biolink-model


Namebiolink-model JSON
Version 4.2.5 PyPI version JSON
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SummaryThe Biolink Model is a high-level data model designed to standardize types and relationships in biological knowledgebases.
upload_time2024-11-11 20:48:43
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docs_urlNone
authorChris Mungall
requires_python<4.0,>=3.9
licenseMIT
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            [![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)
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<img src="src/docs/images/biolink-logo.png" width="20%">

# 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

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    "description": "[![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<img src=\"src/docs/images/biolink-logo.png\" width=\"20%\">\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&t=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\n",
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Chris Mungall
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