AGENTS.md

AGENTS.md for biolink-model

Schema and generated objects for biolink data model and upper ontology

Repo management

This repo uses uv for managing dependencies. Never use commands like pip to add or manage dependencies. uv run is the best way to run things, unless you are using justfile or makefile target

mkdocs is used for documentation.## This is a LinkML Schema repository

Layout:

• src/biolink_model/schema/biolink_model.yaml - LinkML source schema (edit this)
• project - derived files (do not edit these directly, they are derived from the LinkML)
• src/docs - source markdown for documentation
• docs - derived docs - do not edit these directly
• src/data/examples/{valid,invalid} - example data files
  • always include positive examples of each class in the valid subfolder
  • include negative examples for unit tests and to help illustrate pitfalls
  • format is ClassName-{SOMENAME}.yaml
• examples - derived examples. Do not edit these directly

Building and testing:

• just --list to see all commands
• just gen-project to generate project files
• just test to test schema and pos/neg examples
• just lint analogous to ruff for python

These are wrappers on top of existing linkml commands such as gen-project, linkml-convert, linkml-run-examples. You can run the underlying commands (with uv run ...) but in general justfile targets should be favored.

Best practice:

• For full documentation, see https://linkml.io/linkml/
• For schemas with polymorphism, consider using field type marked as a type_designator: true
• Include meaningful descriptions of each element
• always edit biolink-model.yaml in the root of the project.
• map to standards where appropriate (e.g. dcterms)
• Never guess OBO term IDs. Always use the OLS MCP to look for relevant ontology terms
• be proactive in using due diligence to do deep research on the domain, and look at existing standards