CultureBotAI · realmarcin · Jun 16, 2026 · Jun 16, 2026
diff --git a/NEXT_TASKS.md b/NEXT_TASKS.md
@@ -52,13 +52,21 @@ All categories are promoted: the corpus is **427 REVIEWED + 50 DEPRECATED,
 out of scope (see `docs/DEPRECATED_REPLACEMENT_PROPOSAL.md`). No promotion work
 remains.
 
-## 4. Grounding tail + METPO upstream round-trip (deferred)
+## 4. METPO upstream round-trip (BLOCKED on upstream) + residual floor
 
-- Causal-graph grounding stands at **predicates 84% (1082/1284)** and
-  **nodes 61% (1011/1643)**. The remaining residual is non-ontological
-  descriptive phrases / one-off LLM verbs; raising it needs fuzzy matching or
-  new term proposals (diminishing returns, higher risk).
+- Causal-graph grounding now stands at **predicates 85% (1094/1284)** and
+  **nodes 62% (1024/1643)**. The remaining residual is non-ontological
+  graph-narrative phrases (adaptation states, composite descriptors) and vague
+  verbs — these are NOT ontology concepts and should stay as free-text node/edge
+  labels, not be force-matched or proposed. This is the quality floor.
+- Genuinely-novel recurring concepts have been proposed: electron-transfer
+  predicates ([v6](proposals/metpo_traitmech_v6/)) and 2 causal-mechanism
+  classes ([v7](proposals/metpo_traitmech_v7/): salt-in strategy, reductive
+  genome evolution).
 - Upstream submission [berkeleybop/metpo#535](https://github.com/berkeleybop/metpo/issues/535)
-  requests real METPO IDs for cohorts v1-v6 (143 classes + 13 predicates).
-  When minted, run the documented round-trip (swap placeholder
-  `1007xxx`/`2007xxx` for real CURIEs, re-seed).
+  now requests real METPO IDs for cohorts **v1–v7 (145 classes + 13 predicates)**,
+  with concrete suggested mintable ranges from the 2026-06-12 release
+  (classes `1007094–1007238`, predicates `2000735–2000747`). **Blocked on the
+  METPO maintainers minting.** When minted, run the documented round-trip (swap
+  placeholder `1007xxx`/`2007xxx` for real CURIEs in `data/raw/metpo.owl` +
+  groundings, re-seed).
diff --git a/data/traits/ecology/endosymbiosis.yaml b/data/traits/ecology/endosymbiosis.yaml
@@ -1,8 +1,8 @@
 identifier: traitmech:000045
 label: endosymbiosis
 definition: A symbiosis in which the microorganism lives inside the cells or tissues
-  of its host. Obligate intracellular endosymbionts (e.g. of insects) frequently
-  undergo extreme genome reduction.
+  of its host. Obligate intracellular endosymbionts (e.g. of insects) frequently undergo
+  extreme genome reduction.
 definition_source: DOI:10.1038/nrmicro2670
 trait_category: ECOLOGY
 term_kind: CLASS
@@ -15,11 +15,11 @@ synonyms:
   source: DOI:10.1038/nrmicro2670
 evidence:
 - reference: DOI:10.1038/nrmicro2670
-  notes: McCutcheon & Moran, "Extreme genome reduction in symbiotic bacteria",
-    characterize intracellular endosymbionts and their diminished genomes.
+  notes: McCutcheon & Moran, "Extreme genome reduction in symbiotic bacteria", characterize
+    intracellular endosymbionts and their diminished genomes.
 - reference: DOI:10.1038/nrmicro.2017.171
-  notes: Poole et al. describe rhizobia as plant-cell endosymbionts within root
-    nodules, an example of the endosymbiotic lifestyle.
+  notes: Poole et al. describe rhizobia as plant-cell endosymbionts within root nodules,
+    an example of the endosymbiotic lifestyle.
 causal_graphs:
 - graph_id: endosymbiosis_intracellular_genome_reduction
   title: Intracellular endosymbiosis drives extreme genome reduction
@@ -38,17 +38,18 @@ causal_graphs:
   - node_id: reductive_genome_evolution
     label: reductive genome evolution
     node_type: BIOLOGICAL_PROCESS
-    description: Long-term loss of genomic content under relaxed selection and
-      small effective population sizes.
+    description: Long-term loss of genomic content under relaxed selection and small
+      effective population sizes.
+    grounding: METPO:1007721
   edges:
   - subject: intracellular_localization
     predicate: enables
     object: endosymbiosis_trait
     description: Sustained residence inside host cells defines endosymbiosis.
     evidence:
     - reference: DOI:10.1038/nrmicro.2017.171
-      notes: Poole et al. describe rhizobia as plant-cell endosymbionts within
-        root nodules.
