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βš—οΈ CultureMech

Comprehensive Microbial Culture Media Knowledge Graph

A production-ready knowledge base containing 10,657 culture media recipes from 10 major international repositories, with LinkML schema validation, ontology grounding, and browser-based exploration.

License: CC0-1.0 Python

πŸ“Š Current Coverage

Total Recipes: 10,657 culture media formulations

Category Recipes Sources
Bacterial 10,134 MediaDive, TOGO, BacDive, ATCC, NBRC, KOMODO, MediaDB
Algae 242 UTEX, CCAP, SAG
Fungal 119 MediaDive, TOGO
Specialized 99 KOMODO
Archaea 63 MediaDive, TOGO

πŸ“ˆ Detailed Statistics

Recipes by Source

Source Recipes Type Description
KOMODO 3,637 Bacterial Korean microbial media database
MediaDive 3,327 Multi-kingdom DSMZ comprehensive collection
TOGO Medium 2,917 Multi-kingdom Japanese BRCs curated database
MediaDB 469 Defined Chemically defined media
CCAP 113 Algae UK algae & protozoa collection
UTEX 99 Algae University of Texas algae
SAG 30 Algae German algae culture collection
NBRC 2 Bacterial Japanese biological resources
BacDive 1 Bacterial DSMZ cultivation conditions

Medium Composition

Medium Type Recipes Percentage
Complex 8,399 79.3%
Defined 2,196 20.7%

Complex media contain undefined components (e.g., yeast extract, peptone), while defined media have all components chemically specified.

Physical State

State Recipes Percentage
Liquid 10,593 99.98%
Solid (Agar) 2 0.02%

Data Quality Metrics

Metric Value Percentage
Recipes with ingredients 6,815 64.3%
CHEBI-grounded ingredients 3,548 33.5%
Average ingredients/recipe 15.7 -
LinkML validated 10,595 100%

Ontology Grounding:

  • Chemicals: CHEBI (Chemical Entities of Biological Interest)
  • Biological materials: FOODON (Food Ontology), UBERON (Anatomy), ENVO (Environment)
  • Organisms: NCBITaxon (NCBI Taxonomy)
  • Media databases: DSMZ, TOGO, ATCC prefixes

Unmapped Ingredients Tracking System (2026-03-05):

  • 🎯 136 unmapped ingredients identified across 522 media (4.9% of total)
  • πŸ“Š 3,084 total instances requiring ontology term mapping
  • πŸ” Automated detection of numeric placeholders ('1', '2', '3'), generic terms, and empty values
  • πŸ§ͺ Chemical name extraction from notes fields for mapping assistance
  • πŸ“ˆ Priority-based mapping recommendations (critical: 51+ occurrences)
  • See UNMAPPED_INGREDIENTS_SUMMARY.md and docs/unmapped_ingredients_guide.md

Advanced Normalization & SSSOM Enrichment (2026-02):

  • ✨ Integrated MicroMediaParam's production-grade 16-step chemical normalization pipeline
  • πŸ“š 100+ curated biological products (yeast extract, peptone, serum, DNA, agar, etc.)
  • πŸ§ͺ 100+ chemical formula mappings (Fe2(SO4)3 β†’ iron(III) sulfate)
  • πŸ”¬ 15+ buffer abbreviations (HEPES, MES, Tris)
  • πŸ’¨ 11 common laboratory gases (CO2, N2, O2, H2, CH4, etc.)
  • πŸ”€ Unicode dot normalization (5 variants: Β·, ・, β€’, βˆ™, β‹…)
  • πŸ“Š Coverage achieved: 45.6% (2,302 / 5,048 ingredients) - +935 new mappings from baseline
  • πŸ“ˆ 68.4% increase in coverage (27.1% β†’ 45.6%)
  • See PROJECT_STATUS_SUMMARY.md and GAS_MAPPING_SUMMARY.md for details

Enum Normalization (2026-02-20):

  • πŸ”§ Normalized 10,657 YAML files for schema compliance
  • βœ… Fixed capitalization: medium_type (COMPLEX, DEFINED), physical_state (LIQUID, SOLID_AGAR)
  • πŸ“ Recategorized all "imported" files to proper organism types (bacterial, fungal, archaea, algae, specialized)
  • 🎯 100% schema compliance across all enum fields

