CultureMech Media Mapping Guide

Overview

This guide explains how to find and link CultureMech media entries to CommunityMech growth media records.

CultureMech Repository Structure

Repository: https://github.com/CultureBotAI/CultureMech

Media Location: data/normalized_yaml/

Categories:

bacterial/ - Bacterial culture media (DSMZ, ATCC, CCAP, etc.)
fungal/ - Fungal culture media
algae/ - Algal culture media
archaea/ - Archaeal culture media
specialized/ - Multi-domain or specialized media

Finding Media in CultureMech

Method 1: Browse GitHub

Navigate to media directory: https://github.com/CultureBotAI/CultureMech/tree/main/data/normalized_yaml
Select organism category:
- For bacterial community → bacterial/
- For fungal community → fungal/
- For algal community → algae/
- For archaeal community → archaea/
Search for medium:
- Use GitHub's file search (press /)
- Search by:
  - Medium name (e.g., "LB", "M9", "CCAP")
  - Collection ID (e.g., "DSMZ", "ATCC")
  - Original name
Open the YAML file to view details

Method 2: Clone Repository

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

# Search for media by name
cd CultureMech/data/normalized_yaml
grep -r "name: LB" .

# Search for media by collection
grep -r "DSMZ" bacterial/

Method 3: API Search (if available)

# Search using GitHub API
curl -s "https://api.github.com/search/code?q=repo:CultureBotAI/CultureMech+M9+path:data/normalized_yaml" \
  | jq '.items[].name'

Extracting Media Information

Example: CCAP Medium C100

File: data/normalized_yaml/bacterial/CCAP_C100_S_W_AMP.yaml

Contents:

name: S/W + AMP
original_name: S/W + AMP
category: imported
medium_type: COMPLEX
physical_state: LIQUID
ph_range: 7-8
media_term:
  preferred_term: CCAP Medium C100
  term:
    id: mediadive.medium:C100  # ← Use this as culturemech_id
    label: S/W + AMP
notes: 'Source: CCAP | Link: https://www.ccap.ac.uk/...'
ingredients:
  - preferred_term: Soil
    concentration:
      value: variable
      unit: VARIABLE
  - preferred_term: (NH4)MgPO4
    concentration:
      value: '0.01'
      unit: G_PER_L
preparation_steps:
  - step_number: 1
    action: AUTOCLAVE
    description: "Put a layer about 1 cm deep..."

Key Fields to Extract

media_term.term.id → Use as culturemech_id
name → Medium name
ph_range → Use as ph
ingredients → Map to composition
notes → Include in preparation_notes

Mapping to CommunityMech

Step 1: Identify the Medium

From CultureMech YAML:

media_term:
  term:
    id: mediadive.medium:C100
    label: S/W + AMP

Step 2: Construct GitHub URL

Format:

https://github.com/CultureBotAI/CultureMech/blob/main/data/normalized_yaml/{category}/{filename}.yaml

Example:

https://github.com/CultureBotAI/CultureMech/blob/main/data/normalized_yaml/bacterial/CCAP_C100_S_W_AMP.yaml

Step 3: Add to CommunityMech

growth_media:
  - name: CCAP Medium C100 (Soil/Water + AMP)
    culturemech_id: mediadive.medium:C100
    culturemech_url: https://github.com/CultureBotAI/CultureMech/blob/main/data/normalized_yaml/bacterial/CCAP_C100_S_W_AMP.yaml
    ph: "7-8"
    temperature: "20"
    temperature_unit: "°C"
    atmosphere: aerobic
    composition:
      - name: Soil (garden loam)
        concentration: "variable"
      - name: Ammonium magnesium phosphate
        concentration: "0.01"
        unit: "g/L"
    preparation_notes: "See CultureMech for full preparation protocol."

Common Culture Collections in CultureMech

Bacterial Media

DSMZ (German Collection of Microorganisms and Cell Cultures):

Files: bacterial/DSMZ_*.yaml
ID format: mediadive.medium:DSMZ###
Example: DSMZ_Medium_1.yaml

ATCC (American Type Culture Collection):

Files: bacterial/ATCC_*.yaml
ID format: mediadive.medium:ATCC###
Example: ATCC_Medium_1.yaml

CCAP (Culture Collection of Algae and Protozoa):

Files: bacterial/CCAP_*.yaml
ID format: mediadive.medium:C###
Example: CCAP_C100_S_W_AMP.yaml

Fungal Media

CBS (Westerdijk Fungal Biodiversity Institute):

Files: fungal/CBS_*.yaml
ID format: mediadive.medium:CBS###

PDA (Potato Dextrose Agar):

Files: fungal/PDA*.yaml
Common fungal medium

Algal Media

CCAP Algal Media:

Files: algae/CCAP_*.yaml
Specific to photosynthetic organisms

Bulk Mapping Script

For mapping multiple media at once:

#!/usr/bin/env python3
"""Map CultureMech media to CommunityMech communities."""

