Burn down the 11 disposition-typing findings — none of the eight were retypes (#352)

data/traits/environment/nacl_delta_low.yaml

@@ -63,10 +63,6 @@ causal_graphs:
     node_type: CHEMICAL
     description: Accumulation of proline as a compatible solute supporting growth
       at higher NaCl.
-  - node_id: salt_tolerance_breadth
-    label: salt-tolerance breadth
-    node_type: CAPACITY
-    description: Capacity to grow across a range of ambient NaCl concentrations.
   edges:
   - subject: limited_osmoadaptive_flexibility
     predicate: confers
@@ -89,7 +85,7 @@ causal_graphs:
     predicate_id: rdfs:subClassOf
   - subject: ectoine_biosynthesis
     predicate: supports
-    object: salt_tolerance_breadth
+    object: nacl_delta
     description: Ectoine biosynthesis capacity broadens NaCl tolerance; its loss narrows
       the growth range.
     evidence:
@@ -108,7 +104,7 @@ causal_graphs:
         (opuAC, proX/proV/proW) supporting osmoadaptation.
   - subject: trkh_k_uptake
     predicate: supports
-    object: salt_tolerance_breadth
+    object: nacl_delta
     description: TrkH K+ uptake supports intracellular K+ homeostasis enabling salt
       tolerance; its absence may contribute to narrow breadth.
     evidence:
@@ -117,7 +113,7 @@ causal_graphs:
         of compatible solutes and K+ supports salt adaptation.
   - subject: nhac_antiporter
     predicate: supports
-    object: salt_tolerance_breadth
+    object: nacl_delta
     description: NhaC Na+/H+ antiporters support ion homeostasis under salt stress;
       a candidate breadth-expanding mechanism whose absence may contribute to NaCl
       delta low.
@@ -127,24 +123,14 @@ causal_graphs:
         (~3.27 and 3.22-fold).
   - subject: intracellular_proline
     predicate: supports
-    object: salt_tolerance_breadth
+    object: nacl_delta
     description: Increased intracellular proline as a compatible solute supports growth
       at higher NaCl, broadening tolerance.
     evidence:
     - reference: DOI:10.1128/aem.01195-24
       notes: Engineered proline biosynthesis with blocked catabolism increased intracellular
         proline and restored growth at 8% NaCl; supports osmolyte role of proline
         in salt-tolerance breadth.
-  - subject: salt_tolerance_breadth
-    predicate: is a
-    object: nacl_delta
-    description: Salt-tolerance breadth is the capacity quantified by the NaCl-delta
-      phenotype.
-    evidence:
-    - reference: DOI:10.1093/femsre/fuy009
-      notes: Osmoadaptation review frames salinity tolerance breadth as the basis
-        of the NaCl-delta (stenohaline vs euryhaline) distinction.
-    predicate_id: rdfs:subClassOf
 curation_history:
 - timestamp: '2026-05-05T01:35:46.840753+00:00'
   curator: seed_from_metpo
@@ -188,3 +174,17 @@ curation_history:
     or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8
     and v9 and are placeholder ids until METPO mints them.
   llm_assisted: true
+- timestamp: '2026-08-08T05:00:00Z'
+  curator: claude
+  action: MERGE_CAUSAL_NODE
+  changes: 'Merged node salt_tolerance_breadth into nacl_delta and repointed its edges.
+    Issue 352. A FIFTH restatement, caught in review (#360). ''Capacity to grow across
+    a range of ambient NaCl concentrations'' against nacl_delta''s ''Breadth of the
+    growth-supporting NaCl range'' -- the same claim, and nacl_delta is in the same
+    graph already TRAIT and already grounded METPO:1000335. I had retyped it and grounded
+    it METPO:1000622 (halotolerant), which is a DEGREE of tolerance, not a breadth:
+    1000622 is a halophily preference (sub 1000629) while 1000335 is a delta (sub
+    1000532/1000534), so the node''s existing `is a -> nacl_delta` edge asserted halotolerant
+    sub NaCl delta, a subsumption METPO does not have. The absolute-vs-breadth distinction
+    this migration insists on for pH, missed for salt.'
+  llm_assisted: true