✨ Features

βœ… 10,657 recipes - Production-ready dataset from 10 authoritative sources βœ… Four-tier architecture - Clean separation: raw β†’ raw_yaml β†’ normalized_yaml β†’ merge_yaml βœ… Recipe deduplication - Merge recipes with same ingredient sets (~344 unique base formulations) βœ… LinkML schema validation - Comprehensive data quality enforcement βœ… Ontology grounding - CHEBI for chemicals, NCBITaxon for organisms βœ… Full provenance tracking - Complete source attribution and curation history βœ… Automated pipelines - Fetchers, converters, and importers for all sources βœ… Browser interface - Faceted search and filtering βœ… UMAP visualization - Interactive 2D embeddings visualization for exploring media similarity βœ… Knowledge graph export - Biolink-compliant KGX format βœ… Literature verification - 6-tier cascading PDF retrieval for cross-reference validation βœ… ATCC cross-references - Automated equivalency detection with DSMZ media βœ… Unmapped ingredients tracking - Automated detection and prioritization of ingredients needing ontology mapping βœ… Comprehensive documentation - 30+ guides in docs/

πŸš€ Quick Start

Installation

# Clone the repository
git clone https://github.com/CultureBotAI/CultureMech.git
cd CultureMech

# Install dependencies (requires uv)
just install

# Optional: Install Koza for KG export
just install-koza

View the Browser

# Generate browser data from recipes
just gen-browser-data

# Serve locally
just serve-browser

# Open http://localhost:8000/app/

Generate UMAP Visualization

# Generate interactive UMAP visualization (requires KG-Microbe embeddings)
just gen-media-umap /path/to/embeddings.tsv.gz

# View locally
open docs/media_umap.html

# See docs/MEDIA_UMAP_GUIDE.md for detailed instructions

Count Recipes

just count-recipes
# Output:
#   algae:      242
#   bacterial:  10,072
#   fungal:     119
#   archaea:    63
#   specialized: 99
#   Total:      10,595

Validate Recipes

# Validate a single recipe
just validate data/normalized_yaml/bacterial/LB_Broth.yaml

# Validate all recipes
just validate-all

# Schema validation only
just validate-schema data/normalized_yaml/bacterial/LB_Broth.yaml

πŸ“š Data Sources

CultureMech integrates culture media recipes from 10 major international repositories:

Integrated Sources βœ…

Source Recipes Description Status
KOMODO 3,637 Korean microbial media database βœ… Complete
MediaDive (DSMZ) 3,327 German Collection, comprehensive bacterial/fungal media βœ… Complete
TOGO Medium 2,917 Japanese BRCs, curated media database βœ… Complete
MediaDB 469 Chemically defined media database βœ… Complete
CCAP 113 UK Culture Collection of Algae and Protozoa βœ… Complete
UTEX 99 University of Texas algae collection βœ… Complete
SAG 30 German algae culture collection (GΓΆttingen) βœ… Complete
NBRC 2 Japanese NITE Biological Resource Center πŸ”„ Initial
BacDive 1 DSMZ cultivation conditions database πŸ”„ Initial

Planned Expansions πŸš€

Source Potential Description Notes
BacDive ~2,500+ Additional organism-specific cultivation conditions Requires API access
ATCC ~900 American Type Culture Collection media Web scraping needed
NBRC ~420 Additional NITE media formulations Incremental import

Algae Collections (New! πŸŽ‰)

Three major algae culture collections fully integrated:

  • UTEX (Austin, TX): 99 recipes - Full composition details
  • CCAP (Oban, Scotland): 113 recipes - Metadata + PDF references
  • SAG (GΓΆttingen, Germany): 30 recipes - Metadata + PDF references

Total: 242 algae media recipes covering:

  • Freshwater algae (BG-11, Bold's Basal, TAP)
  • Marine phytoplankton (f/2, Erdschreiber's)
  • Cyanobacteria (Spirulina, BG-11 variants)
  • Specialized media (diatoms, euglenoids, volvocales)

See docs/ALGAE_PIPELINE_COMPLETE.md for details.

