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https://biolink.github.io/biolink-model/

Schema and generated objects for biolink data model and upper ontology
https://biolink.github.io/biolink-model/

biolink datamodel gene-ontology json-api knowledge-graphs linkml monarchinitiative ncats ncats-translator neo4j obofoundry owl rdf specification standard yaml

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Schema and generated objects for biolink data model and upper ontology

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# Biolink Model



**Biolink Model:** https://w3id.org/biolink/biolink-model.yaml



Quickstart docs:



For a good overview of the biolink-model, [watch Chris Mungall's talk](https://www.youtube.com/watch?v=RE1hFm8lvJA&t=2s) at ICBO 2020.



- Browse the model: [https://biolink.github.io/biolink-model](https://biolink.github.io/biolink-model)

  - [named thing](https://biolink.github.io/biolink-model/NamedThing/)

  - [association](https://biolink.github.io/biolink-model/Association/)

  - [predicate](https://biolink.github.io/biolink-model/related_to/)



Refer to the following resources for a quick introduction to the Biolink Model:

- [Introduction to the Biolink Datamodel](https://www.slideshare.net/cmungall/introduction-to-the-biolink-datamodel)

- [Biolink Model - A community driven data model for life sciences](https://bit.ly/biolink-model-workshop-biocuration-2020) (Biocuration 2020)

    - Slides: https://bit.ly/biolink-model-workshop-biocuration-2020

    - Video: https://www.youtube.com/watch?v=RE1hFm8lvJA



See 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.



## Introduction



The purpose of the Biolink Model is to provide a high-level datamodel of

biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc),

their properties, relationships, and enumerate ways in which they can be associated.



The representation is independent of storage technology or metamodel (Solr documents, neo4j/property graphs,

RDF/OWL, JSON, CSVs, etc). Different mappings to each of these are provided.



The specification of the Biolink Model is a [single YAML file](biolink-model.yaml) built using [linkml](https://github.com/linkml).

The basic elements of the YAML are:



 - Class Definitions: definitions of upper level *classes* representing both 'named thing' and 'association'

 - 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



The model itself is being used in the following projects:

- [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator)

- [Monarch Initiative](https://monarchinitiative.org/)

- [KG-COVID-19](https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki)

- [KG Microbe](https://github.com/Knowledge-Graph-Hub/kg-microbe)

- [Illuminating the Druggable Genome](https://github.com/Knowledge-Graph-Hub/kg-idg)



## Organization



The main source of truth is [biolink-model.yaml](biolink-model.yaml). This is a YAML file that is intended to

be relatively simple to view and edit in its native form.



The yaml definition is currently used to derive:



  - [JSON Schema](https://github.com/biolink/biolink-model/blob/master/project/jsonschema/biolink_model.schema.json)

  - [Python dataclasses](https://github.com/biolink/biolink-model/blob/master/src/biolink_model/datamodel/model.py)

  - [ProtoBuf definitions](https://github.com/biolink/biolink-model/blob/master/project/protobuf/biolink_model.proto)

  - [GraphQL](https://github.com/biolink/biolink-model/blob/master/project/graphql/biolink_model.graphql)

  - [OWL](https://github.com/biolink/biolink-model/blob/master/project/owl/biolink_model.owl.ttl)

  - [RDF Shape Expressions](https://github.com/biolink/biolink-model/blob/master/project/shex/biolink_model.shex)

  - [JSON-LD context](https://github.com/biolink/biolink-model/blob/master/project/jsonld/biolink_model.context.jsonld)

  - [SHACL Shapes](https://github.com/biolink/biolink-model/blob/master/project/shacl/biolink_model.shacl.ttl)

  - [ShEx Shapes](https://github.com/biolink/biolink-model/blob/master/project/shex/biolink_model.shex)



## Citing Biolink Model

Unni 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).

Biolink 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