From 62a4c60098eaf544fca7dd0add0ae19fa7e5625b Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Mon, 15 Jun 2026 23:56:46 -0700 Subject: [PATCH] Add METPO v7 (2 causal-mechanism classes) + ground 4 residual node concepts MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit New proposal cohort metpo_traitmech_v7 lifts the 2 genuinely-novel recurring causal-graph mechanism concepts from the node residual that have no METPO/GO/ CHEBI/ENVO/PATO home: METPO:1007720 salt-in strategy (5 edges; halophile K+/Cl- osmoadaptation) METPO:1007721 reductive genome evolution (3 edges; gene-loss genome reduction) Parented under METPO:1000059 (phenotype) as a fallback; maintainers may reslot (flagged). robot-validate PASS (ELK no UNSAT, +6). Grounding tail (matching, not proposing) — 2 residual concepts had existing ontology homes after all: hydrostatic pressure -> PATO:0001025 pressure (4 edges) chemotaxis signaling -> GO:0006935 chemotaxis (3 edges) Node grounding 1011 -> 1024 / 1643 (61% -> 62%). The rest of the residual is non-ontological graph-narrative phrases — deliberately left as free-text labels rather than force-matched or proposed. ID ranges reserved against the latest METPO release (2026-06-12, w3id/BioPortal): 1-series used to 1007093, 2-series to 2000734; v7 takes 1007720-1007721 (next free above v5). #535 updated with concrete suggested mintable ranges. validate-strict 0 errors; id-label gate clean; grounding idempotent; pages regen. Co-Authored-By: Claude Fable 5 --- NEXT_TASKS.md | 24 ++++-- data/traits/ecology/endosymbiosis.yaml | 31 ++++--- .../environment/extremely_halophilic.yaml | 7 ++ data/traits/environment/halophilic.yaml | 7 ++ .../traits/environment/nacl_optimum_high.yaml | 7 ++ data/traits/environment/piezotolerant.yaml | 35 ++++---- data/traits/environment/pressure_delta.yaml | 29 ++++--- data/traits/environment/pressure_optimum.yaml | 27 +++--- data/traits/environment/pressure_range.yaml | 19 +++-- data/traits/genomics/genome_size.yaml | 33 +++++--- data/traits/genomics/genome_streamlining.yaml | 26 +++--- data/traits/morphology/flagellated.yaml | 7 ++ data/traits/morphology/motile.yaml | 7 ++ data/traits/morphology/motility.yaml | 7 ++ mappings/node_grounding.tsv | 4 + pages/category/ecology.html | 2 +- pages/category/environment.html | 2 +- pages/category/genomics.html | 2 +- pages/category/metabolism.html | 2 +- pages/category/morphology.html | 2 +- pages/category/observation.html | 2 +- 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+- pages/traits/observation/ph_observation.html | 2 +- .../observation/ph_range_observation.html | 2 +- .../temperature_delta_observation.html | 2 +- .../observation/temperature_observation.html | 2 +- .../temperature_range_observation.html | 2 +- .../physiology/antibiotic_resistance.html | 2 +- pages/traits/physiology/autotrophic.html | 2 +- pages/traits/physiology/bioluminescence.html | 2 +- pages/traits/physiology/carboxydotrophic.html | 2 +- .../traits/physiology/catalase_activity.html | 2 +- .../physiology/chemoautolithotrophic.html | 2 +- pages/traits/physiology/chemoautotrophic.html | 2 +- .../traits/physiology/chemoheterotrophic.html | 2 +- .../physiology/chemolithoautotrophic.html | 2 +- .../physiology/chemolithoheterotrophic.html | 2 +- .../traits/physiology/chemolithotrophic.html | 2 +- .../physiology/chemoorganoheterotrophic.html | 2 +- .../traits/physiology/chemoorganotrophic.html | 2 +- pages/traits/physiology/chemotaxis.html | 2 +- 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| 2 +- .../traits/physiology/photoheterotrophic.html | 2 +- .../physiology/photolithoautotrophic.html | 2 +- .../traits/physiology/photolithotrophic.html | 2 +- .../physiology/photoorganoheterotrophic.html | 2 +- pages/traits/physiology/phototrophic.html | 2 +- pages/traits/physiology/quorum_sensing.html | 2 +- .../traits/physiology/spore_germination.html | 2 +- pages/traits/physiology/stress_response.html | 2 +- pages/traits/physiology/trophic_type.html | 2 +- pages/traits/physiology/urease_activity.html | 2 +- .../viable_but_nonculturable_state.html | 2 +- .../has_maximum_observed_value.html | 2 +- .../has_minimum_observed_value.html | 2 +- .../has_observed_spot_value.html | 2 +- .../quantitative_property/has_value.html | 2 +- .../has_value_comments.html | 2 +- .../is_negative_data.html | 2 +- .../observation_data_property.html | 2 +- pages/traits/upper/biological_process.html | 2 +- pages/traits/upper/chemical_entity.html | 2 +- pages/traits/upper/enzyme.html | 2 +- pages/traits/upper/material_entity.html | 2 +- pages/traits/upper/microbe.html | 2 +- pages/traits/upper/observation.html | 2 +- pages/traits/upper/phenotype.html | 2 +- pages/traits/upper/quality.html | 2 +- pages/umap.html | 2 +- .../metpo_proposal_classes_robot.tsv | 4 + proposals/metpo_traitmech_v7/proposal.md | 84 +++++++++++++++++++ reports/node_grounding_residual.tsv | 4 - 506 files changed, 852 insertions(+), 590 deletions(-) create mode 100644 proposals/metpo_traitmech_v7/metpo_proposal_classes_robot.tsv create mode 100644 proposals/metpo_traitmech_v7/proposal.md diff --git a/NEXT_TASKS.md b/NEXT_TASKS.md index 2d005eaf..7e32f643 100644 --- 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 index 55562035..2682c218 100644 --- 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 @@ -38,8 +38,9 @@ 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 @@ -47,8 +48,8 @@ causal_graphs: 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 index 749032ee..7ac882b2 100644 --- 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 index a63a1ad0..17d6cb7e 100644 --- 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 index 9c468db6..ba16318a 100644 --- 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 index e7b1d653..28879bbe 100644 --- a/data/traits/environment/piezotolerant.yaml +++ b/data/traits/environment/piezotolerant.yaml @@ -17,9 +17,9 @@ 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 @@ -27,8 +27,8 @@ evidence: 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 @@ -47,8 +48,8 @@ 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. @@ -56,20 +57,20 @@ causal_graphs: - 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 @@ -77,3 +78,9 @@ curation_history: 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 index ad8e6f20..f0b6d9b4 100644 --- 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 index 3db0a2bc..09b4a0f1 100644 --- 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 diff --git a/data/traits/environment/pressure_range.yaml b/data/traits/environment/pressure_range.yaml index e1b1070e..0be371b2 100644 --- a/data/traits/environment/pressure_range.yaml +++ b/data/traits/environment/pressure_range.yaml @@ -11,8 +11,8 @@ 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 bounded growth-supporting - pressure span (80-140 MPa), the quantity this phenotype records. + notes: Colwellia marinimaniae MTCD1 illustrates a bounded growth-supporting pressure + span (80-140 MPa), the quantity 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 @@ -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: bounded_growth_span label: growth-permissive pressure span node_type: QUALITY @@ -51,8 +52,8 @@ causal_graphs: - subject: pressure_range_trait predicate: associated with object: bounded_growth_span - description: The pressure range records the bounded interval of permissive - hydrostatic pressures. + description: The pressure range records the bounded interval of permissive hydrostatic + pressures. evidence: - reference: DOI:10.1099/ijsem.0.001671 notes: Colwellia marinimaniae MTCD1 illustrates a bounded growth-supporting @@ -63,8 +64,8 @@ curation_history: curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed quantitative companion trait (growth-supporting pressure span) - mirroring the existing temperature_range / nacl_range pattern, to fill the - pressure coverage gap. + mirroring the existing temperature_range / nacl_range pattern, to fill the pressure + coverage gap. llm_assisted: true - timestamp: '2026-06-09T14:00:00Z' curator: claude @@ -72,3 +73,9 @@ curation_history: changes: Added evidence-backed causal graph (pressure-axis defines bounded growth span) 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/genomics/genome_size.yaml b/data/traits/genomics/genome_size.yaml index c37e963a..252b5979 100644 --- a/data/traits/genomics/genome_size.yaml +++ b/data/traits/genomics/genome_size.yaml @@ -1,8 +1,8 @@ identifier: traitmech:000098 label: genome size -definition: A quantitative genomics property describing the total length of an - organism's genome (typically expressed in megabase pairs), which varies widely - across prokaryotes and reflects lifestyle and evolutionary forces. +definition: A quantitative genomics property describing the total