data/traits/environment/oxygen_preference.yaml

@@ -96,10 +96,6 @@ causal_graphs:
     node_type: GENE_OR_PROTEIN
     description: Enzyme that dismutates superoxide; key oxidative-stress defense.
     grounding: GO:0004784
-  - node_id: oxygen_tolerance
-    label: oxygen tolerance
-    node_type: CAPACITY
-    description: Capacity of a cell to survive exposure to molecular oxygen.
   edges:
   - subject: ambient_oxygen
     predicate: defines
@@ -180,7 +176,7 @@ causal_graphs:
         to O2 or H2O2 stress.
   - subject: detoxifying_enzyme_expression
     predicate: increases
-    object: oxygen_tolerance
+    object: oxygen_preference_trait
     description: A larger detoxifying-enzyme repertoire increases survival under oxygen
       exposure.
     evidence:
@@ -199,7 +195,7 @@ causal_graphs:
     predicate_id: METPO:2007809
   - subject: superoxide_dismutase
     predicate: increases
-    object: oxygen_tolerance
+    object: oxygen_preference_trait
     description: Higher superoxide dismutase activity is associated with higher oxygen
       tolerance.
     evidence:
@@ -300,3 +296,19 @@ curation_history:
     proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints
     them.
   llm_assisted: true
+- timestamp: '2026-08-08T05:00:00Z'
+  curator: claude
+  action: MERGE_CAUSAL_NODE
+  changes: 'Merged node oxygen_tolerance into oxygen_preference_trait and repointed
+    its edges. Issue 352. A SIXTH restatement (#360). METPO:1000601''s own definition
+    is ''an organism''s oxygen requirements OR TOLERANCE for growth'', so ''capacity
+    of a cell to survive exposure to molecular oxygen'' is part of what the anchor
+    already says. I had grounded it METPO:1000609 (aerotolerant), which METPO defines
+    as ''does NOT USE O2 for growth but tolerates its presence'' -- the aerotolerant-anaerobe
+    phenotype, false of the obligate aerobes this node also covers -- and which is
+    itself sub METPO:1000601, making it a sixth child phenotype in a graph that wires
+    the other four in with `is a` and left this one unlinked. aerotolerant.yaml, the
+    record FOR 1000609, has no such node at all: it models the same biology as detoxification
+    processes. Merging attaches the ROS-defence island to the trait, which unlike
+    a retype is a real connectivity gain.'
+  llm_assisted: true

data/traits/environment/ph_delta.yaml

@@ -70,10 +70,6 @@ causal_graphs:
     node_type: PATHWAY
     description: Decarboxylase systems that consume intracellular protons and export
       amines under acid stress.
-  - node_id: low_ph_tolerance
-    label: low-pH tolerance
-    node_type: CAPACITY
-    description: Capacity to grow and survive under acidic external pH.
   - node_id: oxidative_phosphorylation
     label: oxidative phosphorylation
     node_type: BIOLOGICAL_PROCESS
@@ -148,7 +144,7 @@ causal_graphs:
     predicate_id: RO:0002212
   - subject: amino_acid_decarboxylase_acid_resistance
     predicate: increases
-    object: low_ph_tolerance
+    object: ph_delta_trait
     description: Amino-acid decarboxylase acid-resistance systems increase low-pH
       tolerance.
     evidence:
@@ -216,3 +212,17 @@ curation_history:
     is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8
     and are placeholder ids until METPO mints them.
   llm_assisted: true
+- timestamp: '2026-08-08T05:00:00Z'
+  curator: claude
+  action: MERGE_CAUSAL_NODE
+  changes: 'Merged node low_ph_tolerance into ph_delta_trait and repointed its edges.
+    Issue 352. An EIGHTH restatement (#360). I had grounded it METPO:1003008 (acidotolerant)
+    and claimed ''no collision'' with the record''s METPO:1000232 (pH delta). No collision,
+    but the wrong SCOPE: 1003008 is defined as tolerating acid ''WHILE MAINTAINING
+    OPTIMAL GROWTH NEAR NEUTRAL pH'', which excludes the acidophiles this generic
+    pH-delta record covers. A grounding narrower than the node it labels is a false
+    claim about every organism in the excluded part. Also a pure sink. Merging repoints
+    amino_acid_decarboxylase_acid_resistance onto ph_delta_trait, which reads correctly:
+    an acid-resistance system widens the growth-supporting pH range, and a pH delta
+    IS that range.'
+  llm_assisted: true

data/traits/environment/ph_delta_high.yaml

@@ -78,7 +78,7 @@ causal_graphs:
   - node_id: growth_external_ph_5_5_9
     label: growth across external pH 5.5-9.0
     node_type: TRAIT
-    grounding: METPO:1000478
+    grounding: METPO:1000332
     description: Growth supported across the neutralophile external pH range ~5.5-9.0.
   - node_id: constant_pmf
     label: constant proton motive force
@@ -286,3 +286,12 @@ curation_history:
     this record''s own ph_delta_high_trait, so it takes the same METPO:1000478; merging
     the two nodes is tracked in issue 352.'
   llm_assisted: true
+- timestamp: '2026-08-08T05:00:00Z'
+  curator: claude
+  action: REGROUND_CAUSAL_NODE
+  changes: 'Regrounded node growth_external_ph_5_5_9 from METPO:1000478 to METPO:1000332.
+    Issue 352. Shared METPO:1000478 with ph_delta_high_trait, but the two say different
+    things: this node is an ABSOLUTE external range (''~5.5-9.0''), while ph_delta_high_trait
+    is a BREADTH (''approximately 5-9 pH units''), which is what a pH DELTA is. 1000478
+    belongs to the delta; this is a pH range (METPO:1000332).'
+  llm_assisted: true

