{"id":19388838,"url":"https://github.com/linkml/cmdr","last_synced_at":"2025-08-03T23:39:24.535Z","repository":{"id":129702783,"uuid":"610477243","full_name":"linkml/cmdr","owner":"linkml","description":null,"archived":false,"fork":false,"pushed_at":"2025-01-07T21:38:16.000Z","size":1428,"stargazers_count":6,"open_issues_count":4,"forks_count":0,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-07-11T12:55:45.370Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://linkml.io/cmdr/","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/linkml.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","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":"2023-03-06T21:14:18.000Z","updated_at":"2024-12-11T19:10:44.000Z","dependencies_parsed_at":"2025-01-07T22:26:48.938Z","dependency_job_id":"11c9fb0a-d5e4-4213-bb40-399f6e1f3c21","html_url":"https://github.com/linkml/cmdr","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/linkml/cmdr","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linkml%2Fcmdr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linkml%2Fcmdr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linkml%2Fcmdr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linkml%2Fcmdr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/linkml","download_url":"https://codeload.github.com/linkml/cmdr/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linkml%2Fcmdr/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268629566,"owners_count":24281170,"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":"2025-08-03T02:00:12.545Z","response_time":2577,"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":"2024-11-10T10:13:51.150Z","updated_at":"2025-08-03T23:39:24.509Z","avatar_url":"https://github.com/linkml.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CMDR\n\nCMDR (pronunciation: “com-mo-dore” or sometimes “com-man-der”), the Core Model for Data Research, is a LinkML schema/data model for the collection of biological sample data, and its analysis.\n\nThe purpose of this schema is to act as a *base* schema for other LinkML schemas/data models to bootstrap for their specific use case.\n\nThe CMDR data model was inspired by the LinkML [data model](https://github.com/include-dcc/include_linkml) for the INCLUDE project.\n\n## Project Setup\n\n1. Clone *cmdr* project repository\n\n```\n$ git clone https://github.com/linkml/cmdr.git\n```\n\n2. Create virtual environment and install project dependencies\n```\n$ make install\n```\n\n3. Create downstream schema artifacts, run unit tests, and also validate examples/instance data against schema\n```\n$ make test\n```\n\n4. LinkML transformer mapping between source and target schemas on a class\n```\n$ make test_transform\n```\n\n## Website\n\n* [https://linkml.github.io/cmdr](https://linkml.github.io/cmdr)\n\n## Repository Structure\n\n* [examples/](examples/) - example data\n* [project/](project/) - project files (do not edit these)\n* [src/](src/) - source files (edit these)\n    * [cmdr](src/cmdr)\n        * [schema](src/cmdr/schema) -- LinkML schema (edit this)\n* [datamodel](src/cmdr/datamodel) -- Generated python datamodel\n* [tests](tests/) - python tests\n\nWe've added\nsome [HTML visualizastions of data instances](https://htmlpreview.github.io/?https://github.com/linkml/cmdr/blob/master/examples/Container-material-entities.html)!\n\n## Developer Documentation\n\n\u003cdetails\u003e\nUse the `make` command to generate project artefacts:\n\n- `make all`: make everything\n- `make deploy`: deploys site\n\n\u003c/details\u003e\n\n## Credits\n\nthis project was made with [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinkml%2Fcmdr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinkml%2Fcmdr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinkml%2Fcmdr/lists"}