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Link growth media to CultureMech and MediaIngredientMech
Implement complete integration with CultureMech recipe database and MediaIngredientMech ingredient catalog to enrich growth_media data across 21 communities with external identifiers and composition details. Changes: - Add media_linker.py: Fetch/cache/match CultureMech and MediaIngredientMech data - Add link_growth_media.py: CLI for automated media/ingredient linking - Update schema: Add 'from' field to GrowthMediaComponent - Update 21 community YAMLs with growth_media linkage Results: - Media: 18/26 matched to CultureMech (69% success rate) - Ingredients: 57/98 linked to MediaIngredientMech (58% success rate) - 28 new ingredients imported from CultureMech recipes - All changes validated against LinkML schema Technical details: - Token-based fuzzy matching (threshold: 0.85) - Independent matching for media (CultureMech) and ingredients (MediaIngredientMech) - Preserves existing curated data with source tagging - Local index loading for performance (10,657 recipes, 1,108 ingredients) Commands added to justfile: - link-media-dry: Preview changes - link-media: Apply linking - link-media-report: Generate CSV/text reports Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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‎justfile‎

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@@ -149,15 +149,21 @@ apply-batch-repairs REPORT:
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# Link growth media to CultureMech/MediaIngredientMech (dry-run)
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link-media-dry:
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uv run python scripts/link_growth_media.py --dry-run
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uv run python scripts/link_growth_media.py --dry-run \
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--culturemech-index ../../CultureMech/data/normalized_yaml/recipe_index.json \
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--mediaingredientmech-index ../../MediaIngredientMech/data/curated/all_ingredients_index.json
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# Link growth media to CultureMech/MediaIngredientMech (apply)
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link-media:
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uv run python scripts/link_growth_media.py
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uv run python scripts/link_growth_media.py \
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--culturemech-index ../../CultureMech/data/normalized_yaml/recipe_index.json \
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--mediaingredientmech-index ../../MediaIngredientMech/data/curated/all_ingredients_index.json
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# Generate ingredient/media mapping reports
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link-media-report:
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uv run python scripts/link_growth_media.py --dry-run \
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--culturemech-index ../../CultureMech/data/normalized_yaml/recipe_index.json \
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--mediaingredientmech-index ../../MediaIngredientMech/data/curated/all_ingredients_index.json \
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--ingredient-report reports/ingredient_mapping.csv \
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--media-report reports/media_mapping.csv \
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--summary-report reports/media_linking_summary.txt

‎kb/communities/At_RSPHERE_SynCom.yaml‎

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@@ -284,9 +284,8 @@ growth_media:
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incubation_time: '48'
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incubation_time_unit: hours
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vessel_type: agar plates
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preparation_notes: 'Low-nutrient medium used for isolation and maintenance of soil and rhizosphere
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bacteria from Arabidopsis roots. R2A supports slow-growing oligotrophic bacteria common in
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soil environments.
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preparation_notes: 'Low-nutrient medium used for isolation and maintenance of soil and rhizosphere bacteria
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from Arabidopsis roots. R2A supports slow-growing oligotrophic bacteria common in soil environments.
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'
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evidence:
@@ -296,6 +295,61 @@ growth_media:
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snippet: We established Arabidopsis leaf- and root-derived microbiota culture collections representing
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the majority of bacterial species that are reproducibly detectable by culture-independent community
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sequencing
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culturemech_id: CultureMech:002706
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culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:002706
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composition:
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- name: Yeast extract
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concentration: '0.5'
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unit: G_PER_L
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000025
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000025
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- name: Proteose peptone no. 3
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concentration: '0.5'
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unit: G_PER_L
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from: CultureMech
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- name: Casamino acids
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concentration: '0.5'
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unit: G_PER_L
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000173
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000173
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- name: Glucose
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concentration: '0.5'
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unit: G_PER_L
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000138
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000138
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- name: Starch
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concentration: '0.5'
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unit: G_PER_L
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000169
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000169
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- name: Sodium pyruvate
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concentration: '0.3'
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unit: G_PER_L
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000185
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000185
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- name: K2HPO4
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concentration: '0.3'
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unit: G_PER_L
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000122
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000122
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- name: MgSO4 x 7 H2O
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concentration: '0.05'
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unit: G_PER_L
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000118
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000118
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- name: Agar
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concentration: '15'
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unit: G_PER_L
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000119
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000119
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- name: Half-strength Murashige-Skoog medium for Arabidopsis growth
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ph: '5.7'
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temperature: '22'
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light_intensity_unit: μmol photons/m²/s
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vessel_type: square petri plates (vertical orientation)
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preparation_notes: 'Gnotobiotic plant growth system with 0.5× MS medium supplemented with 1% sucrose
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and 0.8% agar. Seeds surface-sterilized prior to inoculation. Plates oriented vertically to
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allow root observation and bacterial colonization tracking.
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and 0.8% agar. Seeds surface-sterilized prior to inoculation. Plates oriented vertically to allow
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root observation and bacterial colonization tracking.
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'
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composition:
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term:
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id: CHEBI:17992
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label: sucrose
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media_ingredient_mech_id: MediaIngredientMech:000214
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000214
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- name: Agar
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concentration: '0.8'
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unit: '%'
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media_ingredient_mech_id: MediaIngredientMech:000119
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000119
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evidence:
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- reference: doi:10.1038/nature16192
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supports: SUPPORT

