lushacao / biolinkml

Biolink modeling language

Binder Link

biolinkml - biolink modeling language

Quickstart docs:

• Browse the model: https://biolink.github.io/biolinkml
  • class definition Class definitions
  • slot definition Class properties
  • type definition Data types
  • schema ddefinition Schema definition

Installation

> pipenv install biolinkml

Examples

FAQ

Why not use X as the modeling framework?

Why invent our own yaml and not use JSON-Schema, SQL, UML, ProtoBuf, OWL, ...

each of these is tied to a particular formalisms. E.g. JSON-Schema to trees. OWL to open world logic. There are various impedance mismatches in converting between these. The goal was to develop something simple and more general that is not tied to any one serialization format or set of assumptions.

There are other projects with similar goals, e.g https://github.com/common-workflow-language/schema_salad

It may be possible to align with these.

Why not use X as the datamodel

Here X may be bioschemas, some upper ontology (BioTop), UMLS metathesaurus, bio*, various other attempts to model all of biology in an object model.

Currently as far as we know there is no existing reference datamodel that is flexible enough to be used here.

Biolink Modeling Language

Type Definitions

typeof: domain: type definition range: type definition description: supertype

base: domain: type definition description: python base type that implements this type definition inherited: true

type uri: domain: type definition range: uri alias: uri description: the URI to be used for the type in semantic web mappings

repr: domain: type definition range: string description: the python representation of this type if different than the base type inherited: true

Slot Definitions