length of an organism's + genome (typically expressed in megabase pairs), which varies widely across prokaryotes + and reflects lifestyle and evolutionary forces. definition_source: DOI:10.1038/nrmicro3331 trait_category: GENOMICS term_kind: CLASS @@ -15,11 +15,11 @@ synonyms: source: DOI:10.1038/nrmicro3331 evidence: - reference: DOI:10.1038/nrmicro3331 - notes: Batut et al. review reductive genome evolution, linking genome size to - population size and lifestyle across prokaryotes. + notes: Batut et al. review reductive genome evolution, linking genome size to population + size and lifestyle across prokaryotes. - reference: DOI:10.1038/ismej.2014.60 - notes: Giovannoni et al. discuss streamlining theory and the small genomes of - abundant free-living microbes. + notes: Giovannoni et al. discuss streamlining theory and the small genomes of abundant + free-living microbes. causal_graphs: - graph_id: genome_size_population_lifestyle title: Genome size reflects effective population size and lifestyle @@ -39,6 +39,7 @@ causal_graphs: label: reductive genome evolution node_type: BIOLOGICAL_PROCESS description: Selective and drift-driven loss of genomic content. + grounding: METPO:1007721 edges: - subject: effective_population_size predicate: regulates @@ -47,8 +48,8 @@ causal_graphs: permits drift-driven loss in symbionts. evidence: - reference: DOI:10.1038/nrmicro3331 - notes: Batut et al. compare reductive genome evolution at both ends of the - population-size spectrum. + notes: Batut et al. compare reductive genome evolution at both ends of the population-size + spectrum. predicate_id: RO:0002211 - subject: reductive_genome_evolution predicate: causes @@ -56,8 +57,8 @@ causal_graphs: description: Reductive evolution sets the observed genome length. evidence: - reference: DOI:10.1038/ismej.2014.60 - notes: Giovannoni et al. link streamlining theory to small genomes in - abundant free-living microbes. + notes: Giovannoni et al. link streamlining theory to small genomes in abundant + free-living microbes. predicate_id: biolink:causes curation_history: - timestamp: '2026-06-05T00:00:00Z' @@ -68,6 +69,12 @@ curation_history: - timestamp: '2026-06-08T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH - changes: Added evidence-backed causal graph (genome size / population-size and - lifestyle) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED. + changes: Added evidence-backed causal graph (genome size / population-size and lifestyle) + with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED. + llm_assisted: true +- timestamp: '2026-06-16T06:54:40Z' + 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/genomics/genome_streamlining.yaml b/data/traits/genomics/genome_streamlining.yaml index 7b6214e7..b5a961d4 100644 --- a/data/traits/genomics/genome_streamlining.yaml +++ b/data/traits/genomics/genome_streamlining.yaml @@ -1,8 +1,8 @@ identifier: traitmech:000099 label: genome streamlining definition: A genomics trait describing selective reduction of genome size and gene - content in free-living microbes with very large effective population sizes, - minimizing the cellular cost of replication and biosynthesis. + content in free-living microbes with very large effective population sizes, minimizing + the cellular cost of replication and biosynthesis. definition_source: DOI:10.1038/ismej.2014.60 trait_category: GENOMICS term_kind: CLASS @@ -39,22 +39,23 @@ causal_graphs: label: reductive genome evolution node_type: BIOLOGICAL_PROCESS description: Selective and drift-driven loss of genomic content. + grounding: METPO:1007721 edges: - subject: oligotrophic_environment predicate: selects for object: streamlining_trait - description: Resource limitation and large Ne favor minimizing cellular cost - via genome reduction. + description: Resource limitation and large Ne favor minimizing cellular cost via + genome reduction. evidence: - reference: DOI:10.1038/ismej.2014.60 - notes: Giovannoni et al. articulate streamlining theory for abundant - oligotrophic microbes. + notes: Giovannoni et al. articulate streamlining theory for abundant oligotrophic + microbes. predicate_id: METPO:2007401 - subject: reductive_genome_evolution predicate: causes object: streamlining_trait - description: Reductive evolution is the population-genetic process realizing - the streamlined-genome phenotype. + description: Reductive