Skip to main content

'A high level datamodel of biological entities and associations'

Project description

Biolink Model Python 3.7 Build Status DOI Join the chat at Regenerate Biolink Model Artifacts Deploy Documentation

Biolink Model

Quickstart docs:

For a good overview of the biolink-model, watch Chris Mungall's talk at ICBO 2020.

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

See also Biolink Model Guidelines for help understanding, curating, and working with the model.


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 built using 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:


The main source of truth is 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:

Make and build instructions

Prerequisites: Python 3.7+ and pipenv

To install pipenv,

pip3 install pipenv

To install the project,

make install

To regenerate artifacts from the Biolink Model YAML,


Note: the Makefile requires the following dependencies to be installed:



Generally install using

pip3 install jsonschema



If you are on a Mac, it can be installed using brew:

brew install jsonschema2pojo

For other OS environments, download the latest release then extract it into your execution path. eg

tar -xvzf jsonschema2pojo-1.0.2.tar.gz
export PATH=$PATH:`pwd`/jsonschema2pojo-1.0.2/bin


See GraphViz site for installation in your operating system.

to regenerate semmeddb exclusion list:

How do I use Biolink Model YAML programmatically?

For operations such as CURIE lookup, finding class by synonyms, get parents, get ancestors, etc. please make use of biolink-model-toolkit. It provides convenience methods for traversing Biolink Model.

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;

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

biolink-model-3.5.4.tar.gz (128.9 kB view hashes)

Uploaded source

Built Distribution

biolink_model-3.5.4-py3-none-any.whl (125.3 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page