From 37448c9246c606c73c292570233075cbae6d9679 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Mon, 25 May 2026 22:01:07 -0700 Subject: [PATCH] =?UTF-8?q?Predicate=20residual=20v5:=20rename=2010=20para?= =?UTF-8?q?phrases=20+=20re-ground=20(=E2=88=9256=20edges)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit One-off migration following the PR #67 pattern — normalizes the next-tier of curator-paraphrased predicate labels to canonical synonyms already in the grounding mappings, then re-runs ground-predicates to fill predicate_id on the 56 affected edges. Renames added to scripts/rename_predicate_labels.py (10 new rules): influences → regulates (7 edges → RO:0002211) determines → causes (6 edges → biolink:causes) sets → defines (6 edges → METPO:2007500) constrains → regulates (6 edges → RO:0002211) input to → participates in (6 edges → biolink:participates_in) powers → enables (6 edges → RO:0002327) organizes → enables (6 edges → RO:0002327) occurs under → occurs in (5 edges → biolink:occurs_in) requires → depends on (4 edges → RO:0002502) triggers → causes (4 edges → biolink:causes) Skipped: engages (vague), incorporated into (wrong-direction), drives production of (too specific). Per-corpus impact: Edges grounded: +56 (from this batch) Distinct labels: −7 Idempotency: re-running both rename and ground-predicates produces no further changes. Verified: - rename --apply → 56 edits, 0 invalid files - ground-predicates --apply → 56 new groundings - validate-strict → 0 ERROR rows / 357 files Co-Authored-By: Claude Opus 4.7 (1M context) --- data/traits/ecology/biosafety_level.yaml | 15 +++++++++- data/traits/environment/aerobic.yaml | 18 ++++++++++-- .../environment/halophily_preference.yaml | 15 +++++++++- data/traits/environment/nacl_optimum.yaml | 15 +++++++++- data/traits/environment/nacl_range.yaml | 18 ++++++++++-- .../environment/obligately_aerobic.yaml | 15 +++++++++- .../environment/obligately_alkaphilic.yaml | 15 +++++++++- .../environment/ph_growth_preference.yaml | 15 +++++++++- data/traits/environment/ph_range.yaml | 18 ++++++++++-- data/traits/environment/stenohaline.yaml | 15 +++++++++- .../environment/temperature_optimum.yaml | 18 ++++++++++-- .../environment/temperature_preference.yaml | 21 ++++++++++++-- .../traits/environment/temperature_range.yaml | 18 ++++++++++-- data/traits/environment/thermotolerant.yaml | 15 +++++++++- data/traits/metabolism/acetogenesis.yaml | 21 ++++++++++++-- .../metabolism/anaerobic_respiration.yaml | 15 +++++++++- .../traits/metabolism/disproportionation.yaml | 15 +++++++++- data/traits/metabolism/homoacetogenesis.yaml | 21 ++++++++++++-- data/traits/metabolism/metabolism.yaml | 15 +++++++++- data/traits/metabolism/methanogenesis.yaml | 15 +++++++++- data/traits/metabolism/syntrophy.yaml | 15 +++++++++- data/traits/morphology/bacillus_shaped.yaml | 15 +++++++++- data/traits/morphology/cell_length.yaml | 15 +++++++++- data/traits/morphology/cell_shape.yaml | 15 +++++++++- data/traits/morphology/cell_width.yaml | 28 ++++++++++++++----- data/traits/morphology/cell_width_small.yaml | 15 +++++++++- data/traits/morphology/crescent_shaped.yaml | 15 +++++++++- data/traits/morphology/filament_shaped.yaml | 15 +++++++++- data/traits/morphology/flagellated.yaml | 15 +++++++++- data/traits/morphology/gliding.yaml | 15 +++++++++- data/traits/morphology/gram_stain.yaml | 18 ++++++++++-- data/traits/morphology/motile.yaml | 15 +++++++++- data/traits/morphology/motility.yaml | 15 +++++++++- data/traits/morphology/rod_shaped.yaml | 15 +++++++++- data/traits/morphology/sphere_shaped.yaml | 15 +++++++++- data/traits/morphology/spiral_shaped.yaml | 15 +++++++++- data/traits/physiology/carboxydotrophic.yaml | 15 +++++++++- data/traits/physiology/methanotrophic.yaml | 15 +++++++++- .../physiology/nutrient_adaptation.yaml | 15 +++++++++- data/traits/physiology/photolithotrophic.yaml | 15 +++++++++- data/traits/physiology/trophic_type.yaml | 21 ++++++++++++-- reports/predicate_grounding_residual.tsv | 10 ------- scripts/rename_predicate_labels.py | 16 +++++++++++ 43 files changed, 625 insertions(+), 71 deletions(-) diff --git a/data/traits/ecology/biosafety_level.yaml b/data/traits/ecology/biosafety_level.yaml index 66c69658..8b75fa18 100644 --- a/data/traits/ecology/biosafety_level.yaml +++ b/data/traits/ecology/biosafety_level.yaml @@ -73,7 +73,7 @@ causal_graphs: description: Proposed enhanced classification beyond BSL-4. edges: - subject: pathogen_hazard_properties - predicate: determines + predicate: causes object: biosafety_level_trait description: Pathogen transmissibility, severity, and treatability jointly determine biosafety-level classification. @@ -82,6 +82,7 @@ causal_graphs: snippet: virulence factors notes: Supports pathogen virulence properties as the biological inputs for hazard-level classification. + predicate_id: biolink:causes - subject: biosafety_level_trait predicate: mandates object: containment_requirements @@ -161,3 +162,15 @@ curation_history: changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×5). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + determines → causes ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:49Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:causes×1). + llm_assisted: true diff --git a/data/traits/environment/aerobic.yaml b/data/traits/environment/aerobic.yaml index 705a5144..23157334 100644 --- a/data/traits/environment/aerobic.yaml +++ b/data/traits/environment/aerobic.yaml @@ -53,7 +53,7 @@ causal_graphs: grounding: METPO:1007504 edges: - subject: aerobic_trait - predicate: requires + predicate: depends on object: molecular_oxygen description: Aerobic growth depends on molecular oxygen availability. evidence: @@ -61,6 +61,7 @@ causal_graphs: snippet: obligate aerobe ... exposed to hypoxia, stops growing notes: Mycobacterium tuberculosis example supports oxygen dependence for aerobic growth. + predicate_id: RO:0002502 - subject: aerobic_trait predicate: has mechanistic process object: aerobic_respiration @@ -71,7 +72,7 @@ causal_graphs: notes: Review supports oxygen-reducing terminal oxidases as core aerobic respiratory enzymes. - subject: aerobic_respiration - predicate: requires + predicate: depends on object: molecular_oxygen description: Aerobic respiration requires oxygen. evidence: @@ -79,6 +80,7 @@ causal_graphs: snippet: transfer electrons from the ETC to O2 notes: Supports molecular oxygen as the terminal acceptor for bacterial respiratory electron transport. + predicate_id: RO:0002502 - subject: molecular_oxygen predicate: acts as object: terminal_electron_acceptor @@ -126,3 +128,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007504×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings: + requires → depends on ×2.