Fetching Data

# Fetch all available sources
just fetch-algae-collections    # UTEX, CCAP, SAG
just fetch-bacdive 100          # BacDive (requires registration)
just fetch-nbrc 50              # NBRC web scraping

# Import to normalized format
just import-algae-collections
just import-bacdive
just import-nbrc

πŸ—οΈ Project Structure

CultureMech/
β”œβ”€β”€ src/culturemech/              # Python package
β”‚   β”œβ”€β”€ schema/                   # LinkML schema definitions
β”‚   β”‚   β”œβ”€β”€ culturemech.yaml     # Main schema (1800+ lines)
β”‚   β”‚   └── unmapped_ingredients_schema.yaml  # Unmapped ingredients schema
β”‚   β”œβ”€β”€ fetch/                    # Data fetchers (10 sources)
β”‚   β”‚   β”œβ”€β”€ utex_fetcher.py      # UTEX algae media
β”‚   β”‚   β”œβ”€β”€ ccap_fetcher.py      # CCAP algae media
β”‚   β”‚   β”œβ”€β”€ sag_fetcher.py       # SAG algae media
β”‚   β”‚   └── ... (7 more fetchers)
β”‚   β”œβ”€β”€ convert/                  # Raw YAML converters
β”‚   β”œβ”€β”€ import/                   # Normalized importers (11 total)
β”‚   β”‚   β”œβ”€β”€ utex_importer.py     # Full UTEX pipeline
β”‚   β”‚   β”œβ”€β”€ ccap_importer.py     # CCAP metadata importer
β”‚   β”‚   β”œβ”€β”€ sag_importer.py      # SAG metadata importer
β”‚   β”‚   └── ... (8 more importers)
β”‚   β”œβ”€β”€ export/                   # Export modules
β”‚   β”‚   β”œβ”€β”€ browser_export.py    # Browser data generator
β”‚   β”‚   └── kgx_export.py        # Knowledge graph export
β”‚   └── render.py                 # HTML page generator
β”‚
β”œβ”€β”€ scripts/                      # Utility scripts
β”‚   β”œβ”€β”€ aggregate_unmapped_ingredients.py  # Aggregate unmapped ingredients
β”‚   └── unmapped_ingredients_stats.py      # Generate statistics reports
β”‚
β”œβ”€β”€ output/                       # Generated outputs
β”‚   └── unmapped_ingredients.yaml # Aggregated unmapped ingredients (502KB)
β”‚
β”œβ”€β”€ data/                         # Three-tier data architecture
β”‚   β”œβ”€β”€ raw/                      # Layer 1: Source files (git ignored)
β”‚   β”‚   β”œβ”€β”€ utex/                # UTEX raw data
β”‚   β”‚   β”œβ”€β”€ ccap/                # CCAP raw data
β”‚   β”‚   β”œβ”€β”€ sag/                 # SAG raw data
β”‚   β”‚   └── ... (10+ sources)
β”‚   β”œβ”€β”€ raw_yaml/                 # Layer 2: Unnormalized YAML (git ignored)
β”‚   └── normalized_yaml/          # Layer 3: Curated recipes (in git)
β”‚       β”œβ”€β”€ algae/               # 242 algae recipes
β”‚       β”œβ”€β”€ bacterial/           # 10,072 bacterial recipes
β”‚       β”œβ”€β”€ fungal/              # 119 fungal recipes
β”‚       β”œβ”€β”€ archaea/             # 63 archaeal recipes
β”‚       └── specialized/         # 99 specialized recipes
β”‚
β”œβ”€β”€ docs/                         # Comprehensive documentation
β”‚   β”œβ”€β”€ QUICK_START.md           # 5-minute getting started
β”‚   β”œβ”€β”€ DATA_LAYERS.md           # Three-tier architecture
β”‚   β”œβ”€β”€ ALGAE_PIPELINE_COMPLETE.md  # Algae integration guide
β”‚   └── ... (27 more docs)
β”‚
β”œβ”€β”€ app/                          # Browser interface
β”‚   β”œβ”€β”€ index.html               # Faceted search UI
β”‚   └── schema.js                # Browser configuration
β”‚
β”œβ”€β”€ tests/                        # Test suite
β”œβ”€β”€ conf/                         # Configuration files
β”œβ”€β”€ project.justfile              # Build automation (80+ commands)
└── pyproject.toml               # Python project config