import yaml
from pathlib import Path

CULTUREMECH_BASE = "https://github.com/CultureBotAI/CultureMech/blob/main/data/normalized_yaml"

def find_culturemech_media(medium_name: str, category: str = "bacterial") -> dict:
    """Search for medium in CultureMech repository."""
    # Clone repo first: git clone https://github.com/CultureBotAI/CultureMech.git

    culturemech_dir = Path("CultureMech/data/normalized_yaml") / category

    for yaml_file in culturemech_dir.glob("*.yaml"):
        with open(yaml_file) as f:
            data = yaml.safe_load(f)

        if medium_name.lower() in data.get("name", "").lower():
            return {
                "culturemech_id": data["media_term"]["term"]["id"],
                "culturemech_url": f"{CULTUREMECH_BASE}/{category}/{yaml_file.name}",
                "name": data["media_term"]["preferred_term"],
                "ph": data.get("ph_range"),
            }

    return None

# Example usage
if __name__ == "__main__":
    result = find_culturemech_media("LB", "bacterial")
    if result:
        print(f"Found: {result['name']}")
        print(f"ID: {result['culturemech_id']}")
        print(f"URL: {result['culturemech_url']}")

Media ID Formats

Different collections use different ID formats:

Collection	ID Format	Example
DSMZ	`mediadive.medium:DSMZ###`	`mediadive.medium:DSMZ1`
ATCC	`mediadive.medium:ATCC###`	`mediadive.medium:ATCC1`
CCAP	`mediadive.medium:C###`	`mediadive.medium:C100`
CBS	`mediadive.medium:CBS###`	`mediadive.medium:CBS1`
Generic	`mediadive.medium:###`	`mediadive.medium:001`

When CultureMech Doesn't Have Your Medium

If your medium is not in CultureMech:

Document it fully in CommunityMech:

growth_media:
  - name: Custom Lab Medium
    # No culturemech_id or culturemech_url
    composition:
      # ... full details

Consider contributing to CultureMech:
- Fork CultureMech repository
- Add your medium in normalized YAML format
- Submit pull request

Reference original source:

preparation_notes: "Custom medium from Smith et al. 2024"
evidence:
  - reference: PMID:12345678
    snippet: "Cells were grown in custom medium..."

Validation

After adding CultureMech links:

# Validate schema
just validate kb/communities/YourCommunity.yaml

# Generate HTML to verify links
just gen-html

# Check generated link
grep "CultureMech" docs/communities/YourCommunity.html

Example Mappings

LB Medium (Luria-Bertani)

CultureMech: bacterial/LB_*.yaml (various versions)

growth_media:
  - name: LB Medium
    culturemech_id: mediadive.medium:LB001
    culturemech_url: https://github.com/CultureBotAI/CultureMech/blob/main/data/normalized_yaml/bacterial/LB_standard.yaml

M9 Minimal Medium

CultureMech: bacterial/M9_*.yaml

growth_media:
  - name: M9 Minimal Medium
    culturemech_id: mediadive.medium:M9001
    culturemech_url: https://github.com/CultureBotAI/CultureMech/blob/main/data/normalized_yaml/bacterial/M9_minimal.yaml

YPD (Yeast Extract Peptone Dextrose)

CultureMech: fungal/YPD_*.yaml

growth_media:
  - name: YPD Medium
    culturemech_id: mediadive.medium:YPD001
    culturemech_url: https://github.com/CultureBotAI/CultureMech/blob/main/data/normalized_yaml/fungal/YPD.yaml

Resources

CultureMech Repository: https://github.com/CultureBotAI/CultureMech
Normalized Media: https://github.com/CultureBotAI/CultureMech/tree/main/data/normalized_yaml
CommunityMech Growth Media Guide: docs/GROWTH_MEDIA_GUIDE.md
Example: examples/growth_media_example.yaml

Questions?

Check existing CultureMech media: Browse repository
Need help finding a medium: Search GitHub issues
Want to add a medium: Fork and submit PR to CultureMech
Integration questions: See docs/GROWTH_MEDIA_GUIDE.md

Last Updated: March 6, 2026 Version: CultureMech Mapping Guide v1.0

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CultureMech Media Mapping Guide

Overview

CultureMech Repository Structure

Finding Media in CultureMech

Method 1: Browse GitHub

Method 2: Clone Repository

Method 3: API Search (if available)

Extracting Media Information

Example: CCAP Medium C100

Key Fields to Extract

Mapping to CommunityMech

Step 1: Identify the Medium

Step 2: Construct GitHub URL

Step 3: Add to CommunityMech

Common Culture Collections in CultureMech

Bacterial Media

Fungal Media

Algal Media

Bulk Mapping Script

Media ID Formats

When CultureMech Doesn't Have Your Medium

Validation

Example Mappings

LB Medium (Luria-Bertani)

M9 Minimal Medium

YPD (Yeast Extract Peptone Dextrose)

Resources

Questions?

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CULTUREMECH_MAPPING_GUIDE.md

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CultureMech Media Mapping Guide

Overview

CultureMech Repository Structure

Finding Media in CultureMech

Method 1: Browse GitHub

Method 2: Clone Repository

Method 3: API Search (if available)

Extracting Media Information

Example: CCAP Medium C100

Key Fields to Extract

Mapping to CommunityMech

Step 1: Identify the Medium

Step 2: Construct GitHub URL

Step 3: Add to CommunityMech

Common Culture Collections in CultureMech

Bacterial Media

Fungal Media

Algal Media

Bulk Mapping Script

Media ID Formats

When CultureMech Doesn't Have Your Medium

Validation

Example Mappings

LB Medium (Luria-Bertani)

M9 Minimal Medium

YPD (Yeast Extract Peptone Dextrose)

Resources

Questions?