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:49Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002502×2). + llm_assisted: true diff --git a/data/traits/environment/halophily_preference.yaml b/data/traits/environment/halophily_preference.yaml index 3638dc81..3a68ee50 100644 --- a/data/traits/environment/halophily_preference.yaml +++ b/data/traits/environment/halophily_preference.yaml @@ -63,7 +63,7 @@ causal_graphs: description: Uptake systems importing osmoprotectants from the environment. edges: - subject: environmental_salinity - predicate: influences + predicate: regulates object: halophily_preference_trait description: Salt concentration determines whether growth requires, tolerates, or avoids salinity. @@ -71,6 +71,7 @@ causal_graphs: - reference: DOI:10.1093/femsre/fuy009 snippet: life at high salt concentrations notes: Review frames halophily as microbial life under high salt concentration. + predicate_id: RO:0002211 - subject: environmental_salinity predicate: causes object: osmotic_stress @@ -167,3 +168,15 @@ curation_history: changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006970×1, CHEBI:65015×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + influences → regulates ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:49Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002211×1). + llm_assisted: true diff --git a/data/traits/environment/nacl_optimum.yaml b/data/traits/environment/nacl_optimum.yaml index 5e7f5277..f64e2ed6 100644 --- a/data/traits/environment/nacl_optimum.yaml +++ b/data/traits/environment/nacl_optimum.yaml @@ -56,13 +56,14 @@ causal_graphs: description: Peak specific growth rate achieved at the optimal NaCl. edges: - subject: ambient_nacl - predicate: triggers + predicate: causes object: osmotic_balance description: External NaCl level engages the osmoadaptive balance machinery. evidence: - reference: DOI:10.1186/1746-1448-4-2 snippet: cope with the high salt concentrations notes: Supports osmotic balance as the response to ambient NaCl. + predicate_id: biolink:causes - subject: compatible_solutes predicate: regulates object: osmotic_balance @@ -146,3 +147,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:65015×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + triggers → causes ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:49Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:causes×1). + llm_assisted: true diff --git a/data/traits/environment/nacl_range.yaml b/data/traits/environment/nacl_range.yaml index 7e4751c5..d49500fe 100644 --- a/data/traits/environment/nacl_range.yaml +++ b/data/traits/environment/nacl_range.yaml @@ -58,7 +58,7 @@ causal_graphs: notes: Supports NaCl as the axis bounding the growth window. predicate_id: METPO:2007500 - subject: low_salt_tolerance - predicate: sets + predicate: defines object: bounded_growth_window description: Tolerance to low salt sets the lower bound of the growth window. evidence: @@ -66,14 +66,16 @@ causal_graphs: snippet: cope with the high salt concentrations notes: Saline-Systems review frames halophily around salt-tolerance mechanisms that span both the lower and upper limits of growth-supporting salinity. + predicate_id: METPO:2007500 - subject: high_salt_tolerance - predicate: sets + predicate: defines object: bounded_growth_window description: Tolerance to high salt sets the upper bound of the growth window. evidence: - reference: DOI:10.1093/femsre/fuy009 snippet: high salt concentrations notes: Supports tolerance to high salt as the upper-bound mechanism. + predicate_id: METPO:2007500 - subject: bounded_growth_window predicate: manifests as object: nacl_range_trait @@ -107,3 +109,15 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings: + sets → defines ×2.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2007500×2). + llm_assisted: true diff --git a/data/traits/environment/obligately_aerobic.yaml b/data/traits/environment/obligately_aerobic.yaml index 93d5acbe..3c8d7748 100644 --- a/data/traits/environment/obligately_aerobic.yaml +++ b/data/traits/environment/obligately_aerobic.yaml @@ -54,7 +54,7 @@ causal_graphs: grounding: METPO:1007500 edges: - subject: obligate_aerobic_trait - predicate: requires + predicate: depends on object: molecular_oxygen description: Obligate aerobic growth depends on oxygen availability. evidence: @@ -62,6 +62,7 @@ causal_graphs: snippet: obligate aerobe ... exposed to hypoxia, stops growing notes: Mycobacterium tuberculosis example supports oxygen requirement in an obligately aerobic bacterium. + predicate_id: RO:0002502 - subject: terminal_oxidases predicate: reduces object: molecular_oxygen @@ -127,3 +128,15 @@ curation_history: changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.' llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + requires → depends on ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002502×1). + llm_assisted: true diff --git a/data/traits/environment/obligately_alkaphilic.yaml b/data/traits/environment/obligately_alkaphilic.yaml index edd977d7..8d909fe8 100644 --- a/data/traits/environment/obligately_alkaphilic.yaml +++ b/data/traits/environment/obligately_alkaphilic.yaml @@ -103,7 +103,7 @@ causal_graphs: snippet: achieve net H+ accumulation notes: Supports proton accumulation by antiporters in alkaliphiles. - subject: proton_coupled_atp_synthase - predicate: constrains + predicate: regulates object: obligately_alkaphilic_trait description: Proton-coupled ATP synthesis at very high pH creates a bioenergetic constraint requiring alkaliphile-specific adaptations. @@ -111,6 +111,7 @@ causal_graphs: - reference: DOI:10.1016/j.bbabio.2010.02.028 snippet: robust H+-coupled ATP synthesis at external pH values > 10 notes: Supports the proton-coupled ATP synthesis challenge in alkaliphiles. + predicate_id: RO:0002211 - subject: cytoplasmic_ph_homeostasis predicate: enables object: obligately_alkaphilic_trait @@ -164,3 +165,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001429×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + constrains → regulates ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002211×1). + llm_assisted: true diff --git a/data/traits/environment/ph_growth_preference.yaml b/data/traits/environment/ph_growth_preference.yaml index b1c9defe..216f4419 100644 --- a/data/traits/environment/ph_growth_preference.yaml +++ b/data/traits/environment/ph_growth_preference.yaml @@ -49,7 +49,7 @@ causal_graphs: grounding: GO:0030641 edges: - subject: environmental_ph - predicate: influences + predicate: regulates object: ph_growth_preference_trait description: Environmental pH determines which pH conditions support growth. evidence: @@ -57,6 +57,7 @@ causal_graphs: snippet: tolerate or grow at external pH values notes: Review frames pH growth as a response to external pH outside the cytoplasmic range. + predicate_id: RO:0002211 - subject: acidic_external_ph predicate: challenges object: cytoplasmic_ph_homeostasis @@ -133,3 +134,15 @@ curation_history: changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001428×1, PATO:0001429×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + influences → regulates ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002211×1). + llm_assisted: true diff --git a/data/traits/environment/ph_range.yaml b/data/traits/environment/ph_range.yaml index d424d23e..23c1cf93 100644 --- a/data/traits/environment/ph_range.yaml +++ b/data/traits/environment/ph_range.yaml @@ -60,7 +60,7 @@ causal_graphs: notes: Supports external pH as the axis bounding the growth window. predicate_id: METPO:2007500 - subject: acid_tolerance - predicate: sets + predicate: defines object: bounded_growth_window description: Acid tolerance sets the lower bound of the pH growth window. evidence: @@ -68,8 +68,9 @@ causal_graphs: snippet: highly impermeable cell membranes notes: Supports envelope proton barriers as the lower-bound mechanism for low-pH growth. + predicate_id: METPO:2007500 - subject: alkaline_tolerance - predicate: sets + predicate: defines object: bounded_growth_window description: Alkaline tolerance sets the upper bound of the pH growth window. evidence: @@ -77,6 +78,7 @@ causal_graphs: snippet: alkaliphiles notes: Supports alkaline-tolerance physiology as the upper-bound mechanism for high-pH growth. + predicate_id: METPO:2007500 - subject: bounded_growth_window predicate: manifests as object: ph_range_trait @@ -110,3 +112,15 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings: + sets → defines ×2.