CultureBotAI · realmarcin · May 24, 2026 · May 24, 2026 · May 24, 2026
diff --git a/docs/cross_repo_linking.md b/docs/cross_repo_linking.md
@@ -299,6 +299,8 @@ All new fields are optional:
 
 ## Validation
 
+### Schema-level tests
+
 Run the cross-repo linking tests:
 
 ```bash
@@ -311,6 +313,31 @@ Test data files are in `tests/data/test_cross_repo_linking/`:
 - `community_no_links.yaml` -- Backward compatibility
 - `community_all_relationship_types.yaml` -- All 5 enum values
 
+### Cross-repo ID validator
+
+`just validate-cross-repo-ids FILE` checks that `culturemech_id` /
+`mediaingredientmech_id` values match their CURIE patterns and, when
+sibling-repo paths are configured, that the referenced IDs actually
+exist in those repos.
+
+```bash
+# Pattern check only (no sibling-repo paths)
+just validate-cross-repo-ids kb/communities/SPRUCE_Peatland_Methane_Cycling_Community.yaml
+
+# Pattern + existence check
+COMMUNITYMECH_SIBLING_REPOS="CultureMech=../CultureMech/kb/media,MediaIngredientMech=../MediaIngredientMech/kb/ingredients" \
+    just validate-cross-repo-ids-all
+```
+
+The validator returns:
+- `error` for malformed CURIEs or IDs missing from a configured sibling repo
+- `info` for IDs whose existence check was skipped because the relevant
+  sibling-repo path wasn't configured
+- nothing if a community has no cross-repo IDs at all
+
+Sibling-repo paths can also be passed via `--culturemech` /
+`--mediaingredientmech` flags to `scripts/validate_cross_repo_ids.py`.
+
 ## See Also
 
 - [Growth Media Linking](media_linking.md) -- Existing cultivation-based linking

diff --git a/justfile b/justfile
@@ -35,6 +35,16 @@ validate-references-all:
         uv run linkml-reference-validator validate data "$file" -s src/communitymech/schema/communitymech.yaml --config conf/reference_validator.yaml
     done
 
+# Validate cross-repo IDs (CultureMech, MediaIngredientMech) in one community file.
+# Pattern checks always run; existence checks run when sibling-repo paths are
+# configured via COMMUNITYMECH_SIBLING_REPOS env (Name=path,Name=path).
+validate-cross-repo-ids FILE:
+    PYTHONPATH=src uv run python scripts/validate_cross_repo_ids.py {{FILE}}
+
+# Validate cross-repo IDs across all community files.
+validate-cross-repo-ids-all:
+    PYTHONPATH=src uv run python scripts/validate_cross_repo_ids.py kb/communities/*.yaml
+
 # Validate ontology terms in a community file
 validate-terms FILE:
     uv run linkml-term-validator validate-data {{FILE}} -s src/communitymech/schema/communitymech.yaml --labels

diff --git a/kb/communities/AMD_Acidophile_Heterotroph_Network.yaml b/kb/communities/AMD_Acidophile_Heterotroph_Network.yaml
@@ -765,7 +765,6 @@ metals_present:
 - COPPER
 - GOLD
 - IRON
-- TITANIUM
 metal_relevance: PRIMARY
 metal_notes: Metal/REE detected via CHEBI terms in metabolites; Metal/REE detected via environmental factor
   measurements; Metal/REE detected via keyword matching in description (context-validated)
diff --git a/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml b/kb/communities/AMD_Nitrososphaerota_Archaeal.yaml
@@ -699,9 +699,7 @@ environmental_factors:
     explanation: Demonstrates value of genomic data for understanding archaeal adaptations
 metals_present:
 - COPPER
-- GOLD
 - IRON
-- TITANIUM
 metal_relevance: PRIMARY
 metal_notes: Metal/REE detected via CHEBI terms in metabolites; Metal/REE detected via environmental factor
   measurements; Metal/REE detected via keyword matching in description (context-validated)
diff --git a/kb/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.yaml b/kb/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.yaml
@@ -179,6 +179,50 @@ environmental_factors:
     snippet: contributions in soil ecosystems remain unknown
     explanation: Supports terrestrial soil as the focus environment.
 growth_media: []
+related_ingredients:
+- preferred_term: acetate
+  chebi_term:
+    id: CHEBI:30089
+    label: acetate
+  relevance: Asgard archaeal acetogens in this wetland soil generate acetate
+    from carbohydrate breakdown via the Wood-Ljungdahl pathway; acetate is
+    therefore both the headline output of Asgard metabolism in this community
+    and the substrate that feeds the co-resident acetoclastic methanogens.
