{"id":15555457,"url":"https://github.com/sckott/gbif-backbone-sql","last_synced_at":"2025-07-04T05:09:13.394Z","repository":{"id":140973481,"uuid":"65834719","full_name":"sckott/gbif-backbone-sql","owner":"sckott","description":"GBIF Darwin Core taxonomic backbone to SQLite","archived":false,"fork":false,"pushed_at":"2024-04-10T20:26:36.000Z","size":42,"stargazers_count":4,"open_issues_count":2,"forks_count":2,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-06-28T10:14:46.056Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Ruby","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/sckott.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,"zenodo":null}},"created_at":"2016-08-16T16:11:02.000Z","updated_at":"2023-02-01T17:49:28.000Z","dependencies_parsed_at":"2025-04-23T19:58:58.241Z","dependency_job_id":null,"html_url":"https://github.com/sckott/gbif-backbone-sql","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/sckott/gbif-backbone-sql","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fgbif-backbone-sql","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fgbif-backbone-sql/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fgbif-backbone-sql/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fgbif-backbone-sql/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sckott","download_url":"https://codeload.github.com/sckott/gbif-backbone-sql/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fgbif-backbone-sql/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263450010,"owners_count":23468154,"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":[],"created_at":"2024-10-02T15:09:24.805Z","updated_at":"2025-07-04T05:09:13.386Z","avatar_url":"https://github.com/sckott.png","language":"Ruby","funding_links":[],"categories":[],"sub_categories":[],"readme":"GBIF taxonomy as SQLite\n=======================\n\n![build-sqlite](https://github.com/ropenscilabs/gbif-backbone-sql/workflows/build-sqlite/badge.svg)\n\nGBIF backbone taxonomy as SQLite DB\n\n__Note:__ The backbone as sqlite is up at \u003chttps://taxize-dbs.s3-us-west-2.amazonaws.com/gbif.zip\u003e -\nYou can continue reading if you want to know the details of how it got there, and/or if you want to\nrun this darwin-core to sql conversion yourself.\n\n## how we do\n\n* download GBIF backbone taxonomy from \u003chttp://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c\u003e as Darwin Core Archive\n* unzip\n* create sqlite DB `gbif.sqlite`\n* import `taxon.txt` into sqlite DB\n* zip up sqlite file\n* upload `gbif.zip` to Amazon S3\n\nAll above is run once per day on [Github Actions](https://github.com/ropenscilabs/gbif-backbone-sql/actions?query=workflow%3Abuild-sqlite)\n\n## Usage\n\ndownload\n\n```\ngit clone https://github.com/ropensci/gbif-backbone-sql.git\ncd gbif-backbone-sql\n```\n\nbundle it\n\n```\nbundle install\n```\n\n```\nrake --tasks\n```\n\n```\nrake clean  # clean files\nrake fetch  # get and unzip backbone\nrake hello  # say hello\nrake s3     # upload database to s3\nrake spine  # get backbone, convert to sql, upload to amazon s3\nrake sql    # create sql database\nrake zip    # create zip file\n```\n\n`rake spine` does all the things\n\nOr, you can do each separately with `rake fetch` then `rake sql`, then `rake zip`, then `rake s3`\n\n### Env vars\n\n`rake s3` requires AWS keys. If you want to upload to AWS, make sure you have env vars\nwith the names `AWS_S3_WRITE_ACCESS_KEY` and `AWS_S3_WRITE_SECRET_KEY`\n\n## Backbone as sqlite\n\n\u003chttps://taxize-dbs.s3-us-west-2.amazonaws.com/gbif.zip\u003e\n\n## info\n\n* GBIF backbone taxonomy citation:\n\n\u003e GBIF Secretariat: GBIF Backbone Taxonomy. doi:10.15468/39omei\nAccessed via http://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c on 2016-08-16\n\n* GBIF backbone taxonomy license: `CC BY 3.0`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsckott%2Fgbif-backbone-sql","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsckott%2Fgbif-backbone-sql","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsckott%2Fgbif-backbone-sql/lists"}