data/traits/environment/ph_delta_low.yaml

@@ -54,10 +54,6 @@ causal_graphs:
     node_type: BIOLOGICAL_PROCESS
     description: Tuning of Delta-psi and Delta-pH components of the proton motive
       force.
-  - node_id: ph_homeostasis_capacity
-    label: pH homeostasis capacity
-    node_type: CAPACITY
-    description: Capacity to balance and maintain cytoplasmic pH under pH stress.
   - node_id: weak_organic_acids
     label: weak organic acids
     node_type: CHEMICAL
@@ -114,7 +110,7 @@ causal_graphs:
     predicate_id: METPO:2007406
   - subject: pmf_architecture
     predicate: determines
-    object: ph_homeostasis_capacity
+    object: cytoplasmic_ph_homeostasis
     description: PMF architecture (Delta-psi and Delta-pH balancing) determines pH
       homeostasis capacity.
     evidence:
@@ -198,3 +194,12 @@ curation_history:
     or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8
     and v9 and are placeholder ids until METPO mints them.
   llm_assisted: true
+- timestamp: '2026-08-08T05:00:00Z'
+  curator: claude
+  action: MERGE_CAUSAL_NODE
+  changes: Merged node ph_homeostasis_capacity into cytoplasmic_ph_homeostasis and
+    repointed its edges. Issue 352. 'Capacity to balance and maintain cytoplasmic
+    pH under pH stress' is cytoplasmic_ph_homeostasis, which is IN THE SAME GRAPH
+    already typed BIOLOGICAL_PROCESS and grounded GO:0051453. Grounding the capacity
+    node to GO:0051453 would have produced a DUPLICATE_GROUNDING against it.
+  llm_assisted: true

data/traits/environment/psychrotolerant.yaml

@@ -85,10 +85,6 @@ causal_graphs:
     label: cryoprotection against freeze-thaw cycles
     node_type: BIOLOGICAL_PROCESS
     description: Protection of cells from damage during freeze-thaw cycling.
-  - node_id: growth_at_4c
-    label: growth at 4 degrees C
-    node_type: CAPACITY
-    description: Ability to grow at refrigeration-range low temperature (4 C).
   edges:
   - subject: low_temperature
     predicate: decreases
@@ -169,15 +165,6 @@ causal_graphs:
     - reference: DOI:10.37256/amtt.5220244537
       notes: EPS surrounding cells play a critical role in cold adaptation by providing
         protection against freeze-thaw cycles and acting as cryoprotectants.
-  - subject: psychrotolerant_trait
-    predicate: has capability
-    object: growth_at_4c
-    description: The psychrotolerant trait entails the capacity to grow at low temperatures
-      such as 4 C while retaining higher optimal temperatures.
-    evidence:
-    - reference: DOI:10.1007/s42770-023-01057-4
-      notes: Psychrotolerant/psychrotroph microbes can grow at 4 C and have optimal
-        growth temperatures above 20 C.
 curation_history:
 - timestamp: '2026-05-05T01:35:46.859611+00:00'
   curator: seed_from_metpo
@@ -282,3 +269,13 @@ curation_history:
     is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8
     and are placeholder ids until METPO mints them.
   llm_assisted: true
+- timestamp: '2026-08-08T05:00:00Z'
+  curator: claude
+  action: DROP_CAUSAL_NODE
+  changes: Dropped node growth_at_4c and its edges. Issue 352. 'Ability to grow at
+    refrigeration-range low temperature (4 C)' IS METPO:1000618 (psychrotolerant),
+    the record's own term and the grounding of psychrotolerant_trait, which is the
+    node it hangs off. A leaf restating its own parent. The parent keeps two other
+    in-edges (cold_shock_response confers, facultative_lipid_remodeling manifests
+    as), so nothing is stranded.
+  llm_assisted: true

