CultureBotAI · realmarcin · Jun 16, 2026 · Jun 16, 2026
diff --git a/data/traits/morphology/capsule.yaml b/data/traits/morphology/capsule.yaml
@@ -50,6 +50,16 @@ causal_graphs:
     node_type: QUALITY
     description: Reduced recognition and clearance by host innate immunity.
   edges:
+  - subject: capsule_assembly
+    predicate: produces
+    object: capsular_polysaccharide
+    description: Capsule biosynthesis synthesizes and exports the high-MW capsular
+      polysaccharide.
+    evidence:
+    - reference: DOI:10.1146/annurev.biochem.75.103004.142545
+      notes: Whitfield reviews biosynthesis, export, and surface assembly of the
+        capsular polysaccharide polymer.
+    predicate_id: biolink:produces
   - subject: capsule_assembly
     predicate: enables
     object: capsule_trait
@@ -86,3 +96,9 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (CHEBI:3379×1).
   llm_assisted: true
+- timestamp: '2026-06-16T00:00:00Z'
+  curator: claude
+  action: FIX_ORPHAN_NODE
+  changes: Connected the previously-orphaned capsular_polysaccharide node via a
+    'produces' (biolink:produces) edge from capsule_assembly.
+  llm_assisted: true
diff --git a/data/traits/physiology/urease_activity.yaml b/data/traits/physiology/urease_activity.yaml
@@ -75,6 +75,16 @@ causal_graphs:
     - reference: DOI:10.1128/mr.53.1.85-108.1989
       notes: Mobley & Hausinger support ammonia release from urea hydrolysis.
     predicate_id: METPO:2000202
+  - subject: urease_function
+    predicate: manifests as
+    object: urease_activity_trait
+    description: Urease enzymatic activity manifests as the observable urease-activity
+      phenotype scored by the diagnostic urease test.
+    evidence:
+    - reference: DOI:10.1128/mr.59.3.451-480.1995
+      notes: Urease activity (urea-to-ammonia hydrolysis raising local pH) is the
+        assayable phenotype used to score urease-positive organisms.
+    predicate_id: METPO:2007400
 curation_history:
 - timestamp: '2026-06-04T00:00:00Z'
   curator: claude
@@ -95,3 +105,10 @@ curation_history:
   changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
     (UniProtKB:A0A090IGX8×1).
   llm_assisted: true
+- timestamp: '2026-06-16T00:00:00Z'
+  curator: claude
+  action: FIX_ORPHAN_NODE
+  changes: Connected the previously-orphaned urease_activity_trait node via a
+    'manifests as' (METPO:2007400) edge from urease_function, so the molecular
+    function links to the observable trait.
+  llm_assisted: true
diff --git a/justfile b/justfile
@@ -48,6 +48,12 @@ audit-writers *args:
 audit-proposals *args:
     uv run python scripts/audit_proposals.py {{args}}
 
+# Structural-integrity audit of causal graphs: flag dangling edges (subject/
+# object not a declared node) and orphan nodes (declared but unreferenced).
+# Emits reports/causal_graph_audit.tsv; exits 1 on any defect.
+audit-graphs *args:
+    uv run python scripts/audit_causal_graphs.py {{args}}
+
 # Verify a METPO ROBOT-template proposal cohort under proposals/.
 # Runs column-count, header, parent integrity, subset tag, and scope-A/C
 # coverage checks. See .claude/skills/metpo-proposal/SKILL.md.
@@ -170,7 +176,7 @@ check: lint test
 # Composite QC: strict closed-schema validation + schema-quality probes +
 # writers audit + proposal citation bar. Mirrors the qc target in
 # MediaIngredientMech / CultureMech.
-qc: validate-strict audit-schema audit-writers audit-proposals
+qc: validate-strict audit-schema audit-writers audit-proposals audit-graphs
 
