{"id":48879420,"url":"https://github.com/obophenotype/ncbitaxon","last_synced_at":"2026-04-16T02:04:52.881Z","repository":{"id":43718994,"uuid":"43841146","full_name":"obophenotype/ncbitaxon","owner":"obophenotype","description":"Build for NCBITaxon","archived":false,"fork":false,"pushed_at":"2025-12-14T13:43:56.000Z","size":5910,"stargazers_count":30,"open_issues_count":28,"forks_count":8,"subscribers_count":11,"default_branch":"master","last_synced_at":"2025-12-16T20:22:02.306Z","etag":null,"topics":["ncbi-taxonomy","obofoundry","ontology","taxonomy"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/obophenotype.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2015-10-07T19:51:40.000Z","updated_at":"2025-12-05T20:15:20.000Z","dependencies_parsed_at":"2023-12-12T16:50:11.294Z","dependency_job_id":"c3548ef0-792c-437b-844e-93aa2abe95c2","html_url":"https://github.com/obophenotype/ncbitaxon","commit_stats":null,"previous_names":[],"tags_count":26,"template":false,"template_full_name":null,"purl":"pkg:github/obophenotype/ncbitaxon","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fncbitaxon","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fncbitaxon/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fncbitaxon/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fncbitaxon/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/obophenotype","download_url":"https://codeload.github.com/obophenotype/ncbitaxon/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/obophenotype%2Fncbitaxon/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31867716,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-15T15:24:51.572Z","status":"online","status_checked_at":"2026-04-16T02:00:06.042Z","response_time":69,"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":["ncbi-taxonomy","obofoundry","ontology","taxonomy"],"created_at":"2026-04-16T02:04:36.319Z","updated_at":"2026-04-16T02:04:52.876Z","avatar_url":"https://github.com/obophenotype.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!--[![Build Status](https://travis-ci.org/obophenotype/ncbitaxon.svg?branch=master)](https://travis-ci.org/obophenotype/ncbitaxon)--\u003e\n[![DOI](https://zenodo.org/badge/13996/obophenotype/ncbitaxon.svg)](https://zenodo.org/badge/latestdoi/13996/obophenotype/ncbitaxon)\n\n\n# Build for NCBITaxon Ontology\n\nThe NCBITaxon ontology is an automatic translation of the [NCBI taxonomy database](http://www.ncbi.nlm.nih.gov/taxonomy) into obo/owl.\n\n# Details\n\nFor details on using the ontology, see the OBO page:\n\nhttp://obofoundry.org/ontology/ncbitaxon.html\n\nThis README details with technical aspects of the build\n\n## Subsets\n\nCurrently there is one subset, ncbitaxon/subsets/taxslim - for details, see [subsets/README.md](subsets/README.md)\n\n## Licensing\n\nThe license for this software is BSD3. See the [LICENSE](LICENSE) file.\n\nNote that the *content* of the ontology is not covered by this software license. The content comes from NCBI.\n\n## Citing the NCBITaxon ontology\n\nbefore citing, ask yourself what the artefact you wish to cite is:\n\n * The NCBI taxonomy **database**\n * The OBO/OWL rendering of the NCBI taxonomy database\n\nThe latter is a fairly trivial translation of the former. If you are in any way citing the *contents* then **you should cite the database**. Currently the most up to date reference is:\n\n * Federhen, Scott. **The NCBI taxonomy database.** *Nucleic acids research 40.D1 (2012): D136-D143.* [http://nar.oxfordjournals.org/content/40/D1/D136.short](http://nar.oxfordjournals.org/content/40/D1/D136.short)\n\nIf you specifically wish to cite the OBO/OWL translation, use the URL for this page\n\n## Editors guide for running releases\n\n### Using gh for releases\n\n1. `sh odk.sh bash` (to enter ODK container)\n   1. `make clean all -B`\n   2. `cd subsets`\n   3. `make all -B`\n   4. `cd ..`\n2. gh release create v2021-06-10\n3. gh release upload v2021-06-10  ncbitaxon.json ncbitaxon.json.gz ncbitaxon.obo ncbitaxon.obo.gz ncbitaxon.owl ncbitaxon.owl.gz subsets/taxslim-disjoint-over-in-taxon.owl subsets/taxslim.obo subsets/taxslim.owl subsets/taxslim.json\n\n### Using Monarch Jenkins\n\n1. Trigger the Jenkins Job on [ci.monarchinitiative.org](https://ci.monarchinitiative.org/view/pipelines/job/ncbi_taxon/)\n2. Download all generated files from the Jenkins job (except for env.txt), including the files in the [subset](https://ci.monarchinitiative.org/view/pipelines/job/ncbi_taxon/lastSuccessfulBuild/artifact/subsets/) directory.\n3. On GitHub, go to [Code](https://github.com/obophenotype/ncbitaxon), and click on [releases](https://github.com/obophenotype/ncbitaxon/releases).\n4. Click \"Draft a new release\". The tag is something like `v2020-02-28`. Provide a title and a meaningful description, and upload all the files downloaded from the Jenkins job above. Hit `Publish release`.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fobophenotype%2Fncbitaxon","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fobophenotype%2Fncbitaxon","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fobophenotype%2Fncbitaxon/lists"}