data/traits/environment/slightly_halophilic.yaml

@@ -43,10 +43,6 @@ causal_graphs:
     label: osmoprotectant transport
     node_type: MOLECULAR_FUNCTION
     description: Uptake of compatible solutes such as glycine betaine.
-  - node_id: salt_tolerance
-    label: salt tolerance
-    node_type: CAPACITY
-    description: Capacity to grow and survive under elevated salinity / salt stress.
   - node_id: ectoine_biosynthesis
     label: ectoine biosynthesis
     node_type: BIOLOGICAL_PROCESS
@@ -131,7 +127,7 @@ causal_graphs:
     predicate_id: RO:0002234
   - subject: ectoine
     predicate: increases
-    object: salt_tolerance
+    object: slightly_halophilic_trait
     description: Accumulation of ectoine as a compatible solute increases salt tolerance.
     evidence:
     - reference: DOI:10.1128/aem.01905-23
@@ -140,7 +136,7 @@ causal_graphs:
     predicate_id: RO:0002213
   - subject: osmoprotectant_transport
     predicate: increases
-    object: salt_tolerance
+    object: slightly_halophilic_trait
     description: Uptake of compatible solutes is a general salt-out osmoadaptation
       strategy that raises salt tolerance.
     evidence:
@@ -274,3 +270,23 @@ curation_history:
     proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints
     them.
   llm_assisted: true
+- timestamp: '2026-08-08T05:00:00Z'
+  curator: claude
+  action: MERGE_CAUSAL_NODE
+  changes: 'Merged node salt_tolerance into slightly_halophilic_trait and repointed
+    its edges. Issue 352. A SEVENTH restatement, caught in the third review round
+    (#360). I had grounded it METPO:1000622 (halotolerant), reasoning that the record
+    is METPO:1000625 (slightly halophilic) so the term is ''distinct''. It is distinct
+    in the worst way: 1000622 and 1000625 are DIRECT SIBLINGS under 1000629 (halophily
+    preference), and 1000622 means ''tolerates high salt but DOES NOT REQUIRE it for
+    growth'' while 1000625 means the organism ''REQUIRES low to moderate salt for
+    optimal growth''. So the node asserted of this record the negation of what the
+    record''s own term says. Distinct is not the test; compatible is. NO CONNECTIVITY
+    CLAIM HERE: the node was already in the trait''s component via osmoprotectant_transport
+    -> compatible_solutes -> osmotic_stress, so merging leaves the graph at 2 components
+    and is a correctness fix, not a structural one. METPO has no generic salt-tolerance
+    disposition to reground to: halotolerant and acidotolerant are the only candidate
+    labels and each already anchors its own record. Recorded as issue #364, which
+    proposes a tolerance axis distinct from the preference axis; nothing under proposals/
+    yet.'
+  llm_assisted: true

data/traits/morphology/non_spore_forming.yaml

@@ -70,10 +70,6 @@ causal_graphs:
     node_type: MOLECULAR_FUNCTION
     description: Reduced or absent activity of the Spo0A master regulator of endospore
       formation.
-  - node_id: loss_sporulation_capacity
-    label: loss of sporulation capacity
-    node_type: CAPACITY
-    description: Loss of the capacity to undergo sporulation.
   - node_id: rap_phosphatases
     label: Rap phosphatases
     node_type: GENE_OR_PROTEIN
@@ -143,22 +139,13 @@ causal_graphs:
     predicate_id: biolink:causes
   - subject: low_spo0a_activity
     predicate: causes
-    object: loss_sporulation_capacity
+    object: non_spore_forming_trait
     description: Low or absent Spo0A activity abolishes sporulation capacity.
     evidence:
     - reference: DOI:10.3389/fmicb.2021.630573
       notes: Spo0A is the master regulator of endospore formation; elevated Spo0A~P
         is required to trigger sporulation.
     predicate_id: biolink:causes
-  - subject: loss_sporulation_capacity
-    predicate: manifests as
-    object: non_spore_forming_trait
-    description: Loss of sporulation capacity manifests the non-spore-forming phenotype.
-    evidence:
-    - reference: DOI:10.3389/fmicb.2021.630573
-      notes: Failure to produce/activate Spo0A prevents sporulation, yielding the
-        non-spore-forming trait.
-    predicate_id: METPO:2007400
   - subject: rap_phosphatases
     predicate: dephosphorylates
     object: spo0f_dephosphorylation
@@ -235,3 +222,13 @@ curation_history:
   changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
     (biolink:causes×2, METPO:2007400×2, RO:0002212×1).
   llm_assisted: true
+- timestamp: '2026-08-08T05:00:00Z'
+  curator: claude
+  action: MERGE_CAUSAL_NODE
+  changes: Merged node loss_sporulation_capacity into non_spore_forming_trait and
+    repointed its edges. Issue 352. 'Loss of the capacity to undergo sporulation'
+    IS the record's own trait (METPO:1000872, non-spore forming), so the only correct
+    grounding duplicates the anchor. Collapsing leaves low_spo0a_activity -causes->
+    non_spore_forming_trait, which is the shape loss_sporulation_genes already uses
+    in this graph.
+  llm_assisted: true