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2007500×2). + llm_assisted: true diff --git a/data/traits/environment/stenohaline.yaml b/data/traits/environment/stenohaline.yaml index 65fc9d09..a10441a7 100644 --- a/data/traits/environment/stenohaline.yaml +++ b/data/traits/environment/stenohaline.yaml @@ -81,7 +81,7 @@ causal_graphs: notes: Supports water flux during osmotic imbalance. predicate_id: RO:0002211 - subject: salinity_adaptation_genes - predicate: constrains + predicate: regulates object: stenohaline_trait description: Salinity adaptation gene repertoires help determine salinity niche breadth; limited repertoires can correspond to narrow tolerance. @@ -90,6 +90,7 @@ causal_graphs: snippet: genes associated with microbial salinity adaptation notes: The constraint direction is inferred from the study's salinity adaptation analysis; kept broad because organism-specific gene sets vary. + predicate_id: RO:0002211 - subject: salinity_shift predicate: exceeds tolerance of object: stenohaline_trait @@ -137,3 +138,15 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + constrains → regulates ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002211×1). + llm_assisted: true diff --git a/data/traits/environment/temperature_optimum.yaml b/data/traits/environment/temperature_optimum.yaml index ba064057..6b4c1269 100644 --- a/data/traits/environment/temperature_optimum.yaml +++ b/data/traits/environment/temperature_optimum.yaml @@ -58,7 +58,7 @@ causal_graphs: description: Peak specific growth rate achieved at the optimal temperature. edges: - subject: ambient_temperature - predicate: influences + predicate: regulates object: membrane_fluidity description: Ambient temperature sets a target membrane fluidity that the cell must match. @@ -66,6 +66,7 @@ causal_graphs: - reference: DOI:10.1146/annurev-micro-091313-103612 snippet: more unsaturated fatty acids notes: Supports temperature as the input to membrane-fluidity adaptation. + predicate_id: RO:0002211 - subject: homoviscous_lipid_composition predicate: regulates object: membrane_fluidity @@ -77,7 +78,7 @@ causal_graphs: notes: Supports homoviscous adaptation as the mechanism setting membrane fluidity. predicate_id: RO:0002211 - subject: ambient_temperature - predicate: influences + predicate: regulates object: enzyme_kinetics description: Ambient temperature scales enzyme turnover rates across the cellular network. @@ -86,6 +87,7 @@ causal_graphs: snippet: energy transducing enzymes notes: Supports temperature as the determinant of enzyme function in adapted organisms. + predicate_id: RO:0002211 - subject: enzyme_kinetics predicate: enables object: maximal_growth_rate @@ -156,3 +158,15 @@ curation_history: changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.' llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings: + influences → regulates ×2.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002211×2). + llm_assisted: true diff --git a/data/traits/environment/temperature_preference.yaml b/data/traits/environment/temperature_preference.yaml index 60049bfc..2b27ea8b 100644 --- a/data/traits/environment/temperature_preference.yaml +++ b/data/traits/environment/temperature_preference.yaml @@ -59,7 +59,7 @@ causal_graphs: description: Rate of population growth under a given temperature regime. edges: - subject: environmental_temperature - predicate: influences + predicate: regulates object: growth_rate description: Microbial growth rate varies with growth temperature. evidence: @@ -67,6 +67,7 @@ causal_graphs: snippet: growth rate vs temperature notes: Study analyzes temperature dependence of microbial growth rates across psychrotrophs, mesophiles, and thermophiles. + predicate_id: RO:0002211 - subject: low_temperature predicate: decreases object: membrane_fluidity @@ -95,7 +96,7 @@ causal_graphs: notes: Review links increased membrane permeability to upper temperature growth limits. - subject: membrane_fluidity - predicate: constrains + predicate: regulates object: temperature_preference_trait description: Temperature preference reflects the range in which membrane function remains compatible with growth. @@ -104,8 +105,9 @@ causal_graphs: snippet: optimizes the performance of cellular physiological processes notes: Review supports membrane fluidity adaptation as a temperature-sensing and response mechanism. + predicate_id: RO:0002211 - subject: protein_stability - predicate: constrains + predicate: regulates object: temperature_preference_trait description: Growth at preferred temperatures requires proteins to remain active and stable. @@ -113,6 +115,7 @@ causal_graphs: - reference: DOI:10.1128/MMBR.65.1.1-43.2001 snippet: molecular mechanisms involved in protein thermostabilization notes: Supports protein stability as a determinant of high-temperature growth. + predicate_id: RO:0002211 curation_history: - timestamp: '2026-05-05T01:35:46.856449+00:00' curator: seed_from_metpo @@ -149,3 +152,15 @@ curation_history: changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.' llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 3 causal-edge predicate label(s) to align with existing groundings: + constrains → regulates ×2; influences → regulates ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002211×3). + llm_assisted: true diff --git a/data/traits/environment/temperature_range.yaml b/data/traits/environment/temperature_range.yaml index 398ab6ce..f9bb6b2b 100644 --- a/data/traits/environment/temperature_range.yaml +++ b/data/traits/environment/temperature_range.yaml @@ -61,21 +61,23 @@ causal_graphs: notes: Supports ambient temperature as the axis bounding the growth window. predicate_id: METPO:2007500 - subject: cold_tolerance - predicate: sets + predicate: defines object: bounded_growth_window description: Cold tolerance sets the lower bound of the temperature growth window. evidence: - reference: DOI:10.1038/sj.embor.7400662 snippet: decreased membrane fluidity notes: Supports cold-end membrane and enzyme adaptation as the lower-bound mechanism. + predicate_id: METPO:2007500 - subject: heat_tolerance - predicate: sets + predicate: defines object: bounded_growth_window description: Heat tolerance sets the upper bound of the temperature growth window. evidence: - reference: DOI:10.1128/MMBR.65.1.1-43.2001 snippet: resistant to irreversible inactivation at high temperatures notes: Supports protein-thermostability physiology as the upper-bound mechanism. + predicate_id: METPO:2007500 - subject: bounded_growth_window predicate: manifests as object: temperature_range_trait @@ -110,3 +112,15 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings: + sets → defines ×2.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (METPO:2007500×2). + llm_assisted: true diff --git a/data/traits/environment/thermotolerant.yaml b/data/traits/environment/thermotolerant.yaml index 53a77c05..cfea784a 100644 --- a/data/traits/environment/thermotolerant.yaml +++ b/data/traits/environment/thermotolerant.yaml @@ -52,13 +52,14 @@ causal_graphs: with obligate thermophiles. edges: - subject: elevated_temperature - predicate: triggers + predicate: causes object: heat_shock_response description: Elevated temperature triggers heat-shock chaperone induction. evidence: - reference: DOI:10.1128/MMBR.65.1.1-43.2001 snippet: resistant to irreversible inactivation at high temperatures notes: Supports protein-stability physiology as a high-temperature response. + predicate_id: biolink:causes - subject: chaperone_proteins predicate: enables object: limited_thermostability @@ -119,3 +120,15 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + triggers → causes ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:causes×1). + llm_assisted: true diff --git a/data/traits/metabolism/acetogenesis.yaml b/data/traits/metabolism/acetogenesis.yaml index d5e9885d..78ea7c9c 100644 --- a/data/traits/metabolism/acetogenesis.yaml +++ b/data/traits/metabolism/acetogenesis.yaml @@ -67,13 +67,14 @@ causal_graphs: description: Primary end product of acetogenesis. edges: - subject: acetogenesis_trait - predicate: occurs under + predicate: occurs in object: anaerobic_condition description: Acetogenesis is typically an anaerobic metabolism. evidence: - reference: DOI:10.1016/j.bbapap.2008.08.012 snippet: grow organisms and work with enzymes under strictly oxygen-free conditions notes: Review emphasizes oxygen-free handling for acetogenic enzymes and organisms. + predicate_id: biolink:occurs_in - subject: acetogenesis_trait predicate: has mechanistic pathway object: wood_ljungdahl_pathway @@ -84,21 +85,23 @@ causal_graphs: snippet: Wood-Ljungdahl Pathway of CO2 Fixation notes: Review title and scope support pathway assignment. - subject: carbon_dioxide - predicate: input to + predicate: participates in object: wood_ljungdahl_pathway description: Carbon dioxide is fixed through the Wood-Ljungdahl pathway. evidence: - reference: DOI:10.1016/j.bbapap.2008.08.012 snippet: CO2 Fixation notes: Supports CO2 as a pathway substrate. + predicate_id: biolink:participates_in - subject: carbon_monoxide - predicate: input to + predicate: participates in object: wood_ljungdahl_pathway description: Carbon monoxide can be converted through the acetogenic pathway. evidence: - reference: DOI:10.1196/annals.1419.015 snippet: convert carbon dioxide and CO into acetyl-CoA notes: Supports CO as a substrate for acetogenic acetyl-CoA synthesis. + predicate_id: biolink:participates_in - subject: wood_ljungdahl_pathway predicate: produces object: acetyl_coa @@ -141,3 +144,15 @@ curation_history: changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01001057×1, GO:0046358×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 3 causal-edge predicate label(s) to align with existing groundings: + input to → participates in ×2; occurs under → occurs in ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:participates_in×2, biolink:occurs_in×1). + llm_assisted: true diff --git a/data/traits/metabolism/anaerobic_respiration.yaml b/data/traits/metabolism/anaerobic_respiration.yaml index 322dca85..4bffffa7 100644 --- a/data/traits/metabolism/anaerobic_respiration.yaml +++ b/data/traits/metabolism/anaerobic_respiration.yaml @@ -55,13 +55,14 @@ causal_graphs: description: Bioenergetic output of respiratory electron transport. edges: - subject: denitrification - predicate: occurs under + predicate: occurs in object: low_oxygen_condition description: Denitrification can occur under anaerobic and microaerophilic conditions. evidence: - reference: DOI:10.1128/mmbr.61.4.533-616.1997 snippet: under anaerobic, microaerophilic, and occasionally aerobic conditions notes: Supports low-oxygen context for denitrification. + predicate_id: biolink:occurs_in - subject: nitrogen_oxides predicate: acts as object: terminal_electron_acceptor @@ -112,3 +113,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007504×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + occurs under → occurs in ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:occurs_in×1). + llm_assisted: true diff --git a/data/traits/metabolism/disproportionation.yaml b/data/traits/metabolism/disproportionation.yaml index 7fcdbfa0..e3f12927 100644 --- a/data/traits/metabolism/disproportionation.yaml +++ b/data/traits/metabolism/disproportionation.yaml @@ -65,7 +65,7 @@ causal_graphs: description: Enzymatic route proposed for some sulfur disproportionators. edges: - subject: disproportionation_trait - predicate: occurs under + predicate: occurs in object: anoxic_condition description: Sulfur disproportionation is commonly observed as anaerobic microbial metabolism. @@ -74,6 +74,7 @@ causal_graphs: snippet: microbiologically catalyzed chemolithotrophic process notes: Supports microbial sulfur disproportionation under non-oxygenated sulfur cycling contexts. + predicate_id: biolink:occurs_in - subject: inorganic_sulfur_intermediate predicate: serves as electron donor and acceptor object: disproportionation_trait @@ -169,3 +170,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:33542×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + occurs under → occurs in ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:occurs_in×1). + llm_assisted: true diff --git a/data/traits/metabolism/homoacetogenesis.yaml b/data/traits/metabolism/homoacetogenesis.yaml index 05a8c60e..a2362cfe 100644 --- a/data/traits/metabolism/homoacetogenesis.yaml +++ b/data/traits/metabolism/homoacetogenesis.yaml @@ -75,13 +75,14 @@ causal_graphs: description: Energy carrier conserved during acetate formation. edges: - subject: homoacetogenesis_trait - predicate: occurs under + predicate: occurs in object: anaerobic_condition description: Homoacetogenesis is an anaerobic acetogenic metabolism. evidence: - reference: DOI:10.1023/A:1020514617738 snippet: obligately anaerobic bacteria notes: Supports anaerobic context for acetogens. + predicate_id: biolink:occurs_in - subject: homoacetogenesis_trait predicate: has mechanistic pathway object: wood_ljungdahl_pathway @@ -91,13 +92,14 @@ causal_graphs: snippet: Wood-Ljungdahl pathway notes: Supports pathway assignment for acetogens. - subject: carbon_dioxide - predicate: input to + predicate: participates in object: wood_ljungdahl_pathway description: CO2 is reduced through the Wood-Ljungdahl pathway. evidence: - reference: DOI:10.1016/j.tibtech.2019.05.008 snippet: carbon dioxide are reduced notes: Supports CO2 as substrate. + predicate_id: biolink:participates_in - subject: molecular_hydrogen predicate: provides electrons for object: wood_ljungdahl_pathway @@ -107,13 +109,14 @@ causal_graphs: snippet: acetyl-CoA from CO or CO2 + H2 notes: Supports H2 as an electron donor with CO2. - subject: carbon_monoxide - predicate: input to + predicate: participates in object: wood_ljungdahl_pathway description: CO can serve as a C1 input or intermediate for acetyl-CoA synthesis. evidence: - reference: DOI:10.1016/j.bbapap.2008.08.012 snippet: acetyl-CoA from CO or CO2 + H2 notes: Supports CO as substrate or intermediate. + predicate_id: biolink:participates_in - subject: wood_ljungdahl_pathway predicate: produces object: acetyl_coa @@ -172,3 +175,15 @@ curation_history: changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01001057×1, GO:0046358×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 3 causal-edge predicate label(s) to align with existing groundings: + input to → participates in ×2; occurs under → occurs in ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:participates_in×2, biolink:occurs_in×1). + llm_assisted: true diff --git a/data/traits/metabolism/metabolism.yaml b/data/traits/metabolism/metabolism.yaml index 74ec6e01..2fbd65c5 100644 --- a/data/traits/metabolism/metabolism.yaml +++ b/data/traits/metabolism/metabolism.yaml @@ -72,7 +72,7 @@ causal_graphs: notes: Supports ATP and reducing power as canonical outputs of catabolism. predicate_id: METPO:2000202 - subject: atp_and_reducing_power - predicate: powers + predicate: enables object: biosynthesis description: ATP and reducing power fuel biosynthetic reactions. evidence: @@ -80,6 +80,7 @@ causal_graphs: snippet: ATP synthesis notes: Supports ATP-driven biosynthesis as the central coupling of energy to anabolism. + predicate_id: RO:0002327 - subject: biosynthesis predicate: enables object: cellular_growth @@ -128,3 +129,15 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:47Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + powers → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/metabolism/methanogenesis.yaml b/data/traits/metabolism/methanogenesis.yaml index f7025454..4bf3bfb6 100644 --- a/data/traits/metabolism/methanogenesis.yaml +++ b/data/traits/metabolism/methanogenesis.yaml @@ -72,7 +72,7 @@ causal_graphs: description: Primary reduced carbon end product. edges: - subject: methanogenesis_trait - predicate: occurs under + predicate: occurs in object: anoxic_habitat description: Hydrogenotrophic methanogenesis is associated with anoxic habitats. evidence: @@ -80,6 +80,7 @@ causal_graphs: snippet: terminal step of microbial biomass degradation in anoxic habitats notes: Review places hydrogenotrophic methanogenesis in anoxic microbial biomass degradation. + predicate_id: biolink:occurs_in - subject: carbon_dioxide predicate: reduced with electron donor object: molecular_hydrogen @@ -138,3 +139,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A099T5Q9×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + occurs under → occurs in ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:occurs_in×1). + llm_assisted: true diff --git a/data/traits/metabolism/syntrophy.yaml b/data/traits/metabolism/syntrophy.yaml index 5745f69b..5f5b578d 100644 --- a/data/traits/metabolism/syntrophy.yaml +++ b/data/traits/metabolism/syntrophy.yaml @@ -98,13 +98,14 @@ causal_graphs: snippet: live at the limits of what is thermodynamically possible notes: Supports the thermodynamic constraint that product removal relieves. - subject: molecular_hydrogen - predicate: input to + predicate: participates in object: methanogenesis description: Hydrogen can feed methanogenesis in syntrophic communities. evidence: - reference: DOI:10.1038/nrmicro2166 snippet: syntrophic methanogenic communities notes: Supports hydrogen-linked electron flow into methanogenic partners. + predicate_id: biolink:participates_in curation_history: - timestamp: '2026-05-05T01:35:46.936190+00:00' curator: seed_from_metpo @@ -123,3 +124,15 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:consumes×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + input to → participates in ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:participates_in×1). + llm_assisted: true diff --git a/data/traits/morphology/bacillus_shaped.yaml b/data/traits/morphology/bacillus_shaped.yaml index 8e6d03dc..d90f0d52 100644 --- a/data/traits/morphology/bacillus_shaped.yaml +++ b/data/traits/morphology/bacillus_shaped.yaml @@ -53,13 +53,14 @@ causal_graphs: grounding: UniProtKB:C0LUM8 edges: - subject: mreB - predicate: organizes + predicate: enables object: rod_complex description: MreB organizes rod-shape elongation machinery. evidence: - reference: DOI:10.1146/annurev-cellbio-010521-010834 snippet: MreB filaments interact with Rod complexes notes: Supports MreB-Rod complex interaction in rod-shape regulation. + predicate_id: RO:0002327 - subject: rod_complex predicate: directs object: peptidoglycan_synthesis @@ -147,3 +148,15 @@ curation_history: changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2×1, UniProtKB:C0LUM8×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + organizes → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/morphology/cell_length.yaml b/data/traits/morphology/cell_length.yaml index 492f4c8b..bd73c043 100644 --- a/data/traits/morphology/cell_length.yaml +++ b/data/traits/morphology/cell_length.yaml @@ -80,13 +80,14 @@ causal_graphs: snippet: FtsZ ring at the future division site notes: Supports FtsZ-ring assembly as the proximate divisome event. - subject: division_site_placement - predicate: triggers + predicate: causes object: cytokinesis description: Division-site placement directs constriction and cytokinesis. evidence: - reference: DOI:10.1038/nrmicro2671 snippet: directs cell division notes: Supports division-site placement as the trigger for cytokinesis. + predicate_id: biolink:causes - subject: cytokinesis predicate: resets object: cell_length_trait @@ -113,3 +114,15 @@ curation_history: changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326×1, RO:0002211×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + triggers → causes ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:causes×1). + llm_assisted: true diff --git a/data/traits/morphology/cell_shape.yaml b/data/traits/morphology/cell_shape.yaml index c2f87feb..9ca65987 100644 --- a/data/traits/morphology/cell_shape.yaml +++ b/data/traits/morphology/cell_shape.yaml @@ -84,7 +84,7 @@ causal_graphs: notes: Supports PBPs in peptidoglycan synthesis/remodeling. predicate_id: biolink:catalyzes - subject: peptidoglycan_synthesis - predicate: determines + predicate: causes object: cell_shape_trait description: Spatial regulation of wall synthesis determines growth morphology. evidence: @@ -92,6 +92,7 @@ causal_graphs: snippet: peptidoglycan synthesis to bacterial growth and morphology notes: Review supports regulated peptidoglycan synthesis as a determinant of morphology. + predicate_id: biolink:causes - subject: mreB predicate: positions object: peptidoglycan_synthesis @@ -168,3 +169,15 @@ curation_history: changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2×1, UniProtKB:C0LUM8×1, UniProtKB:A0A2N9AY16×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + determines → causes ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:causes×1). + llm_assisted: true diff --git a/data/traits/morphology/cell_width.yaml b/data/traits/morphology/cell_width.yaml index a84cc0d6..97688b0e 100644 --- a/data/traits/morphology/cell_width.yaml +++ b/data/traits/morphology/cell_width.yaml @@ -20,9 +20,9 @@ evidence: causal_graphs: - graph_id: cell_width_mreb_lateral_wall title: Cell-width control by MreB-directed lateral cell-wall assembly - description: DOI-backed graph linking MreB cytoskeletal organization, - Rod-complex peptidoglycan synthesis, and turgor-balanced wall mechanics to - the observed cell-width phenotype. + description: DOI-backed graph linking MreB cytoskeletal organization, Rod-complex + peptidoglycan synthesis, and turgor-balanced wall mechanics to the observed cell-width + phenotype. nodes: - node_id: cell_width_trait label: cell width @@ -48,7 +48,7 @@ causal_graphs: description: Internal hydrostatic pressure pushing against the cell wall. edges: - subject: mreb_cytoskeleton - predicate: organizes + predicate: enables object: rod_complex_pg description: MreB filaments organize Rod-complex peptidoglycan synthesis along the cylinder. @@ -56,6 +56,7 @@ causal_graphs: - reference: DOI:10.1146/annurev-cellbio-101011-155745 snippet: MreB-directed peptidoglycan synthesis notes: Supports MreB as the organizer of lateral PG synthesis. + predicate_id: RO:0002327 - subject: rod_complex_pg predicate: builds object: peptidoglycan_cell_wall @@ -66,13 +67,14 @@ causal_graphs: snippet: rod-shape is maintained notes: Supports lateral PG assembly as the wall-building activity. - subject: peptidoglycan_cell_wall - predicate: constrains + predicate: regulates object: cell_width_trait description: The peptidoglycan sacculus constrains cell width against turgor. evidence: - reference: DOI:10.1038/nrmicro3088 snippet: rod-shape is maintained notes: Supports the cell wall as the structural constraint on width. + predicate_id: RO:0002211 - subject: turgor_pressure predicate: balances object: peptidoglycan_cell_wall @@ -91,6 +93,18 @@ curation_history: - timestamp: '2026-05-11T22:30:00-07:00' curator: claude action: CURATED_CAUSAL_GRAPH - changes: Added DOI-backed causal graph linking MreB cytoskeleton, Rod-complex - peptidoglycan synthesis, cell wall, and turgor balance to cell width. + changes: Added DOI-backed causal graph linking MreB cytoskeleton, Rod-complex peptidoglycan + synthesis, cell wall, and turgor balance to cell width. + llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings: + organizes → enables ×1; constrains → regulates ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1, RO:0002211×1). llm_assisted: true diff --git