πŸ“– Documentation

Comprehensive documentation is available in the docs/ directory:

Getting Started

Architecture

Integration Guides

Data Quality & Enrichment

🧬 Recipe Format

Recipes are stored as YAML files following the LinkML schema:

name: BG-11 Medium
category: algae
medium_type: COMPLEX
physical_state: LIQUID

description: Standard cyanobacteria medium from UTEX Culture Collection

ingredients:
  - agent_term:
      preferred_term: NaNO3
    amount: 1.5 g/L

  - agent_term:
      preferred_term: K2HPO4
    amount: 0.04 g/L

preparation_steps:
  - step_number: 1
    instruction: Dissolve all ingredients in distilled water

  - step_number: 2
    instruction: Autoclave at 121Β°C for 20 minutes

# Algae-specific fields
light_intensity: 50-100 ¡mol photons m⁻² s⁻¹
light_cycle: 12:12 or 16:8 light:dark
temperature_range: 15-30Β°C depending on species

applications:
  - Algae cultivation
  - Cyanobacteria culture
  - Phytoplankton research

curation_history:
  - curator: utex-import
    date: '2026-01-28'
    action: Imported from UTEX Culture Collection

references:
  - reference_id: UTEX:bg-11-medium
  - reference_id: https://utex.org/products/bg-11-medium

See data/normalized_yaml/ for complete examples.

πŸ”¬ Data Model

LinkML Schema

The schema (src/culturemech/schema/culturemech.yaml) defines:

Key Classes:

  • MediaRecipe - Root entity (one per YAML file)
  • IngredientDescriptor - Chemicals with CHEBI terms
  • OrganismDescriptor - Target organisms with NCBITaxon IDs
  • SolutionDescriptor - Stock solutions
  • PreparationStep - Ordered protocol steps
  • MediaVariant - Related formulations

Ontology Bindings:

  • CHEBI - Chemical ingredients
  • NCBITaxon - Target organisms
  • UO - Units of measurement
  • Source databases - DSMZ, TOGO, ATCC, UTEX, CCAP, SAG

Enums:

  • MediumTypeEnum: DEFINED, COMPLEX, MINIMAL, SELECTIVE, DIFFERENTIAL, ENRICHMENT
  • PhysicalStateEnum: LIQUID, SOLID_AGAR, SEMISOLID, BIPHASIC
  • PreparationActionEnum: DISSOLVE, MIX, HEAT, AUTOCLAVE, FILTER_STERILIZE
  • SterilizationMethodEnum: AUTOCLAVE, FILTER, DRY_HEAT, TYNDALLIZATION

Algae-Specific Extensions

Added fields for algae culture conditions:

  • light_intensity - Β΅mol photons m⁻² s⁻¹
  • light_cycle - Photoperiod (e.g., "16:8 light:dark")
  • light_quality - Light source type
  • temperature_range - Cultivation temperature
  • salinity - Marine vs freshwater
  • aeration - COβ‚‚ supplementation
  • culture_vessel - Flask, tube, bioreactor

βœ… Data Quality

Three-Tier Architecture

Layer 1: raw/          β†’ Raw source files (JSON, TSV, SQL)
         ↓
Layer 2: raw_yaml/     β†’ Unnormalized YAML (preserves original structure)
         ↓
Layer 3: normalized_yaml/ β†’ LinkML-validated, ontology-grounded recipes

Benefits:

  • Reproducible pipeline from source to curated data
  • Easy to re-import with schema changes
  • Clear separation of concerns
  • Version control on curated layer only

Validation

# Full validation (schema + ontologies)
just validate data/normalized_yaml/algae/BG-11_Medium.yaml

# Schema validation only
just validate-schema data/normalized_yaml/algae/BG-11_Medium.yaml

# Validate all recipes
just validate-all

Provenance

Every recipe includes:

  • Source database attribution
  • Fetch date and version
  • Import date and curator
  • Cross-references to original sources
  • PDF URLs for detailed protocols (CCAP/SAG)

πŸ”¬ Literature Verification

NEW (2026-02-20): CultureMech now includes a comprehensive literature verification system for validating cross-references through scientific papers.

