{"id":13318248,"url":"https://github.com/cmungall/obo-metadata","last_synced_at":"2025-06-10T12:38:57.602Z","repository":{"id":66914416,"uuid":"480429890","full_name":"cmungall/obo-metadata","owner":"cmungall","description":"EXPERIMENTAL obo metadata repo","archived":false,"fork":false,"pushed_at":"2022-04-12T15:29:20.000Z","size":1255,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-04T23:13:50.861Z","etag":null,"topics":["linkml","metadata","obofoundry"],"latest_commit_sha":null,"homepage":"https://cmungall.github.io/obo-metadata/","language":"Jupyter Notebook","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/cmungall.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}},"created_at":"2022-04-11T15:03:02.000Z","updated_at":"2022-04-11T19:21:44.000Z","dependencies_parsed_at":"2023-05-13T23:00:12.892Z","dependency_job_id":null,"html_url":"https://github.com/cmungall/obo-metadata","commit_stats":{"total_commits":10,"total_committers":1,"mean_commits":10.0,"dds":0.0,"last_synced_commit":"0aa2af7adc1c17ffa5add0192d06c31f0f7d3897"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fobo-metadata","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fobo-metadata/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fobo-metadata/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fobo-metadata/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmungall","download_url":"https://codeload.github.com/cmungall/obo-metadata/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fobo-metadata/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259077732,"owners_count":22801991,"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":["linkml","metadata","obofoundry"],"created_at":"2024-07-29T18:29:51.791Z","updated_at":"2025-06-10T12:38:57.561Z","avatar_url":"https://github.com/cmungall.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# obo-metadata\n\nThis is a demonstration project on how to create a metadata SCHEMA for OBO that can be\nused for constraint checking.\n\nThe intended workflow is:\n\n * The core properties are [maintained in a google sheet](https://docs.google.com/spreadsheets/d/1YU_58PB-TaxlvJ5oIneUig8kB8CbmHyR30hUqfD0ZtE/edit) and synced with COGs\n * The sheet is compiled to different products including:\n     1. a SCHEMA that can be used for VALIDATION\n     2. OWL AnnotationProperties (omo.owl) that can be IMPORTED in different ontologies\n\n\nCurrently, the format of the schema is LinkML yaml. This can be used to generate different\nvaldation schemas\n\n - SHACL\n - JSON-Schema\n - LinkML itself\n\n\nAs a DEMO FLAGSHIP APPLICATION the\n[OAK](https://incatools.github.io/ontology-access-kit/) library and\ncommand line tool implements an efficient OMO checker that takes as input:\n\n 1. the OMO LinkML schema\n 2. a SQLite version of an ontology created using rdftab\n\nAnd produces a report\n\n## Schema\n\n- [google sheets](https://docs.google.com/spreadsheets/d/1YU_58PB-TaxlvJ5oIneUig8kB8CbmHyR30hUqfD0ZtE/edit) (partial)\n- [obo-metadata.yaml](src/linkml/obo-metadata.yaml)\n\n## Examples\n\nSee [examples](examples)\n\n## OBO Report\n\nPRELIMINARY!!!\n\n- [sheet](https://docs.google.com/spreadsheets/d/1Er8xYeKMvKKo-MGQf7w9jUgCWTOZwprDq9Td2Nuu4Po/edit#gid=488211236)\n- analysis [notebooks](notebooks)\n\n## Manifest\n\n * Generated docs: [cmungall.github.io/obo-metadata/](https://cmungall.github.io/obo-metadata/)\n     * Example property: https://cmungall.github.io/obo-metadata/definition/\n     * Example metaclass: https://cmungall.github.io/obo-metadata/Class/\n * Source: [src/linkml/](src/linkml/)\n * Analysis (v preliminary)\n     * [notebooks](notebooks)\n * Derived files: [project](https://github.com/cmungall/obo-metadata/tree/main/project)\n     * Schemasheets: TODO: sync w COGS [project/sheets](project/sheets)\n     * JSON-Schema [project/json-schema](project/jsonschema)\n     * etc\n\n\n## How to validate\n\nYou will need to:\n\n 1. Install OAK\n 2. Obtain the SQLite version of the ontology(ies) to be validated\n 3. Run on command line\n\nSee:\n\n * [howtos/validate-an-obo-ontology](https://incatools.github.io/ontology-access-kit/howtos/validate-an-obo-ontology.html)\n * In: [OAK](https://github.com/INCATools/ontology-access-kit/)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmungall%2Fobo-metadata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmungall%2Fobo-metadata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmungall%2Fobo-metadata/lists"}