From d23f1e0ffe93c509833557ee2eb2335f20285644 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Thu, 8 Oct 2026 10:05:09 -0700
Subject: [PATCH] Bound wine, Mankai and fungal-leaching mechanisms (batch123)
---
...pecies_Strain_Substitution_Consortium.html | 68 +-
...Yeast_ThreeSpecies_Contact_Consortium.html | 60 +-
...ffia_Mankai_Endosphere_Cobamide_Guild.html | 46 +-
...oridium_Talaromyces_Fungal_Consortium.html | 94 +-
.../2026-10-08T164943Z-codex-71bcd5.yaml | 27 +
.../2026-10-08T164944Z-codex-cf55bb.yaml | 27 +
.../2026-10-08T164944Z-codex-638dc2.yaml | 26 +
.../2026-10-08T164944Z-codex-c1ca0f.yaml | 27 +
...pecies_Strain_Substitution_Consortium.yaml | 104 +-
...Yeast_ThreeSpecies_Contact_Consortium.yaml | 84 +-
...ffia_Mankai_Endosphere_Cobamide_Guild.yaml | 104 +-
...oridium_Talaromyces_Fungal_Consortium.yaml | 121 +-
references_cache/PMID_42784437.txt | 9 +-
reports/causal_graph_review/README.md | 29 +
.../adversarial-review-20261008-batch123.yaml | 437 +++++++
.../cache-provenance-20261008-batch123.json | 318 +++++
.../20261008-four-records-batch123.yaml | 754 +++++++++++
reports/causal_graph_review/inventory.tsv | 8 +-
reports/causal_graph_review/summary.json | 4 +-
.../validation-20261008-batch123.json | 1105 +++++++++++++++++
tests/test_causal_review_batch123.py | 176 +++
21 files changed, 3431 insertions(+), 197 deletions(-)
create mode 100644 history/records/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium/2026-10-08T164943Z-codex-71bcd5.yaml
create mode 100644 history/records/Wine_Yeast_ThreeSpecies_Contact_Consortium/2026-10-08T164944Z-codex-cf55bb.yaml
create mode 100644 history/records/Wolffia_Mankai_Endosphere_Cobamide_Guild/2026-10-08T164944Z-codex-638dc2.yaml
create mode 100644 history/records/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium/2026-10-08T164944Z-codex-c1ca0f.yaml
create mode 100644 reports/causal_graph_review/adversarial-review-20261008-batch123.yaml
create mode 100644 reports/causal_graph_review/cache-provenance-20261008-batch123.json
create mode 100644 reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
create mode 100644 reports/causal_graph_review/validation-20261008-batch123.json
create mode 100644 tests/test_causal_review_batch123.py
diff --git a/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html b/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html
index 1df6c580d..d7ca1a779 100644
--- a/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html
+++ b/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html
@@ -708,7 +708,7 @@ Ecological Interactions
- Removing a species or substituting one of the two strains representing a species significantly changed population dynamics, growth behavior, and metabolic output across the five-species wine yeast consortium.
+ Species drop-out and strain substitution changed population succession, fermentation kinetics and metabolic outputs in the defined five-species synthetic-must panel. These are positive composition-perturbation effects, not identified molecular mechanisms. All tested consortia completed fermentation within the observation period; changed kinetics should not be equated with failure to finish fermentation.
@@ -748,16 +748,29 @@ Evidence
+
+
+
+ "the molecular mechanisms underlying the observed species- and strain-dependent effects were not addressed in the present work."
+
+
+
-
Fermentation sugar utilization and population measurements together supported competitive interactions among the wine yeast species.
+
PARTIAL: drop-out-associated sugar-preference shifts and compensatory relative-abundance changes support the authors' competition interpretation, principally among L. thermotolerans, S. bacillaris and T. delbrueckii. These consortium-level observations do not resolve a direct inhibitory agent or establish every pairwise relationship. ARISA measures relative DNA-based succession, not absolute viable population size; viable plating provides complementary evidence. Contact, toxins and nitrogen preferences remain candidate mechanisms, not demonstrated causes here.
@@ -790,7 +803,7 @@
Evidence
PMID:42784437
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"Sugar utilization and population data jointly revealed competitive interactions among species"
@@ -805,7 +818,7 @@ Evidence
- Strain substitutions in the non-Saccharomyces members shifted metabolic output more broadly than the S. cerevisiae strain, while chemical profiles tracked the species and strain identities assembled into each consortium.
+ Among the particular strains tested, non-Saccharomyces substitutions affected a broader range of final metabolites than switching the S. cerevisiae strain. The latter still had detectable effects and was not metabolically silent. This result is panel- and synthetic-must-specific, not a universal ordering of species importance or a demonstration that strain effects share one mechanism.