6-Tier Cascading PDF Retrieval

The system attempts to retrieve PDFs from multiple sources in order:

  1. Direct Publisher Access - ASM, PLOS, Frontiers, MDPI, Nature, Science, Elsevier
  2. PubMed Central (PMC) - NCBI idconv API
  3. Unpaywall API - Open access aggregator
  4. Semantic Scholar - Open PDF endpoint
  5. Sci-Hub Fallback - Optional, disabled by default (requires explicit opt-in)
  6. Web Search - arXiv, bioRxiv, Europe PMC

Key Features

  • βœ… Legal sources first - Always tries publisher, PMC, Unpaywall, and Semantic Scholar before fallback
  • βœ… Sci-Hub opt-in only - Disabled by default, requires --enable-scihub-fallback flag
  • βœ… Full provenance - Tracks which tier successfully retrieved each PDF
  • βœ… Evidence extraction - 8 regex patterns for detecting media equivalencies
  • βœ… Batch processing - Verify multiple candidates efficiently
  • βœ… Caching layer - Metadata and PDFs cached locally to avoid repeated requests

Usage Examples

# Generate ATCC-DSMZ cross-reference candidates (name-based matching only)
python -m culturemech.enrich.atcc_crossref_builder generate

# Verify candidates using legal sources only (no Sci-Hub)
python -m culturemech.enrich.atcc_crossref_builder generate \
    --verify-literature

# Verify with Sci-Hub fallback enabled (explicit opt-in)
python -m culturemech.enrich.atcc_crossref_builder generate \
    --verify-literature \
    --enable-scihub-fallback

# Configure via environment variables
export ENABLE_SCIHUB_FALLBACK=true
export LITERATURE_EMAIL="your@email.com"
export FALLBACK_PDF_MIRRORS="https://sci-hub.se,https://sci-hub.st"
python -m culturemech.enrich.atcc_crossref_builder generate --verify-literature

Institutional Compliance

⚠️ Important: The Sci-Hub fallback tier is disabled by default and requires explicit opt-in. Use may violate publisher agreements or local laws. Users are responsible for compliance with institutional policies.

Safety features:

  • Default: use_fallback_pdf=False
  • Legal sources exhausted first
  • Clear warnings when Sci-Hub is enabled
  • Full provenance tracking
  • No auto-distribution of PDFs

See IMPLEMENTATION_SUMMARY.md for complete documentation.

🌐 Browser Interface

The faceted search browser (app/index.html) provides:

  • Full-text search - Name, organism, ingredient, application
  • Faceted filtering - Category, type, state, organisms, sterilization
  • Real-time filtering - Instant results from 10,595 recipes
  • External links - CHEBI, NCBITaxon, source databases
  • Mobile responsive - Works on all devices

Generate browser data:

just gen-browser-data
just serve-browser
# Open http://localhost:8000/app/

πŸ”§ Development

Common Commands

just --list              # Show all 80+ commands
just count-recipes       # Count recipes by category
just fetch-utex          # Fetch UTEX algae media
just import-utex         # Import UTEX to normalized format
just validate-all        # Validate all recipes
just gen-browser-data    # Generate browser search data
just test                # Run test suite

Cross-Reference & Enrichment

# Generate ATCC-DSMZ cross-reference candidates
python -m culturemech.enrich.atcc_crossref_builder generate \
    --output data/curation/atcc_candidates.json

# Verify candidates via literature search (legal sources only)
python -m culturemech.enrich.atcc_crossref_builder generate \
    --verify-literature

# Verify with Sci-Hub fallback (opt-in, requires explicit flag)
python -m culturemech.enrich.atcc_crossref_builder generate \
    --verify-literature \
    --enable-scihub-fallback

# Normalize enum values (medium_type, physical_state, category)
python -m culturemech.enrich.normalize_enums --dry-run  # Preview changes
python -m culturemech.enrich.normalize_enums            # Apply changes

# Aggregate unmapped ingredients for mapping prioritization
python scripts/aggregate_unmapped_ingredients.py --verbose --min-occurrences 2

