MediaIngredientMech

LLM-assisted curation system for media ingredient ontology mappings.

Overview

MediaIngredientMech provides a structured workflow for curating media ingredient ontology mappings with full audit trails. It manages 995 mapped and 136 unmapped ingredients aggregated from 10,657 media recipes in CultureMech.

Key Features:

• Ingredient-centric data model with LinkML schemas
• Interactive CLI for ontology mapping curation
• LLM assistance tracking in curation events
• Comprehensive validation (schema + ontology terms)
• Full audit trail for all curation actions
• YAML-based data storage with version control

Quick Start

Installation

# Clone repository
cd /Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/MediaIngredientMech

# Install with dev dependencies
just install

# Generate LinkML dataclasses
just gen-schema

Import Data

# Import from CultureMech (995 mapped + 136 unmapped = 1,131 total)
just import-data

# Validate imported data
just validate-all

Curate Ingredients

# Create snapshot before curation
just snapshot

# Launch interactive curation CLI
just curate

# Generate progress report
just report

Architecture

Data Sources:

• CultureMech/output/mapped_ingredients.yaml → 995 mapped ingredients
• CultureMech/output/unmapped_ingredients.yaml → 136 unmapped ingredients

Schema:

• IngredientRecord: Root class with mapping status, synonyms, curation history
• OntologyMapping: CHEBI/FOODON term mappings with quality ratings
• CurationEvent: Audit trail with LLM assistance tracking

Workflow:

1. Import data from CultureMech
2. Curate unmapped ingredients (sorted by occurrence count)
3. Validate ontology terms via OAK/OLS
4. Record curation events with timestamps
5. Export validated mappings back to CultureMech

Project Structure

MediaIngredientMech/
├── src/mediaingredientmech/
│   ├── schema/              # LinkML schemas
│   ├── curation/            # Core curation logic
│   ├── validation/          # Schema & ontology validators
│   ├── export/              # Report generation
│   └── utils/               # YAML I/O, ontology client
├── data/
│   ├── curated/             # Working data (version controlled)
│   └── snapshots/           # Timestamped backups (excluded from git)
├── scripts/                 # CLI tools
├── tests/                   # Test suite
└── docs/                    # Documentation

Documentation

• Curation Guide - Step-by-step curation workflow
• Schema Reference - Data model documentation
• Workflows - Common operations and integration

Development

# Run tests with coverage
just test-cov

# Format code
just format

# Lint code
just lint

# Run all quality checks
just check

License

CC0-1.0 - Public Domain Dedication