evolution is the population-genetic process realizing the + streamlined-genome phenotype. evidence: - reference: DOI:10.1038/nrmicro3331 notes: Batut et al. compare reductive genome evolution across the bacterial @@ -71,6 +72,11 @@ curation_history: curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (oligotrophic selection / reductive - evolution) with METPO/biolink predicate groundings; promoted PROPOSED to - REVIEWED. + evolution) with METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED. + llm_assisted: true +- timestamp: '2026-06-16T06:54:40Z' + 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/morphology/flagellated.yaml b/data/traits/morphology/flagellated.yaml index 3b7effa3..15b37ee4 100644 --- a/data/traits/morphology/flagellated.yaml +++ b/data/traits/morphology/flagellated.yaml @@ -53,6 +53,7 @@ causal_graphs: label: chemotaxis signaling node_type: BIOLOGICAL_PROCESS description: Regulation of flagellar rotation and movement direction. + grounding: GO:0006935 edges: - subject: flagellar_filament predicate: enables @@ -134,3 +135,9 @@ curation_history: changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009420×1, GO:0009424×1). llm_assisted: true +- timestamp: '2026-06-16T06:54:40Z' + curator: claude + action: GROUND_CAUSAL_NODES + changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv + (GO:0006935×1). + llm_assisted: true diff --git a/data/traits/morphology/motile.yaml b/data/traits/morphology/motile.yaml index 3c680744..07f93d1c 100644 --- a/data/traits/morphology/motile.yaml +++ b/data/traits/morphology/motile.yaml @@ -56,6 +56,7 @@ causal_graphs: label: chemotaxis signaling node_type: BIOLOGICAL_PROCESS description: Regulatory system that biases movement toward favorable conditions. + grounding: GO:0006935 edges: - subject: metabolic_energy predicate: generates @@ -157,3 +158,9 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1). llm_assisted: true +- timestamp: '2026-06-16T06:54:40Z' + curator: claude + action: GROUND_CAUSAL_NODES + changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv + (GO:0006935×1). + llm_assisted: true diff --git a/data/traits/morphology/motility.yaml b/data/traits/morphology/motility.yaml index 5a4891b9..08abdc52 100644 --- a/data/traits/morphology/motility.yaml +++ b/data/traits/morphology/motility.yaml @@ -56,6 +56,7 @@ causal_graphs: node_type: BIOLOGICAL_PROCESS description: Signal transduction that changes motility direction in response to environmental cues. + grounding: GO:0006935 edges: - subject: flagellar_motor predicate: enables @@ -141,3 +142,9 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1). llm_assisted: true +- timestamp: '2026-06-16T06:54:40Z' + curator: claude + action: GROUND_CAUSAL_NODES + changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv + (GO:0006935×1). + llm_assisted: true diff --git a/mappings/node_grounding.tsv b/mappings/node_grounding.tsv index a9fb3332..22765f4a 100644 --- a/mappings/node_grounding.tsv +++ b/mappings/node_grounding.tsv @@ -143,3 +143,7 @@ phenazine biosynthesis BIOLOGICAL_PROCESS GO:0002047 phenazine biosynthetic proc type iv pilus CELLULAR_LOCALIZATION GO:0044096 type IV pilus skos:exactMatch GO high exact GO-CC term via kg-microbe merged-kg (normalized match, verified) habitat ENVIRONMENTAL_FACTOR ENVO:01000739 habitat skos:exactMatch ENVO medium exact ENVO term (generic) via kg-microbe merged-kg (normalized match, verified) ultraviolet radiation ENVIRONMENTAL_FACTOR ENVO:21001216 ultraviolet radiation skos:exactMatch ENVO high exact ENVO term via kg-microbe merged-kg (normalized match, verified) +hydrostatic pressure ENVIRONMENTAL_FACTOR PATO:0001025 pressure skos:closeMatch PATO high grounding-tail: PATO pressure quality +chemotaxis signaling BIOLOGICAL_PROCESS GO:0006935 chemotaxis skos:closeMatch GO medium grounding-tail: GO chemotaxis (signal-transduction sense) +salt-in strategy BIOLOGICAL_PROCESS METPO:1007720 salt-in strategy skos:exactMatch METPO high proposed upstream in proposals/metpo_traitmech_v7 +reductive genome evolution BIOLOGICAL_PROCESS METPO:1007721 reductive genome evolution skos:exactMatch METPO high proposed upstream in proposals/metpo_traitmech_v7 diff --git a/pages/category/ecology.html b/pages/category/ecology.html index f622fb1c..da2a6c75 100644 --- a/pages/category/ecology.html +++ b/pages/category/ecology.html @@ -244,7 +244,7 @@

ECOLOGY (26)