# View unmapped ingredients statistics
python scripts/unmapped_ingredients_stats.py --top 20

# View full aggregated data
less output/unmapped_ingredients.yaml

# Read the comprehensive guide
cat docs/unmapped_ingredients_guide.md

# Read the executive summary
cat UNMAPPED_INGREDIENTS_SUMMARY.md

Adding New Recipes

  1. Create YAML file in appropriate category:

    cp data/normalized_yaml/bacterial/LB_Broth.yaml \
       data/normalized_yaml/bacterial/Your_Medium.yaml
  2. Edit following schema structure

  3. Validate:

    just validate data/normalized_yaml/bacterial/Your_Medium.yaml
  4. Regenerate browser:

    just gen-browser-data

Running Tests

# All tests
just test

# With coverage
just test-cov

# Specific test
pytest tests/test_kgx_export.py

🎯 Use Cases

For Researchers

  • Find media recipes for specific organisms
  • Compare formulations across culture collections
  • Access detailed protocols with preparation steps
  • Discover alternatives through variant relationships

For Culture Collections

  • Standardize media recipe formats
  • Cross-reference with other collections
  • Track provenance and curation history
  • Export to knowledge graphs for integration

For Bioinformaticians

  • Query via KG using Biolink model
  • Link organisms to cultivation conditions
  • Analyze ingredients with CHEBI ontology
  • Build applications on structured data

πŸ“Š Statistics

$ just count-recipes
Recipe count by category:

  algae:        242
  archaea:       63
  bacterial:  10,134
  fungal:       119
  specialized:   99

Total recipes:  10,657

Data Quality:

  • βœ… 100% schema-validated
  • βœ… 100% enum compliance (10,657 files normalized)
  • βœ… Full source attribution
  • βœ… Comprehensive provenance tracking
  • βœ… LinkML compliance

Pipeline Coverage:

  • βœ… 10 data sources integrated
  • βœ… 11 import pipelines operational
  • βœ… 3 algae collections (UTEX, CCAP, SAG)
  • βœ… Automated fetch β†’ convert β†’ import workflow

Enrichment Features:

  • βœ… Literature verification with 6-tier PDF retrieval
  • βœ… ATCC-DSMZ cross-reference detection
  • βœ… Automated enum normalization
  • βœ… Evidence extraction from scientific papers
  • βœ… Unmapped ingredients aggregation and tracking (136 ingredients, 3,084 instances)

🀝 Contributing

We welcome contributions! Ways to contribute:

  1. Add recipes - Create YAML files following the schema
  2. Enhance existing recipes - Add ontology terms, preparation details
  3. Report issues - Found errors or have suggestions?
  4. Improve documentation - Help make guides clearer
  5. Add data sources - Know of other culture media databases?

See CONTRIBUTING.md for detailed guidelines.

Pull Request Process

  1. Fork the repository
  2. Create a feature branch
  3. Make your changes
  4. Validate: just validate-all
  5. Test: just test
  6. Submit pull request

πŸ”— Related Resources

Culture Collections

Ontologies

Related Projects

πŸ“„ License

CC0

This work is dedicated to the public domain under CC0 1.0 Universal.

You are free to:

  • Use for any purpose
  • Modify and distribute
  • Use commercially
  • No attribution required (but appreciated!)

πŸ“ Citation

If you use CultureMech in your research, please cite:

@software{culturemech2026,
  title = {CultureMech: A Comprehensive Microbial Culture Media Knowledge Graph},
  author = {CultureBotAI},
  year = {2026},
  url = {https://github.com/CultureBotAI/CultureMech},
  note = {10,595 culture media recipes from 10 international repositories}
}

πŸ™ Acknowledgments

Data Sources: DSMZ, TOGO, ATCC, NBRC, BacDive, KOMODO, UTEX, CCAP, SAG, MediaDB

Architecture: Inspired by the dismech project

Ontologies: CHEBI, NCBITaxon, UO

Community: KG-Hub, LinkML, Biolink Model

πŸ“§ Contact


Built with ❀️ for microbiology research

10,657 recipes β€’ 10 sources β€’ Production ready β€’ Public domain

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Microbial Culture Media Knowledge Graph - Comprehensive collection of 10,000+ culture media recipes from major international repositories with LinkML schema, ontology grounding, and browser-based exploration

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