 # --- id↔label correspondence gate (vendored byte-identical across the Mech repos) ---
 

diff --git a/pages/category/ecology.html b/pages/category/ecology.html
@@ -244,7 +244,7 @@ <h1>ECOLOGY <span class="meta">(26)</span></h1>
 </main>
 <footer class="site-footer">
   <div class="wrap">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/category/environment.html b/pages/category/environment.html
@@ -1004,7 +1004,7 @@ <h1>ENVIRONMENT <span class="meta">(121)</span></h1>
 </main>
 <footer class="site-footer">
   <div class="wrap">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/category/genomics.html b/pages/category/genomics.html
@@ -188,7 +188,7 @@ <h1>GENOMICS <span class="meta">(19)</span></h1>
 </main>
 <footer class="site-footer">
   <div class="wrap">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/category/metabolism.html b/pages/category/metabolism.html
@@ -1180,7 +1180,7 @@ <h1>METABOLISM <span class="meta">(143)</span></h1>
 </main>
 <footer class="site-footer">
   <div class="wrap">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/category/morphology.html b/pages/category/morphology.html
@@ -740,7 +740,7 @@ <h1>MORPHOLOGY <span class="meta">(88)</span></h1>
 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/category/observation.html b/pages/category/observation.html
@@ -196,7 +196,7 @@ <h1>OBSERVATION <span class="meta">(20)</span></h1>
 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/category/physiology.html b/pages/category/physiology.html
@@ -396,7 +396,7 @@ <h1>PHYSIOLOGY <span class="meta">(45)</span></h1>
 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/category/quantitative_property.html b/pages/category/quantitative_property.html
@@ -92,7 +92,7 @@ <h1>QUANTITATIVE_PROPERTY <span class="meta">(7)</span></h1>
 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/category/upper.html b/pages/category/upper.html
@@ -100,7 +100,7 @@ <h1>UPPER <span class="meta">(8)</span></h1>
 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/index.html b/pages/index.html
@@ -114,7 +114,7 @@ <h2>About</h2>
 </main>
 <footer class="site-footer">
   <div class="wrap">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/animal_pathogen.html b/pages/traits/ecology/animal_pathogen.html
@@ -661,7 +661,7 @@ <h2>kg-microbe</h2>
 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/biofilm_formation.html b/pages/traits/ecology/biofilm_formation.html
@@ -597,7 +597,7 @@ <h2>kg-microbe</h2>
 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/biosafety_level.html b/pages/traits/ecology/biosafety_level.html
@@ -717,7 +717,7 @@ <h2>kg-microbe</h2>
 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/biosafety_level_1.html b/pages/traits/ecology/biosafety_level_1.html
@@ -603,7 +603,7 @@ <h2>kg-microbe</h2>
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 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/biosafety_level_2.html b/pages/traits/ecology/biosafety_level_2.html
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/biosafety_level_3.html b/pages/traits/ecology/biosafety_level_3.html
@@ -605,7 +605,7 @@ <h2>kg-microbe</h2>
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 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/biosafety_level_4.html b/pages/traits/ecology/biosafety_level_4.html
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 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/biosafety_level_5.html b/pages/traits/ecology/biosafety_level_5.html
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 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/commensalism.html b/pages/traits/ecology/commensalism.html
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 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/endosymbiosis.html b/pages/traits/ecology/endosymbiosis.html
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 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/free_living.html b/pages/traits/ecology/free_living.html
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 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/gut_associated.html b/pages/traits/ecology/gut_associated.html
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 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/habitat_association.html b/pages/traits/ecology/habitat_association.html
@@ -618,7 +618,7 @@ <h2>kg-microbe</h2>
 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/host_associated.html b/pages/traits/ecology/host_associated.html
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 </main>
 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/human_pathogen.html b/pages/traits/ecology/human_pathogen.html
@@ -655,7 +655,7 @@ <h2>kg-microbe</h2>
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 <footer class="site-footer">
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/mutualism.html b/pages/traits/ecology/mutualism.html
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/nitrogen_fixing_symbiosis.html b/pages/traits/ecology/nitrogen_fixing_symbiosis.html
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/opportunistic_pathogen.html b/pages/traits/ecology/opportunistic_pathogen.html
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     · 477 TraitRecords
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diff --git a/pages/traits/ecology/parasitism.html b/pages/traits/ecology/parasitism.html
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     · 477 TraitRecords
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diff --git a/pages/traits/ecology/pathogenic_to_host.html b/pages/traits/ecology/pathogenic_to_host.html
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     · 477 TraitRecords
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diff --git a/pages/traits/ecology/plant_pathogen.html b/pages/traits/ecology/plant_pathogen.html
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/predatory_bacterium.html b/pages/traits/ecology/predatory_bacterium.html
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     · 477 TraitRecords
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diff --git a/pages/traits/ecology/rhizosphere_association.html b/pages/traits/ecology/rhizosphere_association.html
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     · 477 TraitRecords
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diff --git a/pages/traits/ecology/saprotrophy.html b/pages/traits/ecology/saprotrophy.html
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     · 477 TraitRecords
     · embedding coverage 98.3%

diff --git a/pages/traits/ecology/soil_dwelling.html b/pages/traits/ecology/soil_dwelling.html
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     · 477 TraitRecords
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