LinkML Common Modeling Elements and Types (COMET)
https://linkml.github.io/linkml-common
The schema.org project is a great resource for high level annotation of web pages and other resources. LinkML-Common differs from schema.org in a number of ways
- Opinionated
- schema.org is great for annotating data with minimum fuss
- LinkML-Common enforces a more constrained data model, and is a validation-first framework
- Focused on Science, Technology, Engineering, Mathematics, and Scholarly Communication
- schema.org has excellent broad coverage of a number of domains
- LinkML-Common has a focus on science and adjacent domains. There is more emphasis on modeling investigations, and adhering to ontologies such as the Ontology for Biomedical Investigations
LinkML-Common has a broader remit than healthcare or clinical research data models. However, it is intended to give broad coverage in these domains, and to be extensible. We aim to provide rigorous computable transformations between COMET and these models
Biolink is a Knowledge Graph model that emphasizes shared knowledge entities such as genes, diseases, drugs. These are largely not modeled to any great extent in COMET, and the idea is that these models can be combined.
Yes! If you don't like our modeling, the idea is to use LinkML-Transformer to profile, extend, and adapt the modeling elements here.
Note that like COMET, LinkML-Transformer is not yet mature and is under active development.
We also provide Pydantic, OWL, JSON-Schema, and many other representations.
- examples/ - example data
- project/ - project files (do not edit these)
- src/ - source files (edit these)
- tests/ - Python tests
make all: make everythingmake deploy: deploys site
This project was made with linkml-project-cookiecutter.