CLAUDE.md

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

This is a LinkML schema project for common value sets. It consists primarily of LinkML enum (static and dynamic) definitions, organized by domain

Project Structure

Schema Files

• Main schema: src/valuesets/schema/valuesets.yaml -- this just imports
• Schema modules in: src/valuesets/schema/
  • core.yaml - Core definitions
  • bio/
    • MORE TO COME
  • healthcare.yaml - Healthcare-related value sets
  • investigation.yaml - Investigation-related value sets
  • statistics.yaml - Statistics-related value sets
  • types.yaml - Type definitions

Note: we will probably start nesting some of these more

Editing

After every edit, always check you didn't make a mistake by running just site

Additionally, validate your schema changes with just validate to ensure they conform to LinkML specifications.

DO NOT edit generated artefacts

Guidelines

• Enums should be organized by domain
• Using CamelCase for all enum names
• PERMISSIBLE_VALUES in upper case by default, except when existing standard exists

Linking to ontology terms

• use meaning: to map to an ontology term
• use OBO preferantially
• use CURIEs, with prefixes declared in header.

ALWAYS check IDs, NEVER guess them. Use OLS to check.

Development Commands

All commands are managed through the just command runner:

• Run tests: just test
• Run linting: just lint
• Validate schema: just validate - Validates LinkML schema definitions

Generated Code

• Python datamodel: src/valuesets/datamodel/
  • Auto-generated from schema - do not edit directly
• Project artifacts: project/ directory (git-ignored by default)