BioSim Schema Documentation

BioSim Schema provides a LinkML-based, reusable metadata model for biomolecular simulation data, with tooling to validate terms and generate downstream artefacts for BioSimDR workflows. These docs are for schema users and contributors: they explain installation, day-to-day usage, contribution workflows, generation/CI behavior, and where to find the schema reference.

Contents:

• Installation
  • Requirements
  • Install from source
  • Optional dependency groups
• Usage
  • Common generation workflow
  • Command reference
  • Validate example data
• Contributing to BioSim Schema
  • What is LinkML
  • How this Schema is Designed
  • How to Propose Changes
• Development Workflow
  • Set up Development Environment
  • Simple Example: Add a New Term
  • How Schema Changes Propagate to Downstream Artefacts
  • Submitting Changes
  • Minimal Local Workflow
  • Docs
  • Schema validation tests
  • Pre-commit behavior
  • CI and Quality Gates
• Schema
  • Why this schema exists
  • How the schema is organized
  • How to read the autogenerated reference