{"id":13557390,"url":"https://github.com/biolink/biolink-model","last_synced_at":"2025-05-15T10:06:51.523Z","repository":{"id":38083673,"uuid":"112995625","full_name":"biolink/biolink-model","owner":"biolink","description":"Schema and generated objects for biolink data model and upper ontology","archived":false,"fork":false,"pushed_at":"2025-05-15T01:43:37.000Z","size":321384,"stargazers_count":196,"open_issues_count":150,"forks_count":78,"subscribers_count":24,"default_branch":"master","last_synced_at":"2025-05-15T02:33:44.659Z","etag":null,"topics":["biolink","datamodel","gene-ontology","json-api","knowledge-graphs","linkml","monarchinitiative","ncats","ncats-translator","neo4j","obofoundry","owl","rdf","specification","standard","yaml"],"latest_commit_sha":null,"homepage":"https://biolink.github.io/biolink-model/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biolink.png","metadata":{"files":{"readme":"README.md","changelog":"ChangeLog","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2017-12-04T04:45:18.000Z","updated_at":"2025-05-15T01:43:41.000Z","dependencies_parsed_at":"2022-07-26T10:32:51.155Z","dependency_job_id":"c8d11b7f-fb04-4261-a49b-8c44308fbd8d","html_url":"https://github.com/biolink/biolink-model","commit_stats":{"total_commits":2625,"total_committers":62,"mean_commits":42.33870967741935,"dds":0.5596190476190477,"last_synced_commit":"e2a5167acf1a9bea9574724e3a9c2b3086649ced"},"previous_names":[],"tags_count":105,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biolink%2Fbiolink-model","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biolink%2Fbiolink-model/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biolink%2Fbiolink-model/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biolink%2Fbiolink-model/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biolink","download_url":"https://codeload.github.com/biolink/biolink-model/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254264731,"owners_count":22041789,"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":["biolink","datamodel","gene-ontology","json-api","knowledge-graphs","linkml","monarchinitiative","ncats","ncats-translator","neo4j","obofoundry","owl","rdf","specification","standard","yaml"],"created_at":"2024-08-01T12:04:19.328Z","updated_at":"2025-05-15T10:06:46.507Z","avatar_url":"https://github.com/biolink.png","language":"Python","readme":"[![Biolink Model](https://img.shields.io/github/v/release/biolink/biolink-model?style=flat-square)](https://img.shields.io/github/v/release/biolink/biolink-model?style=flat-square)\n[![Python 3.9](https://img.shields.io/badge/python-3.9+-blue)](https://img.shields.io/badge/python-3.9+-blue)\n[![DOI](https://zenodo.org/badge/112995625.svg)](https://zenodo.org/badge/latestdoi/112995625)\n\n\n\u003cimg src=\"src/docs/images/biolink-logo.png\" width=\"20%\"\u003e\n\n# Biolink Model\n\n**Biolink Model:** https://w3id.org/biolink/biolink-model.yaml\n\nQuickstart docs:\n\nFor a good overview of the biolink-model, [watch Chris Mungall's talk](https://www.youtube.com/watch?v=RE1hFm8lvJA\u0026t=2s) at ICBO 2020.\n\n- Browse the model: [https://biolink.github.io/biolink-model](https://biolink.github.io/biolink-model)\n  - [named thing](https://biolink.github.io/biolink-model/NamedThing/)\n  - [association](https://biolink.github.io/biolink-model/Association/)\n  - [predicate](https://biolink.github.io/biolink-model/related_to/)\n\n\nRefer to the following resources for a quick introduction to the Biolink Model:\n- [Introduction to the Biolink Datamodel](https://www.slideshare.net/cmungall/introduction-to-the-biolink-datamodel)\n- [Biolink Model - A community driven data model for life sciences](https://bit.ly/biolink-model-workshop-biocuration-2020) (Biocuration 2020)\n    - Slides: https://bit.ly/biolink-model-workshop-biocuration-2020\n    - Video: https://www.youtube.com/watch?v=RE1hFm8lvJA\n\nSee also the Biolink Model Documentation for help in [understanding](https://biolink.github.io/biolink-model/), [curating](https://biolink.github.io/biolink-model/curating-the-model/), and [working](https://biolink.github.io/biolink-model/working-with-the-model/) with the model.\n\n\n## Introduction\n\nThe purpose of the Biolink Model is to provide a high-level datamodel of\nbiological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc),\ntheir properties, relationships, and enumerate ways in which they can be associated.\n\nThe representation is independent of storage technology or metamodel (Solr documents, neo4j/property graphs,\nRDF/OWL, JSON, CSVs, etc). Different mappings to each of these are provided.\n\nThe specification of the Biolink Model is a [single YAML file](biolink-model.yaml) built using [linkml](https://github.com/linkml).\nThe basic elements of the YAML are:\n\n - Class Definitions: definitions of upper level *classes* representing both 'named thing' and 'association'\n - Slot Definitions: definitions of *slots* (aka properties) that can be used to relate members of these classes to other classes or data types. Slots collectively refer to predicates, node properties, and edge properties\n\nThe model itself is being used in the following projects:\n- [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator)\n- [Monarch Initiative](https://monarchinitiative.org/)\n- [KG-COVID-19](https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki)\n- [KG Microbe](https://github.com/Knowledge-Graph-Hub/kg-microbe)\n- [Illuminating the Druggable Genome](https://github.com/Knowledge-Graph-Hub/kg-idg)\n\n\n## Organization\n\nThe main source of truth is [biolink-model.yaml](biolink-model.yaml). This is a YAML file that is intended to\nbe relatively simple to view and edit in its native form.\n\nThe yaml definition is currently used to derive:\n\n  - [JSON Schema](https://github.com/biolink/biolink-model/blob/master/project/jsonschema/biolink_model.schema.json)\n  - [Python dataclasses](https://github.com/biolink/biolink-model/blob/master/src/biolink_model/datamodel/model.py)\n  - [ProtoBuf definitions](https://github.com/biolink/biolink-model/blob/master/project/protobuf/biolink_model.proto)\n  - [GraphQL](https://github.com/biolink/biolink-model/blob/master/project/graphql/biolink_model.graphql)\n  - [OWL](https://github.com/biolink/biolink-model/blob/master/project/owl/biolink_model.owl.ttl)\n  - [RDF Shape Expressions](https://github.com/biolink/biolink-model/blob/master/project/shex/biolink_model.shex)\n  - [JSON-LD context](https://github.com/biolink/biolink-model/blob/master/project/jsonld/biolink_model.context.jsonld)\n  - [SHACL Shapes](https://github.com/biolink/biolink-model/blob/master/project/shacl/biolink_model.shacl.ttl)\n  - [ShEx Shapes](https://github.com/biolink/biolink-model/blob/master/project/shex/biolink_model.shex)\n\n\n## Citing Biolink Model\nUnni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ, The Biomedical Data Translator Consortium (2022).\nBiolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. Wiley; 2022 Jun 6; https://onlinelibrary.wiley.com/doi/10.1111/cts.13302 \n","funding_links":[],"categories":["Python","others"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiolink%2Fbiolink-model","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiolink%2Fbiolink-model","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiolink%2Fbiolink-model/lists"}