a/data/traits/morphology/cell_width_small.yaml b/data/traits/morphology/cell_width_small.yaml index 944f824e..6532c525 100644 --- a/data/traits/morphology/cell_width_small.yaml +++ b/data/traits/morphology/cell_width_small.yaml @@ -43,13 +43,14 @@ causal_graphs: description: MreB-organized lateral peptidoglycan assembly. edges: - subject: mreb_cytoskeleton - predicate: organizes + predicate: enables object: rod_complex_pg description: MreB organizes lateral PG synthesis along the cylinder. evidence: - reference: DOI:10.1146/annurev-cellbio-101011-155745 snippet: MreB-directed peptidoglycan synthesis notes: Supports MreB as the lateral PG organizer. + predicate_id: RO:0002327 - subject: rod_complex_pg predicate: produces object: cell_width_small_trait @@ -86,3 +87,15 @@ curation_history: changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + organizes → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/morphology/crescent_shaped.yaml b/data/traits/morphology/crescent_shaped.yaml index 1257f0e6..d27b448b 100644 --- a/data/traits/morphology/crescent_shaped.yaml +++ b/data/traits/morphology/crescent_shaped.yaml @@ -58,7 +58,7 @@ causal_graphs: notes: Supports crescentin as an inner-curvature-localized shape protein. predicate_id: biolink:located_in - subject: crescentin - predicate: constrains + predicate: regulates object: peptidoglycan_growth_bias description: Crescentin mechanically constrains cell-wall growth to create differential curvature. @@ -66,6 +66,7 @@ causal_graphs: - reference: DOI:10.1038/emboj.2009.61 snippet: mechanical control of cell growth notes: Supports a mechanical growth-control role for crescentin. + predicate_id: RO:0002211 - subject: peptidoglycan_growth_bias predicate: generates object: crescent_cell_curvature @@ -114,3 +115,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A2N9AY16×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + constrains → regulates ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002211×1). + llm_assisted: true diff --git a/data/traits/morphology/filament_shaped.yaml b/data/traits/morphology/filament_shaped.yaml index 022df500..0bdca36d 100644 --- a/data/traits/morphology/filament_shaped.yaml +++ b/data/traits/morphology/filament_shaped.yaml @@ -68,7 +68,7 @@ causal_graphs: notes: Supports DivIVA as a polarity determinant in Streptomyces. predicate_id: biolink:located_in - subject: scy - predicate: organizes + predicate: enables object: apical_polarisome description: Scy is a component of the tip-organizing center controlling polar growth. @@ -76,6 +76,7 @@ causal_graphs: - reference: DOI:10.1371/journal.pgen.1002423 snippet: tip organizing center notes: Supports Scy/DivIVA assemblies in Streptomyces polarized growth. + predicate_id: RO:0002327 - subject: apical_polarisome predicate: recruits object: apical_peptidoglycan_synthesis @@ -145,3 +146,15 @@ curation_history: changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:Q1IYG2×1, UniProtKB:A0A191V3Q4×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + organizes → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/morphology/flagellated.yaml b/data/traits/morphology/flagellated.yaml index cd97d0a9..1f674b95 100644 --- a/data/traits/morphology/flagellated.yaml +++ b/data/traits/morphology/flagellated.yaml @@ -78,13 +78,14 @@ causal_graphs: snippet: reversible rotary motor notes: Supports basal body motor rotation of flagella. - subject: ion_motive_force - predicate: powers + predicate: enables object: stator_complex description: Ion flux through stator complexes powers torque generation. evidence: - reference: DOI:10.3389/fmicb.2021.659464 snippet: relationship between the IMF and the functioning notes: Supports ion motive force coupling to flagellar motor function. + predicate_id: RO:0002327 - subject: chemotaxis_signaling predicate: regulates object: flagellated_trait @@ -113,3 +114,15 @@ curation_history: changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1, RO:0002211×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + powers → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/morphology/gliding.yaml b/data/traits/morphology/gliding.yaml index 721e837a..0946982e 100644 --- a/data/traits/morphology/gliding.yaml +++ b/data/traits/morphology/gliding.yaml @@ -85,13 +85,14 @@ causal_graphs: notes: Supports linkage between type IX secretion and gliding machinery. predicate_id: RO:0002326 - subject: proton_motive_force - predicate: powers + predicate: enables object: gliding_motility_machinery description: Proton motive force can power gliding motility motors. evidence: - reference: DOI:10.1038/s41579-021-00626-4 snippet: proton-driven motor that powers type 9 secretion and gliding motility notes: Supports proton-driven gliding machinery in reviewed systems. + predicate_id: RO:0002327 curation_history: - timestamp: '2026-05-05T01:35:46.907644+00:00' curator: seed_from_metpo @@ -122,3 +123,15 @@ curation_history: changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.' llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + powers → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/morphology/gram_stain.yaml b/data/traits/morphology/gram_stain.yaml index d069ad53..58d81427 100644 --- a/data/traits/morphology/gram_stain.yaml +++ b/data/traits/morphology/gram_stain.yaml @@ -90,7 +90,7 @@ causal_graphs: snippet: alcohol-acetone decolorization notes: Supports decolorization as a chemical step differentiating Gram reactions. - subject: outer_membrane - predicate: influences + predicate: regulates object: gram_stain_trait description: The Gram-negative outer membrane contributes to dye loss and counterstain appearance. @@ -98,8 +98,9 @@ causal_graphs: - reference: DOI:10.1038/s41579-019-0201-x snippet: defining feature of the Gram-negative cell envelope notes: Supports the outer membrane as a defining Gram-negative envelope feature. + predicate_id: RO:0002211 - subject: peptidoglycan_cell_wall - predicate: determines + predicate: causes object: gram_stain_trait description: Peptidoglycan thickness and envelope architecture determine Gram stain outcome. @@ -107,6 +108,7 @@ causal_graphs: - reference: DOI:10.3109/10520299609117151 snippet: mechanism of the Gram stain notes: Supports cell-wall mediated Gram reaction. + predicate_id: biolink:causes curation_history: - timestamp: '2026-05-05T01:35:46.901879+00:00' curator: seed_from_metpo @@ -126,3 +128,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019867×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings: + influences → regulates ×1; determines → causes ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002211×1, biolink:causes×1). + llm_assisted: true diff --git a/data/traits/morphology/motile.yaml b/data/traits/morphology/motile.yaml index cf04fde3..3c680744 100644 --- a/data/traits/morphology/motile.yaml +++ b/data/traits/morphology/motile.yaml @@ -67,13 +67,14 @@ causal_graphs: notes: Supports energy transduction from ion gradients into motor function. predicate_id: biolink:produces - subject: ion_motive_force - predicate: powers + predicate: enables object: flagellar_motor description: Ion motive force powers rotation of the flagellar motor. evidence: - reference: DOI:10.3389/fmicb.2021.659464 snippet: The Dynamic Ion Motive Force Powering notes: Review directly addresses ion motive force powering flagellar motors. + predicate_id: RO:0002327 - subject: flagellar_motor predicate: enables object: motile_trait @@ -144,3 +145,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:R6TBR9×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + powers → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/morphology/motility.yaml b/data/traits/morphology/motility.yaml index 9302e5b5..5a4891b9 100644 --- a/data/traits/morphology/motility.yaml +++ b/data/traits/morphology/motility.yaml @@ -87,13 +87,14 @@ causal_graphs: notes: Supports gliding as an active bacterial movement mechanism. predicate_id: RO:0002327 - subject: ion_motive_force - predicate: powers + predicate: enables object: flagellar_motor description: Ion motive force powers rotation of many bacterial flagellar motors. evidence: - reference: DOI:10.3389/fmicb.2021.659464 snippet: relationship between the IMF and the functioning notes: Supports ion motive force powering the bacterial flagellar motor. + predicate_id: RO:0002327 - subject: chemotaxis_signaling predicate: regulates object: motility_trait @@ -128,3 +129,15 @@ curation_history: changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:R6TBR9×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + powers → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:50Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/morphology/rod_shaped.yaml b/data/traits/morphology/rod_shaped.yaml index 261a5abe..4074d43c 100644 --- a/data/traits/morphology/rod_shaped.yaml +++ b/data/traits/morphology/rod_shaped.yaml @@ -60,13 +60,14 @@ causal_graphs: grounding: UniProtKB:C0LUM8 edges: - subject: mreB - predicate: organizes + predicate: enables object: rod_complex description: MreB organizes rod-shape elongation machinery. evidence: - reference: DOI:10.1146/annurev-cellbio-010521-010834 snippet: MreB filaments interact with Rod complexes notes: Supports MreB-Rod complex interaction in rod-shape regulation. + predicate_id: RO:0002327 - subject: rod_complex predicate: directs object: peptidoglycan_synthesis @@ -158,3 +159,15 @@ curation_history: changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1B1UYY2×1, UniProtKB:C0LUM8×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + organizes → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:51Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/morphology/sphere_shaped.yaml b/data/traits/morphology/sphere_shaped.yaml index 63db7997..9d339dc1 100644 --- a/data/traits/morphology/sphere_shaped.yaml +++ b/data/traits/morphology/sphere_shaped.yaml @@ -51,13 +51,14 @@ causal_graphs: description: Sidewall growth mode that lengthens rods. edges: - subject: ftsZ_division_ring - predicate: organizes + predicate: enables object: septal_peptidoglycan_synthesis description: The FtsZ division ring organizes septal wall synthesis. evidence: - reference: DOI:10.1038/nrmicro1205 snippet: FtsZ collaborates with penicillin binding proteins notes: Supports FtsZ-PBP cooperation in division-associated shape generation. + predicate_id: RO:0002327 - subject: septal_peptidoglycan_synthesis predicate: builds object: peptidoglycan_cell_wall @@ -110,3 +111,15 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + organizes → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:51Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/morphology/spiral_shaped.yaml b/data/traits/morphology/spiral_shaped.yaml index a7ca47fb..9dcbefc5 100644 --- a/data/traits/morphology/spiral_shaped.yaml +++ b/data/traits/morphology/spiral_shaped.yaml @@ -54,7 +54,7 @@ causal_graphs: movement. edges: - subject: curvature_scaffold - predicate: influences + predicate: regulates object: peptidoglycan_remodeling description: Shape scaffolds or complexes bias wall remodeling to create curved and spiral forms. @@ -62,6 +62,7 @@ causal_graphs: - reference: DOI:10.1371/journal.pbio.1002565 snippet: cytoplasmic scaffolding proteins ... participate in helical morphogenesis notes: Supports scaffold involvement in helical or spiral morphogenesis. + predicate_id: RO:0002211 - subject: peptidoglycan_remodeling predicate: enables object: helical_curvature @@ -117,3 +118,15 @@ curation_history: changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:associated_with×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + influences → regulates ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:51Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002211×1). + llm_assisted: true diff --git a/data/traits/physiology/carboxydotrophic.yaml b/data/traits/physiology/carboxydotrophic.yaml index 96640553..c216bfdf 100644 --- a/data/traits/physiology/carboxydotrophic.yaml +++ b/data/traits/physiology/carboxydotrophic.yaml @@ -110,13 +110,14 @@ causal_graphs: notes: Supports respiratory-chain coupling in aerobic CO-utilizing bacteria. predicate_id: METPO:2007402 - subject: respiratory_chain - predicate: requires + predicate: depends on object: co_insensitive_terminal_oxidase description: CO-utilizing bacteria use a CO-insensitive terminal oxidase branch. evidence: - reference: DOI:10.1111/j.1574-6968.1986.tb01858.x snippet: CO-insensitive terminal oxidase notes: Supports terminal oxidase adaptation for CO metabolism. + predicate_id: RO:0002502 - subject: respiratory_chain predicate: generates object: proton_motive_force @@ -188,3 +189,15 @@ curation_history: changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.' llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + requires → depends on ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:51Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002502×1). + llm_assisted: true diff --git a/data/traits/physiology/methanotrophic.yaml b/data/traits/physiology/methanotrophic.yaml index d983b1a4..13da88f9 100644 --- a/data/traits/physiology/methanotrophic.yaml +++ b/data/traits/physiology/methanotrophic.yaml @@ -126,13 +126,14 @@ causal_graphs: notes: Supports methanol dehydrogenase as the next step. predicate_id: METPO:2000016 - subject: formaldehyde - predicate: input to + predicate: participates in object: formaldehyde_assimilation description: Formaldehyde can be assimilated through RuMP or serine pathways. evidence: - reference: DOI:10.1039/D3CY00737E snippet: RuMP pathway and the serine pathway notes: Supports formaldehyde assimilation routes in methanotrophs. + predicate_id: biolink:participates_in - subject: methanotrophic_trait predicate: produces object: carbon_dioxide @@ -179,3 +180,15 @@ curation_history: changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0A3YNQ7×1, UniProtKB:A0A010SCY7×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + input to → participates in ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:51Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:participates_in×1). + llm_assisted: true diff --git a/data/traits/physiology/nutrient_adaptation.yaml b/data/traits/physiology/nutrient_adaptation.yaml index d6a76d1d..d8c8e24e 100644 --- a/data/traits/physiology/nutrient_adaptation.yaml +++ b/data/traits/physiology/nutrient_adaptation.yaml @@ -58,7 +58,7 @@ causal_graphs: description: Adaptation favoring efficient growth in nutrient-poor conditions. edges: - subject: ambient_nutrient_concentration - predicate: triggers + predicate: causes object: nutrient_sensing description: Ambient nutrient levels are detected by cellular sensing systems. evidence: @@ -66,6 +66,7 @@ causal_graphs: snippet: high (copiotrophic) or low (oligotrophic) nutrient concentrations notes: Supports nutrient concentration as the environmental driver of the adaptation axis. + predicate_id: biolink:causes - subject: nutrient_sensing predicate: controls object: resource_allocation @@ -139,3 +140,15 @@ curation_history: changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400×2, RO:0002211×1). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + triggers → causes ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:51Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:causes×1). + llm_assisted: true diff --git a/data/traits/physiology/photolithotrophic.yaml b/data/traits/physiology/photolithotrophic.yaml index 79f93c78..cf60e4c9 100644 --- a/data/traits/physiology/photolithotrophic.yaml +++ b/data/traits/physiology/photolithotrophic.yaml @@ -114,13 +114,14 @@ causal_graphs: notes: Supports donor oxidation during anoxygenic photosynthesis. predicate_id: METPO:2007402 - subject: light - predicate: powers + predicate: enables object: anoxygenic_photosynthesis description: Light powers anoxygenic photosynthetic electron transport. evidence: - reference: DOI:10.3390/antiox10060829 snippet: deriving energy from photosynthesis notes: Supports photosynthetic energy capture in photolithotrophic sulfur bacteria. + predicate_id: RO:0002327 - subject: carbon_dioxide predicate: fixed during object: anoxygenic_photosynthesis @@ -186,3 +187,15 @@ curation_history: changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: biomass: BIOLOGICAL_PROCESS → CHEMICAL ×1.' llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: + powers → enables ×1.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:51Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (RO:0002327×1). + llm_assisted: true diff --git a/data/traits/physiology/trophic_type.yaml b/data/traits/physiology/trophic_type.yaml index 450a2d24..88689f9f 100644 --- a/data/traits/physiology/trophic_type.yaml +++ b/data/traits/physiology/trophic_type.yaml @@ -80,7 +80,7 @@ causal_graphs: description: Chemical-energy-driven trophic phenotype. edges: - subject: carbon_source_use - predicate: determines + predicate: causes object: trophic_type_trait description: Carbon-source utilization defines the auto/heterotrophy axis of the trophic classification. @@ -88,8 +88,9 @@ causal_graphs: - reference: DOI:10.1146/annurev.micro.61.080706.093130 snippet: carbon source notes: Supports carbon-source utilization as a primary trophic-type axis. + predicate_id: biolink:causes - subject: energy_source_use - predicate: determines + predicate: causes object: trophic_type_trait description: Energy-source utilization defines the photo/chemotrophy axis of the trophic classification. @@ -97,8 +98,9 @@ causal_graphs: - reference: DOI:10.1146/annurev.micro.61.080706.093130 snippet: energy source notes: Supports energy-source utilization as a primary trophic-type axis. + predicate_id: biolink:causes - subject: electron_donor_use - predicate: determines + predicate: causes object: trophic_type_trait description: Electron-donor utilization defines the litho/organotrophy axis of the trophic classification. @@ -106,6 +108,7 @@ causal_graphs: - reference: DOI:10.1146/annurev.micro.61.080706.093130 snippet: electron donor notes: Supports electron-donor utilization as a primary trophic-type axis. + predicate_id: biolink:causes - subject: encoded_metabolic_pathways predicate: realizes object: trophic_type_trait @@ -171,3 +174,15 @@ curation_history: changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×4). llm_assisted: true +- timestamp: '2026-05-26T05:00:48Z' + curator: claude + action: RENAME_PREDICATE_LABELS + changes: 'Renamed 3 causal-edge predicate label(s) to align with existing groundings: + determines → causes ×3.' + llm_assisted: true +- timestamp: '2026-05-26T05:00:51Z' + curator: claude + action: GROUND_CAUSAL_PREDICATES + changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv + (biolink:causes×3). + llm_assisted: true diff --git a/reports/predicate_grounding_residual.tsv b/reports/predicate_grounding_residual.tsv index f36deee5..3f93fef3 100644 --- a/reports/predicate_grounding_residual.tsv +++ b/reports/predicate_grounding_residual.tsv @@ -1,19 +1,9 @@ predicate_label edge_count example_files -influences 7 data/traits/environment/halophily_preference.yaml|data/traits/environment/ph_growth_preference.yaml|data/traits/environment/temperature_optimum.yaml engages 7 data/traits/environment/nacl_optimum_mid1.yaml|data/traits/environment/ph_optimum_mid2.yaml|data/traits/environment/temperature_optimum_low.yaml -determines 6 data/traits/ecology/biosafety_level.yaml|data/traits/morphology/cell_shape.yaml|data/traits/morphology/gram_stain.yaml -sets 6 data/traits/environment/nacl_range.yaml|data/traits/environment/ph_range.yaml|data/traits/environment/temperature_range.yaml -constrains 6 data/traits/environment/obligately_alkaphilic.yaml|data/traits/environment/stenohaline.yaml|data/traits/environment/temperature_preference.yaml -input to 6 data/traits/metabolism/acetogenesis.yaml|data/traits/metabolism/homoacetogenesis.yaml|data/traits/metabolism/syntrophy.yaml -powers 6 data/traits/metabolism/metabolism.yaml|data/traits/morphology/flagellated.yaml|data/traits/morphology/gliding.yaml -organizes 6 data/traits/morphology/bacillus_shaped.yaml|data/traits/morphology/cell_width.yaml|data/traits/morphology/cell_width_small.yaml imports 5 data/traits/environment/alkaphilic.yaml|data/traits/environment/euryhaline.yaml|data/traits/environment/halophily_preference.yaml -occurs under 5 data/traits/metabolism/acetogenesis.yaml|data/traits/metabolism/anaerobic_respiration.yaml|data/traits/metabolism/disproportionation.yaml incorporated into 5 data/traits/physiology/autotrophic.yaml|data/traits/physiology/chemoheterotrophic.yaml|data/traits/physiology/chemoorganoheterotrophic.yaml drives production of 5 data/traits/physiology/chemolithoheterotrophic.yaml|data/traits/physiology/chemoorganotrophic.yaml|data/traits/physiology/chemotrophic.yaml -requires 4 data/traits/environment/aerobic.yaml|data/traits/environment/obligately_aerobic.yaml|data/traits/physiology/carboxydotrophic.yaml decreases 4 data/traits/environment/facultative_psychrophilic.yaml|data/traits/environment/psychrophilic.yaml|data/traits/environment/psychrotolerant.yaml -triggers 4 data/traits/environment/nacl_optimum.yaml|data/traits/environment/thermotolerant.yaml|data/traits/morphology/cell_length.yaml prevents 4 data/traits/morphology/non_motile.yaml|data/traits/morphology/non_spore_forming.yaml initiates 4 data/traits/morphology/sporulation.yaml|data/traits/physiology/photoheterotrophic.yaml|data/traits/physiology/photoorganoheterotrophic.yaml can proceed through 4 data/traits/physiology/chemoheterotrophic.yaml|data/traits/physiology/chemoorganoheterotrophic.yaml diff --git a/scripts/rename_predicate_labels.py b/scripts/rename_predicate_labels.py index 53935ad6..dbdea203 100644 --- a/scripts/rename_predicate_labels.py +++ b/scripts/rename_predicate_labels.py @@ -46,11 +46,27 @@ # Rename map: old label → (new label, target CURIE the new label grounds to). # The CURIE column is informational — the actual grounding happens via the # separate ground_causal_predicates.py pass after this script runs. +# +# First 4 rows landed in PR #67 (predicate residual v3). The next 10 +# rows landed in the predicate residual v5 batch — each chosen so its +# corpus usage maps cleanly to an existing grounded predicate. RENAMES: dict[str, tuple[str, str]] = { + # predicate residual v3 (PR #67) cohort "supports": ("enables", "RO:0002327"), "drives": ("regulates", "RO:0002211"), "maintains": ("regulates", "RO:0002211"), "shapes": ("causes", "biolink:causes"), + # predicate residual v5 cohort + "influences": ("regulates", "RO:0002211"), # env-axis → trait-pref edges + "powers": ("enables", "RO:0002327"), # ATP/PMF → process edges + "input to": ("participates in", "biolink:participates_in"), # substrate → pathway + "determines": ("causes", "biolink:causes"), # X-utilization → trophic-type + "sets": ("defines", "METPO:2007500"), # tolerance → bounded-window + "constrains": ("regulates", "RO:0002211"), # X → Y where X bounds Y + "organizes": ("enables", "RO:0002327"), # cytoskeleton → process edges + "occurs under": ("occurs in", "biolink:occurs_in"), # process → condition + "triggers": ("causes", "biolink:causes"), # signal → response + "requires": ("depends on", "RO:0002502"), # process → cofactor/substrate }