‎kb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml‎

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@@ -243,7 +243,12 @@ growth_media:
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inoculum_unit: μg chlorophyll/mL
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incubation_time: '17'
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incubation_time_unit: days
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preparation_notes: 'Medium prepared for sustained algal-bacterial hydrogen production. Mannitol and yeast extract are added to support bacterial growth and enhance H2 production. Cultures start under aerobic conditions and transition to anaerobic conditions for hydrogen production. Sulfur deprivation may be used to induce anaerobiosis and activate hydrogenase in Chlamydomonas. High-cell density cultures (76.7 μg/mL chlorophyll) produce 313 mL H2/L over 17 days, while low-cell density cultures (10 μg/mL chlorophyll) produce 163.5 mL H2/L over 25 days.
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preparation_notes: 'Medium prepared for sustained algal-bacterial hydrogen production. Mannitol and
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yeast extract are added to support bacterial growth and enhance H2 production. Cultures start under
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aerobic conditions and transition to anaerobic conditions for hydrogen production. Sulfur deprivation
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may be used to induce anaerobiosis and activate hydrogenase in Chlamydomonas. High-cell density cultures
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(76.7 μg/mL chlorophyll) produce 313 mL H2/L over 17 days, while low-cell density cultures (10 μg/mL
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chlorophyll) produce 163.5 mL H2/L over 25 days.
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'
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composition:
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term:
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id: CHEBI:9754
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label: tris(hydroxymethyl)aminomethane
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from: community_curated
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- name: Acetate (carbon source)
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concentration: '17'
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unit: mM
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term:
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id: CHEBI:30089
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label: acetate
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from: community_curated
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- name: Mannitol
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concentration: '20'
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unit: mM
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term:
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id: CHEBI:16899
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label: mannitol
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from: community_curated
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media_ingredient_mech_id: MediaIngredientMech:000308
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000308
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- name: Yeast extract
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concentration: '0.1'
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unit: percent (w/v)
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term:
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id: CHEBI:89981
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label: yeast extract
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from: community_curated
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media_ingredient_mech_id: MediaIngredientMech:000025
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000025
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- name: Ammonium chloride (nitrogen source)
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concentration: '7.5'
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unit: mM
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term:
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id: CHEBI:31206
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label: ammonium chloride
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from: community_curated
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- name: Potassium phosphate
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concentration: '1.0'
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unit: mM
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term:
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id: CHEBI:131527
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label: dipotassium hydrogen phosphate
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from: community_curated
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media_ingredient_mech_id: MediaIngredientMech:000630
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000630
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- name: Magnesium sulfate
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concentration: '0.4'
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unit: mM
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term:
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id: CHEBI:32599
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label: magnesium sulfate
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from: community_curated
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media_ingredient_mech_id: MediaIngredientMech:000174
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000174
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- name: Calcium chloride
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concentration: '0.34'
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unit: mM
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term:
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id: CHEBI:3312
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label: calcium dichloride
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from: community_curated
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media_ingredient_mech_id: MediaIngredientMech:000484
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000484
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- name: See source for composition
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concentration: variable
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unit: VARIABLE
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000002
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000002
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evidence:
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- reference: PMID:38159768
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supports: SUPPORT
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evidence_source: IN_VITRO
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snippet: When incubated in mannitol- and yeast extract-containing medium, this bacterial community can promote and sustain algal hydrogen production up to 313 mL H2·L-1 for 17 days and 163.5 mL H2·L-1 for 25 days in high-cell (76.7 μg·mL-1 of initial chlorophyll) and low-cell density (10 μg·mL-1 of initial chlorophyll) algal cultures, respectively
347+
snippet: When incubated in mannitol- and yeast extract-containing medium, this bacterial community
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can promote and sustain algal hydrogen production up to 313 mL H2·L-1 for 17 days and 163.5 mL H2·L-1
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for 25 days in high-cell (76.7 μg·mL-1 of initial chlorophyll) and low-cell density (10 μg·mL-1
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of initial chlorophyll) algal cultures, respectively
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explanation: Establishes mannitol and yeast extract as key medium components for sustained H2 production
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culturemech_id: CultureMech:000139
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culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:000139
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metals_present:
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- TITANIUM
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metal_relevance: SIGNIFICANT

