATools","download_url":"https://codeload.github.com/INCATools/ontology-term-usage/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/INCATools%2Fontology-term-usage/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286079811,"owners_count":27282121,"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","status":"online","status_checked_at":"2025-11-25T02:00:05.816Z","response_time":54,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2025-03-01T06:38:01.890Z","updated_at":"2025-11-25T04:09:25.095Z","avatar_url":"https://github.com/INCATools.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ontology_term_usage\n\nPython wrapper to different clients to determine how a particular term is used.\n\nOne use case is for ontology developers who want to obsolete a term but need to know how it is used.\n\nFor example, if GO wanted to obsolete \"apoptosis\", GO editors could query for GO:0006915 and see\nwhich ontologies use it.\n\nFor more context see:\n\n - [obo#1630](https://github.com/OBOFoundry/OBOFoundry.github.io/pull/1630)\n\nDemo server (NOT STABLE):\n\n* https://v61vbincq3.execute-api.us-east-1.amazonaws.com/staging/docs\n* https://v61vbincq3.execute-api.us-east-1.amazonaws.com/staging/usage/GO:0006915\n\n\nServices wrapped:\n\n* ontobee\n* ubergraph (subset of OBO)\n* go (for annotations and go-cams)\n* uniprot sparql endpoint (for annotations)\n\nPlanned:\n\n* bioportal\n\nFor more details, see inline docs and tests\n\nNo CLI yet. We will implement using click\n\nDemo:\n\n```bash\npoetry run pytest -s\n```\n\n## Caveats\n\nIt is actually quite hard to determine whether a term is used. Many ontologies do not put their \"complete\" versions forward as the main\nURL that is loaded into services like OLS, Ontobee, Bioportal,\nin particular, the inter-ontology axioms this tool queries may be missing.\n\nUbergraph gets around this partially by having its own configuration\nthat may load additional axioms - but ubergraph may not have all of obo\n\n## API\n\nTo run the API locally:\n\n```bash\nmake app\n```\n\n * Docs: http://127.0.0.1:8000/docs\n * Find usages: http://127.0.0.1:8000/usage/GO:0007588\n\nDeployment on AWS via serverless:\n\nFollow \n\nhttps://adem.sh/blog/tutorial-fastapi-aws-lambda-serverless\n\nfor serverless/lambda deployment\n\nType\n\n```bash\nmake deploy\n```\n\n## Future plans\n\n - It may be better to wrap this into a generic obolibrary python package\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fincatools%2Fontology-term-usage","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fincatools%2Fontology-term-usage","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fincatools%2Fontology-term-usage/lists"}