+  evidence:
+  - reference: PMID:39085194
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: carbohydrate breakdown to acetate and formate
+    explanation: Anchors acetate as the central Asgard metabolic output that
+      modulates downstream methanogenesis substrates in wetland soil.
+- preferred_term: formate
+  chebi_term:
+    id: CHEBI:15740
+    label: formate
+  relevance: Formate co-produced with acetate is a major C1 substrate for
+    hydrogenotrophic and formate-utilizing methanogens, defining a second
+    Asgard-mediated methanogenesis-substrate channel in this community.
+  evidence:
+  - reference: PMID:39085194
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: carbohydrate breakdown to acetate and formate
+    explanation: Anchors formate as the second Asgard-derived methanogenesis
+      substrate alongside acetate.
+- preferred_term: dihydrogen
+  chebi_term:
+    id: CHEBI:18276
+    label: dihydrogen
+  relevance: Expression of [NiFe]-hydrogenases by both Atabeyarchaeia and
+    Freyarchaeia genomes implicates H2 cycling as a core Asgard activity in
+    this wetland soil; any cultivation medium designed around the community
+    would need an H2 headspace.
+  evidence:
+  - reference: PMID:39085194
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: expression of genes for [NiFe]-hydrogenases
+    explanation: Anchors H2 cycling as an in situ expressed Asgard activity.
 external_resources:
 - name: Primary publication for the Asgard wetland soil methanogenesis-substrate
     community

diff --git a/kb/communities/At_RSPHERE_SynCom.yaml b/kb/communities/At_RSPHERE_SynCom.yaml
@@ -427,8 +427,7 @@ environmental_factors:
     plant-microbe interactions, and synthetic community design
 
     '
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: INCIDENTAL
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected
   via keyword matching in description (context-validated)
diff --git a/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml b/kb/communities/Australian_Lead_Zinc_Polymetallic.yaml
@@ -966,10 +966,8 @@ environmental_factors:
     explanation: Documents long-term weathering profile development
 metals_present:
 - COPPER
-- GOLD
 - IRON
 - LEAD
-- TITANIUM
 - ZINC
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via CHEBI terms in metabolites; Metal/REE detected via environmental factor

diff --git a/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml b/kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml
@@ -544,9 +544,7 @@ environmental_factors:
       was narrated for plausible real-world use
     explanation: Describes REE mineralogy at Bayan Obo
 metals_present:
-- GOLD
 - IRON
-- TITANIUM
 rare_earth_elements_present:
 - CERIUM
 - LANTHANUM

diff --git a/kb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml b/kb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml
@@ -351,7 +351,6 @@ growth_media:
     explanation: Establishes mannitol and yeast extract as key medium components for sustained H2 production
   culturemech_id: CultureMech:000139
   culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:000139
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements
diff --git a/kb/communities/Chlamydomonas_Methylobacterium_Mutualism.yaml b/kb/communities/Chlamydomonas_Methylobacterium_Mutualism.yaml
@@ -327,6 +327,5 @@ growth_media:
   culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:000139
 metals_present:
 - IRON
-- TITANIUM
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements
diff --git a/kb/communities/Chlorella_Rhizobium_Bioflocculation.yaml b/kb/communities/Chlorella_Rhizobium_Bioflocculation.yaml
@@ -234,7 +234,6 @@ environmental_factors:
     explanation: Co-culture timing optimized for maximum harvesting efficiency
 metals_present:
 - IRON
-- TITANIUM
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected via keyword
   matching in description (context-validated)
diff --git a/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml b/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml
@@ -610,7 +610,6 @@ environmental_factors:
 metals_present:
 - CHROMIUM
 - IRON
-- TITANIUM
 metal_relevance: PRIMARY
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected via keyword
   matching in description (context-validated)
diff --git a/kb/communities/Cinnamate_Degradation_Consortium.yaml b/kb/communities/Cinnamate_Degradation_Consortium.yaml
@@ -182,8 +182,7 @@ environmental_factors:
     complete mineralization to methane
 
     '
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected via keyword
   matching in description (context-validated)
diff --git a/kb/communities/Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community.yaml b/kb/communities/Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community.yaml
@@ -257,6 +257,54 @@ environmental_factors:
     snippet: emissions of carbon dioxide, methane, and nitrous oxide
     explanation: Supports greenhouse gas endpoints.