‎kb/communities/Chlamydomonas_Methylobacterium_Mutualism.yaml‎

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light_regime: continuous illumination
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light_intensity: '100'
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light_intensity_unit: μmol photons/m²/s
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preparation_notes: 'TAP medium is the standard maintenance medium for Chlamydomonas reinhardtii. For nitrogen stress experiments, cultures are grown in nitrogen-depleted TAP medium to induce the mutualistic interaction with Methylobacterium. The medium contains Tris buffer for pH stability and acetate as a carbon source. Ammonium serves as the nitrogen source under normal conditions, but is omitted or depleted to create nitrogen stress.
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preparation_notes: 'TAP medium is the standard maintenance medium for Chlamydomonas reinhardtii. For
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nitrogen stress experiments, cultures are grown in nitrogen-depleted TAP medium to induce the mutualistic
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interaction with Methylobacterium. The medium contains Tris buffer for pH stability and acetate as
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a carbon source. Ammonium serves as the nitrogen source under normal conditions, but is omitted or
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depleted to create nitrogen stress.
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'
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composition:
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term:
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id: CHEBI:9754
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label: tris(hydroxymethyl)aminomethane
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from: community_curated
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- name: Acetate (carbon source)
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concentration: '17'
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unit: mM
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term:
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id: CHEBI:30089
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label: acetate
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from: community_curated
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- name: Ammonium chloride (nitrogen source)
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concentration: '7.5'
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unit: mM
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term:
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id: CHEBI:31206
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label: ammonium chloride
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from: community_curated
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- name: Potassium phosphate
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concentration: '1.0'
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unit: mM
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term:
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id: CHEBI:131527
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label: dipotassium hydrogen phosphate
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from: community_curated
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media_ingredient_mech_id: MediaIngredientMech:000630
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000630
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- name: Magnesium sulfate
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concentration: '0.4'
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unit: mM
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term:
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id: CHEBI:32599
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label: magnesium sulfate
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from: community_curated
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media_ingredient_mech_id: MediaIngredientMech:000174
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000174
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- name: Calcium chloride
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concentration: '0.34'
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unit: mM
@@ -293,12 +306,25 @@ growth_media:
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term:
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id: CHEBI:3312
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label: calcium dichloride
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from: community_curated
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media_ingredient_mech_id: MediaIngredientMech:000484
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000484
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- name: See source for composition
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concentration: variable
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unit: VARIABLE
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from: CultureMech
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media_ingredient_mech_id: MediaIngredientMech:000002
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media_ingredient_mech_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients/MediaIngredientMech:000002
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evidence:
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- reference: PMID:29385570
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supports: SUPPORT
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evidence_source: IN_VITRO
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snippet: The model alga Chlamydomonas reinhardtii can grow efficiently on several inorganic nitrogen sources (e.g
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explanation: Establishes TAP medium as the growth medium for studying nitrogen metabolism and stress responses
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snippet: The model alga Chlamydomonas reinhardtii can grow efficiently on several inorganic nitrogen
323+
sources (e.g
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explanation: Establishes TAP medium as the growth medium for studying nitrogen metabolism and stress
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responses
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culturemech_id: CultureMech:000139
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culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:000139
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metals_present:
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- IRON
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- TITANIUM

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