biolinkml is a general purpose modeling language following object-oriented and ontological principles. Models are authored in YAML. A variety of artefacts can be generated from the model, including ShEx, JSON-Schema, OWL, Python dataclasses, UML diagrams, Markdown pages for deployment in a GitHub pages site, and more.
biolinkml is used for development of the BioLink Model, but the framework is general purpose and can be used for any kind of modeling.
For an example, see the Jupyter notebook example
> pipenv install biolinkml
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.
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.
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