 growth_media: []
+related_ingredients:
+- preferred_term: sulfate
+  chebi_term:
+    id: CHEBI:16189
+    label: sulfate
+  relevance: Sulfate is the explicitly manipulated ion in this microcosm
+    experiment; an environment-analog cultivation medium for this community
+    would need sulfate as a controllable variable rather than a fixed
+    background anion, since the study disentangles sulfate effects from other
+    seawater ions on the community.
+  evidence:
+  - reference: PMID:38628812
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: tease apart the effects of sulfate from other seawater ions
+    explanation: Anchors sulfate as the central controllable environmental
+      variable for any medium designed to dogfood this community.
+- preferred_term: seawater ions
+  chebi_term:
+    id: CHEBI:26710
+    label: sodium chloride
+  relevance: Artificial-seawater ions (NaCl as the representative bulk salt)
+    drove the community shifts and GHG emission changes more strongly than
+    sulfate alone; any cultivation medium for this community would need a
+    seawater-equivalent ion background, not just sulfate.
+  evidence:
+  - reference: PMID:38628812
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: other ions present in seawater, not sulfate, drive ecological and
+      biogeochemical responses to seawater intrusion
+    explanation: Anchors NaCl-dominated artificial seawater (representative
+      bulk seawater-ion mixture) as the primary driver of community responses.
+- preferred_term: methane
+  chebi_term:
+    id: CHEBI:16183
+    label: methane
+  relevance: Methane is one of the headline greenhouse gas emission endpoints
+    monitored across all microcosm treatments; an environment-analog medium
+    targeting this community would need methane in the headspace as a key
+    quantitative endpoint.
+  evidence:
+  - reference: PMID:38628812
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: emissions of carbon dioxide, methane, and nitrous oxide
+    explanation: Anchors methane as a measured greenhouse gas endpoint of this
+      microcosm community.
 associated_datasets: []
 external_resources:
 - name: Primary publication for coastal forested wetland seawater-ion microcosms

diff --git a/kb/communities/Copper_Biomining_Heap_Leach.yaml b/kb/communities/Copper_Biomining_Heap_Leach.yaml
@@ -566,7 +566,6 @@ environmental_factors:
 metals_present:
 - COPPER
 - IRON
-- TITANIUM
 metal_relevance: PRIMARY
 metal_notes: Metal/REE detected via CHEBI terms in metabolites; Metal/REE detected via environmental factor
   measurements; Metal/REE detected via keyword matching in description (context-validated)

diff --git a/kb/communities/DVM_Triculture.yaml b/kb/communities/DVM_Triculture.yaml
@@ -375,7 +375,6 @@ environmental_factors:
     snippet: We find that tri-cultures with both routes increase methane production by almost twofold
       compared to co-cultures and are stable in the absence of sulfate
     explanation: Quantifies enhanced productivity from tri-culture interactions
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements
diff --git a/kb/communities/Dangl_SynComm_35.yaml b/kb/communities/Dangl_SynComm_35.yaml
@@ -541,7 +541,6 @@ environmental_factors:
     evidence_source: IN_VITRO
     snippet: Suppressors and nonsuppressors co-occur in the root microbiome and the
       presence of the former can enhance the colonization ability of the latter
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: INCIDENTAL
 metal_notes: Metal/REE detected via environmental factor measurements
diff --git a/kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml b/kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml
@@ -239,7 +239,6 @@ environmental_factors:
     explanation: Quantifies growth conditions for the syntrophic consortium
 metals_present:
 - IRON
-- TITANIUM
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected via keyword
   matching in description (context-validated)

diff --git a/kb/communities/Ewaste_Bioleaching_Consortium.yaml b/kb/communities/Ewaste_Bioleaching_Consortium.yaml
@@ -570,7 +570,6 @@ metals_present:
 - NICKEL
 - PALLADIUM
 - SILVER
-- TITANIUM
 - ZINC
 metal_relevance: PRIMARY
 metal_notes: Metal/REE detected via CHEBI terms in metabolites; Metal/REE detected via environmental factor

diff --git a/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml b/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml
@@ -472,7 +472,6 @@ environmental_factors:
 metals_present:
 - COPPER
 - IRON
-- TITANIUM
 metal_relevance: PRIMARY
 metal_notes: Metal/REE detected via CHEBI terms in metabolites; Metal/REE detected via environmental factor
   measurements; Metal/REE detected via keyword matching in description (context-validated)

diff --git a/kb/communities/GLBRC_Populus_Variovorax_SynCom28.yaml b/kb/communities/GLBRC_Populus_Variovorax_SynCom28.yaml
@@ -833,7 +833,6 @@ external_resources:
   resource_id: zenodo.17466836
   url: https://zenodo.org/records/17466836
   description: Reproducible workflow and supplemental tables including strain metadata for the DefCom.