+      notes: Poole et al. describe rhizobia as plant-cell endosymbionts within root
+        nodules.
     predicate_id: RO:0002327
   - subject: endosymbiosis_trait
     predicate: causes
@@ -57,8 +58,8 @@ causal_graphs:
       reduction in obligate endosymbionts.
     evidence:
     - reference: DOI:10.1038/nrmicro2670
-      notes: McCutcheon & Moran review extreme genome reduction in obligate
-        symbiotic bacteria.
+      notes: McCutcheon & Moran review extreme genome reduction in obligate symbiotic
+        bacteria.
     predicate_id: biolink:causes
 curation_history:
 - timestamp: '2026-06-02T00:00:00Z'
@@ -73,3 +74,9 @@ curation_history:
   changes: Added evidence-backed causal graph (intracellular endosymbiosis / genome
     reduction) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.
   llm_assisted: true
+- timestamp: '2026-06-16T06:54:39Z'
+  curator: claude
+  action: GROUND_CAUSAL_NODES
+  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
+    (METPO:1007721×1).
+  llm_assisted: true
diff --git a/data/traits/environment/extremely_halophilic.yaml b/data/traits/environment/extremely_halophilic.yaml
@@ -45,6 +45,7 @@ causal_graphs:
     label: salt-in strategy
     node_type: BIOLOGICAL_PROCESS
     description: Intracellular inorganic salt accumulation for osmotic balance.
+    grounding: METPO:1007720
   - node_id: acidic_halophilic_proteins
     label: acidic halophilic proteins
     node_type: GENE_OR_PROTEIN
@@ -128,3 +129,9 @@ curation_history:
   changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
     (METPO:2007401×1).
   llm_assisted: true
+- timestamp: '2026-06-16T06:54:39Z'
+  curator: claude
+  action: GROUND_CAUSAL_NODES
+  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
+    (METPO:1007720×1).
+  llm_assisted: true
diff --git a/data/traits/environment/halophilic.yaml b/data/traits/environment/halophilic.yaml
@@ -51,6 +51,7 @@ causal_graphs:
     label: salt-in strategy
     node_type: BIOLOGICAL_PROCESS
     description: Intracellular inorganic ion accumulation for osmotic balance.
+    grounding: METPO:1007720
   edges:
   - subject: high_salt_environment
     predicate: selects for
@@ -153,3 +154,9 @@ curation_history:
   changes: Overwrote 2 causal-node grounding(s) to corrected CURIEs (phase-2 id-label
     fix; verified vs OAK).
   llm_assisted: true
+- timestamp: '2026-06-16T06:54:39Z'
+  curator: claude
+  action: GROUND_CAUSAL_NODES
+  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
+    (METPO:1007720×1).
+  llm_assisted: true
diff --git a/data/traits/environment/nacl_optimum_high.yaml b/data/traits/environment/nacl_optimum_high.yaml
@@ -49,6 +49,7 @@ causal_graphs:
     node_type: BIOLOGICAL_PROCESS
     description: Intracellular K+ accumulation balancing high external NaCl osmotic
       activity.
+    grounding: METPO:1007720
   edges:
   - subject: hypersaline_nacl
     predicate: selects for
@@ -102,3 +103,9 @@ curation_history:
   changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
     (METPO:2007401×1).
   llm_assisted: true
+- timestamp: '2026-06-16T06:54:39Z'
+  curator: claude
+  action: GROUND_CAUSAL_NODES
+  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
+    (METPO:1007720×1).
+  llm_assisted: true
diff --git a/data/traits/environment/piezotolerant.yaml b/data/traits/environment/piezotolerant.yaml
@@ -17,18 +17,18 @@ evidence:
 - reference: DOI:10.3389/fmolb.2022.1058381
   snippet: Microorganisms adapted to HHP are usually known as piezophiles, referring
     to their preference for high pressure
-  notes: Pressure-adaptation review distinguishes piezotolerant organisms, which
-    withstand high hydrostatic pressure but grow at similar or faster rates at
-    atmospheric pressure, from obligate piezophiles.
+  notes: Pressure-adaptation review distinguishes piezotolerant organisms, which withstand
+    high hydrostatic pressure but grow at similar or faster rates at atmospheric pressure,
+    from obligate piezophiles.
 - reference: DOI:10.1099/ijsem.0.001671
   snippet: growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C
   notes: Provides the contrasting obligate-piezophile reference point against which
     piezotolerant (atmospheric-capable) growth is defined.
 causal_graphs:
 - graph_id: piezotolerance_pressure_range
   title: 'Piezotolerance: growth across atmospheric and elevated pressures'
-  description: Evidence-backed causal sketch linking adaptation to elevated
-    hydrostatic pressure to growth that is sustained at atmospheric pressure.
