linkml-aop

A LinkML schema for Adverse Outcome Pathways, with EMOD - Evidence Model - expansions.

Website

Coming soon...

Repository Structure

• examples/ - example data
• inputs/ - raw input files (e.g. schemauto-generated YAML)
• project/ - project files (do not edit these)
• src/ - source files (edit these)
  • linkml_aop
    • schema -- LinkML schemas
    • datamodel -- generated Python datamodel
    • scripts -- curation and utility scripts
    • curation -- domain constants, definitions, and enums used by scripts
• tests/ - Python tests

Curation Workflow

The schemauto generated schema, inputs/emod_3-26-26_linkml.yml, is based on the AOP-Wiki EMOD 3.0 application MySQL DB schema that is under development for prototyping purposes. It serves as the basis for the src/linkml_aop/schema/aop_emod_linkml.yaml, that was generated from the schemauto file by applying the transformations in src/linkml_aop/scripts/curate_emod_linkml.py.

To add or revise schema definitions and enumerations:

Optional first step - generate a new EMOD input schema by pointing to the EMOD 3.0 MySQL instance (permissions needed)

1. Edit src/linkml_aop/curation/aop_definitions_and_enums.py with new or updated definitions/enums.

2. Run the curation script to regenerate the schema:

   uv run python -m linkml_aop.scripts.curate_emod_linkml inputs/<input_file>.yml src/linkml_aop/schema/aop_emod_linkml.yaml

3. Review the changes in src/linkml_aop/schema/aop_emod_linkml.yaml.

Developer Documentation

Commands

This LinkML project uses the command runner just which is a better choice than make on Windows. To generate project artefacts, run:

• just --list: list all pre-defined tasks
• just all: make everything
• just deploy: deploys site

Credits

This project was started from: linkml-project-cookiecutter.

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