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: INCIDENTAL
 metal_notes: Metal/REE detected via environmental factor measurements
diff --git a/kb/communities/GLBRC_UFMP_Fermentation_Community.yaml b/kb/communities/GLBRC_UFMP_Fermentation_Community.yaml
@@ -462,9 +462,7 @@ associated_datasets:
 
       '
     explanation: Links the metagenome dataset to the UFMP fermentation community study
-metals_present:
-- GOLD
-- TITANIUM
+metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected via keyword
   matching in description (context-validated)
diff --git a/kb/communities/GOM_Oil_Degrading_Consortium.yaml b/kb/communities/GOM_Oil_Degrading_Consortium.yaml
@@ -174,8 +174,7 @@ environmental_factors:
   description: 'Designed for practical application in bioremediation of oil-contaminated marine environments
 
     '
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected via keyword
   matching in description (context-validated)
diff --git a/kb/communities/Geobacter_Clostridium_DIET.yaml b/kb/communities/Geobacter_Clostridium_DIET.yaml
@@ -437,7 +437,6 @@ growth_media:
     explanation: Establishes anaerobic requirement maintained using Hungate technique
   culturemech_id: CultureMech:015432
   culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:015432
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements
diff --git a/kb/communities/Geobacter_Methanosaeta_DIET.yaml b/kb/communities/Geobacter_Methanosaeta_DIET.yaml
@@ -293,8 +293,7 @@ growth_media:
       specialized medium
   culturemech_id: CultureMech:015435
   culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:015435
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected
   via keyword matching in description (context-validated)
diff --git a/kb/communities/Geobacter_Methanosarcina_DIET.yaml b/kb/communities/Geobacter_Methanosarcina_DIET.yaml
@@ -336,8 +336,7 @@ growth_media:
     explanation: Confirms ethanol as electron donor and DIET mechanism in coculture
   culturemech_id: CultureMech:015434
   culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:015434
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: SIGNIFICANT
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected
   via keyword matching in description (context-validated)
diff --git a/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml b/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml
@@ -725,7 +725,6 @@ environmental_factors:
 metals_present:
 - COPPER
 - IRON
-- TITANIUM
 - ZINC
 metal_relevance: PRIMARY
 metal_notes: Metal/REE detected via CHEBI terms in metabolites; Metal/REE detected via environmental factor

diff --git a/kb/communities/Industrial_Bioreactor_Consortium.yaml b/kb/communities/Industrial_Bioreactor_Consortium.yaml
@@ -999,9 +999,7 @@ environmental_factors:
     explanation: Links high Fe³⁺ to Ferroplasma competitive advantage
 metals_present:
 - COPPER
-- GOLD
 - IRON
-- TITANIUM
 metal_relevance: PRIMARY
 metal_notes: Metal/REE detected via CHEBI terms in metabolites; Metal/REE detected via environmental factor
   measurements; Metal/REE detected via keyword matching in description (context-validated)
diff --git a/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml b/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml
@@ -671,7 +671,6 @@ environmental_factors:
     '
 metals_present:
 - IRON
-- TITANIUM
 rare_earth_elements_present:
 - DYSPROSIUM
 - ERBIUM

diff --git a/kb/communities/Lotus_LjSC3.yaml b/kb/communities/Lotus_LjSC3.yaml
@@ -597,7 +597,6 @@ environmental_factors:
     interactions relevant to sustainable agriculture and reduced fertilizer use
 
     '
-metals_present:
-- TITANIUM
+metals_present: []
 metal_relevance: INCIDENTAL
 metal_notes: Metal/REE detected via environmental factor measurements