+  description: Evidence-backed causal sketch linking adaptation to elevated hydrostatic
+    pressure to growth that is sustained at atmospheric pressure.
   nodes:
   - node_id: piezotolerant_trait
     label: piezotolerant
@@ -39,6 +39,7 @@ causal_graphs:
     label: hydrostatic pressure
     node_type: ENVIRONMENTAL_FACTOR
     description: Ambient hydrostatic pressure imposed on the cell.
+    grounding: PATO:0001025
   - node_id: membrane_adaptation
     label: membrane lipid adaptation
     node_type: BIOLOGICAL_PROCESS
@@ -47,33 +48,39 @@ causal_graphs:
   - subject: hydrostatic_pressure
     predicate: regulates
     object: membrane_adaptation
-    description: Hydrostatic pressure modulates membrane fluidity, prompting
-      adaptive lipid composition.
+    description: Hydrostatic pressure modulates membrane fluidity, prompting adaptive
+      lipid composition.
     evidence:
     - reference: DOI:10.3389/fmolb.2022.1058381
       notes: HHP adaptation involves unsaturated and branched-chain fatty acids.
     predicate_id: RO:0002211
   - subject: membrane_adaptation
     predicate: enables
     object: piezotolerant_trait
-    description: Membrane adaptation supports growth across the pressure range
-      atmospheric ↔ high.
+    description: Membrane adaptation supports growth across the pressure range atmospheric
+      ↔ high.
     evidence:
     - reference: DOI:10.1099/ijsem.0.001671
-      notes: Contrast with obligate piezophiles (growth limited to 80-140 MPa)
-        defines piezotolerant as the atmospheric-capable phenotype.
+      notes: Contrast with obligate piezophiles (growth limited to 80-140 MPa) defines
+        piezotolerant as the atmospheric-capable phenotype.
     predicate_id: RO:0002327
 curation_history:
 - timestamp: '2026-05-28T00:00:00Z'
   curator: claude
   action: PROPOSED_FROM_RESEARCH
-  changes: Proposed candidate ENVIRONMENT trait (pressure-tolerant growth) from
-    literature research to complete the pressure-preference axis alongside
-    piezophilic and obligately piezophilic.
+  changes: Proposed candidate ENVIRONMENT trait (pressure-tolerant growth) from literature
+    research to complete the pressure-preference axis alongside piezophilic and obligately
+    piezophilic.
   llm_assisted: true
 - timestamp: '2026-06-09T14:00:00Z'
   curator: claude
   action: CURATED_CAUSAL_GRAPH
   changes: Added evidence-backed causal graph (membrane adaptation across pressure
     range) with RO predicate groundings; promoted PROPOSED to REVIEWED.
   llm_assisted: true
+- timestamp: '2026-06-16T06:54:39Z'
+  curator: claude
+  action: GROUND_CAUSAL_NODES
+  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
+    (PATO:0001025×1).
+  llm_assisted: true
diff --git a/data/traits/environment/pressure_delta.yaml b/data/traits/environment/pressure_delta.yaml
@@ -1,7 +1,7 @@
 identifier: traitmech:000006
 label: pressure delta
-definition: A pressure phenotype with numerical limits expressing the breadth
-  (maximum minus minimum) of hydrostatic pressure supporting growth of an organism.
+definition: A pressure phenotype with numerical limits expressing the breadth (maximum
+  minus minimum) of hydrostatic pressure supporting growth of an organism.
 definition_source: DOI:10.3389/fmolb.2022.1058381
 trait_category: ENVIRONMENT
 term_kind: CLASS
@@ -16,8 +16,8 @@ evidence:
     span as a derived descriptor of pressure-adaptation flexibility.
 - reference: DOI:10.1099/ijsem.0.001671
   snippet: growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C
-  notes: The 80-140 MPa span of Colwellia marinimaniae MTCD1 (delta = 60 MPa)
-    illustrates the breadth this phenotype records.
+  notes: The 80-140 MPa span of Colwellia marinimaniae MTCD1 (delta = 60 MPa) illustrates
+    the breadth this phenotype records.
 causal_graphs:
 - graph_id: pressure_delta_breadth_descriptor
   title: 'Pressure delta: breadth of the pressure-tolerance span'
@@ -34,11 +34,11 @@ causal_graphs:
     label: hydrostatic pressure
     node_type: ENVIRONMENTAL_FACTOR
     description: Ambient hydrostatic pressure imposed on the cell.
+    grounding: PATO:0001025
   - node_id: pressure_tolerance_breadth
     label: pressure-tolerance breadth
     node_type: QUALITY
-    description: Width of the hydrostatic-pressure interval over which growth is
-      sustained.
+    description: Width of the hydrostatic-pressure interval over which growth is sustained.
   edges:
   - subject: hydrostatic_pressure
     predicate: defines
@@ -63,14 +63,19 @@ curation_history:
 - timestamp: '2026-05-28T00:00:00Z'
   curator: claude
   action: PROPOSED_FROM_RESEARCH
-  changes: Proposed quantitative companion trait (pressure-tolerance breadth)
-    mirroring the existing temperature_delta / nacl_delta pattern, to fill the
-    pressure coverage gap.
+  changes: Proposed quantitative companion trait (pressure-tolerance breadth) mirroring
+    the existing temperature_delta / nacl_delta pattern, to fill the pressure coverage
+    gap.
   llm_assisted: true
 - timestamp: '2026-06-09T14:00:00Z'
   curator: claude
   action: CURATED_CAUSAL_GRAPH
-  changes: Added evidence-backed causal graph (pressure-axis defines tolerance
-    breadth) with METPO/biolink predicate groundings; promoted PROPOSED to
-    REVIEWED.
+  changes: Added evidence-backed causal graph (pressure-axis defines tolerance breadth)
+    with METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.
+  llm_assisted: true
+- timestamp: '2026-06-16T06:54:39Z'
+  curator: claude
+  action: GROUND_CAUSAL_NODES
+  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
+    (PATO:0001025×1).
   llm_assisted: true
diff --git a/data/traits/environment/pressure_optimum.yaml b/data/traits/environment/pressure_optimum.yaml
@@ -1,7 +1,7 @@
 identifier: traitmech:000004
 label: pressure optimum
-definition: A pressure phenotype with numerical limits giving the hydrostatic
-  pressure at which an organism grows fastest.
+definition: A pressure phenotype with numerical limits giving the hydrostatic pressure
+  at which an organism grows fastest.
 definition_source: DOI:10.1099/ijsem.0.001671
 trait_category: ENVIRONMENT
 term_kind: CLASS
@@ -11,13 +11,13 @@ parent_traits:
 evidence:
 - reference: DOI:10.1099/ijsem.0.001671
   snippet: growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C
-  notes: Colwellia marinimaniae MTCD1 illustrates a measurable pressure optimum
-    (120 MPa), the quantitative value this phenotype records.
+  notes: Colwellia marinimaniae MTCD1 illustrates a measurable pressure optimum (120
+    MPa), the quantitative value this phenotype records.
 - reference: DOI:10.3389/fmolb.2022.1058381
   snippet: Microorganisms adapted to HHP are usually known as piezophiles, referring
     to their preference for high pressure
-  notes: Pressure-adaptation review supports an organism-specific optimal growth
-    pressure as the defining quantity for piezophile classification.
+  notes: Pressure-adaptation review supports an organism-specific optimal growth pressure
+    as the defining quantity for piezophile classification.
 causal_graphs:
 - graph_id: pressure_optimum_balanced_adaptation
   title: Pressure-optimum balanced adaptation
@@ -33,6 +33,7 @@ causal_graphs:
     label: hydrostatic pressure
     node_type: ENVIRONMENTAL_FACTOR
     description: Ambient hydrostatic pressure imposed on the cell.
+    grounding: PATO:0001025
   - node_id: maximal_growth_rate
     label: maximal growth rate
     node_type: BIOLOGICAL_PROCESS
@@ -41,12 +42,12 @@ causal_graphs:
   - subject: hydrostatic_pressure
     predicate: defines
     object: pressure_optimum_trait
-    description: The hydrostatic-pressure axis defines the value at which growth
-      is fastest.
+    description: The hydrostatic-pressure axis defines the value at which growth is
+      fastest.
     evidence:
     - reference: DOI:10.3389/fmolb.2022.1058381
-      notes: Pressure-adaptation review supports an organism-specific optimal
-        growth pressure as the defining piezophile quantity.
+      notes: Pressure-adaptation review supports an organism-specific optimal growth
+        pressure as the defining piezophile quantity.
     predicate_id: METPO:2007500
   - subject: pressure_optimum_trait
     predicate: associated with
@@ -72,3 +73,9 @@ curation_history:
   changes: Added evidence-backed causal graph (pressure-axis defines optimum) with
     METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.
   llm_assisted: true
+- timestamp: '2026-06-16T06:54:39Z'
+  curator: claude
+  action: GROUND_CAUSAL_NODES
+  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
+    (PATO:0001025×1).
+  llm_assisted: true