@@ -868,21 +881,56 @@ Evidence
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
KNOWLEDGE_GAP
OPEN
- Which exact strain names or culture-collection accessions correspond to the two Saccharomyces cerevisiae, Lachancea thermotolerans, Hanseniaspora uvarum, Starmerella bacillaris, and Torulaspora delbrueckii isolates used in the five-species strain-substitution panel, and which medium and incubation parameters were used for the fermentation assays?
+ How should the ten reported strains and synthetic-must assay context be represented in the canonical species-level record?
-
The PubMed abstract for PMID:42784437 identifies the five species and states that each was represented by two phenotypically diverging strains, but it does not name the ten strains, their accessions, the exact fermentation medium, temperature, or timing.
+
The primary article Table 1 names the ten strains, and Methods supplies the synthetic-must assay conditions. The earlier abstract-only gap therefore concerns canonical strain and methods curation rather than missing source information. These non-graph fields require a separate evidence-backed update; species identities and the existing engineering-design block are preserved in this graph repair.
Attaches to: taxonomy#Saccharomyces cerevisiae, taxonomy#Lachancea thermotolerans, taxonomy#Hanseniaspora uvarum, taxonomy#Starmerella bacillaris, taxonomy#Torulaspora delbrueckii
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which mechanisms account for the composition-dependent fermentation phenotypes?
+
+
Drop-outs and substitutions establish composition effects but not their molecular mediators. Relative succession is not a complete pairwise interaction matrix, and non-significant statistical interactions are not proof of absence. Do not transfer contact or toxin mechanisms from other systems to this panel.
+
+
Attaches to: ecological_interactions#Species drop-out and strain-substitution output shifts, ecological_interactions#Inferred interspecies sugar-utilization competition, ecological_interactions#Non-Saccharomyces strain-dependent metabolic tuning
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
the molecular mechanisms underlying the observed species- and strain-dependent effects were not addressed in the present work.
+
+
+
+
@@ -1142,7 +1190,7 @@ Environmental Factors
processes.push("fermentation");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1174,7 +1222,7 @@ Environmental Factors
nodes.push({
id: intId,
- label: "Interspecies sugar-utilization competition",
+ label: "Inferred interspecies sugar-utilization competition",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html b/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html
index 9819243d6..ada44bdb6 100644
--- a/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html
+++ b/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html
@@ -619,7 +619,7 @@ Ecological Interactions
- When all three yeasts shared the same YNB vessel, direct contact favored S. cerevisiae growth and S. cerevisiae established numerical dominance by the end of the 12 h observation period.
+ In the direct-contact treatment, the three yeast strains shared each YNB vessel while the membrane and recirculation system was retained. S. cerevisiae growth was favored and it established numerical dominance by the end of the 12 h observation period. This positive treatment effect does not identify a necessary contact-sensing gene or demonstrate that the same mechanism operates in every strain.
@@ -680,7 +680,7 @@ Evidence
- When the three yeasts were physically separated but shared filtered medium, T. delbrueckii dominated early biomass growth while L. thermotolerans growth was lower than in the direct-contact mixed culture.
+ Physical separation with shared filtered medium favored early T. delbrueckii growth while L. thermotolerans declined more than in direct contact. HYPOTHESIZED: medium-mediated suppression of L. thermotolerans by T. delbrueckii could explain the pattern. Neither a killer toxin nor a specific inhibitory metabolite was established as its cause, and indirect pairwise confirmation was still needed. No pairwise causal arrow is inferred from this comparison.
@@ -726,7 +726,7 @@ Evidence
PMID:42176030
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"T. delbrueckii likely suppresses growth of L. thermotolerans through a medium-mediated mechanism."
@@ -741,7 +741,7 @@ Evidence
- Extracellular amino acid concentrations differed between direct and indirect contact fermentations after 5 h; the measured serine, glycine, valine, aspartic acid, and arginine concentrations were higher in the indirect-contact condition, with no significant difference after 9 h.
+ Extracellular amino acid concentrations differed between direct and indirect contact fermentations after 5 h; the measured serine, glycine, valine, aspartic acid, and arginine concentrations were higher in the indirect-contact condition, with no significant difference after 9 h. The difference does not by itself demonstrate increased secretion, reduced uptake or cross-feeding; secretion, cell death and partial lysis remain possible contributors. YNB already supplied histidine, methionine and tryptophan.
@@ -783,6 +783,19 @@ Evidence
+
+
+
+ "No statistically significant differences between these conditions were observed after 9 h"
+
+
+
@@ -828,7 +841,7 @@ Associated Datasets
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -843,6 +856,41 @@
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which medium-mediated process explains the indirect-contact growth shift?
+
+
The three-species treatment comparison supports contrasting growth patterns. It does not isolate a T. delbrueckii inhibitor, and the paper explicitly requires indirect pairwise confirmation. Transcriptional differences, including HXT and HPF1 responses, are not selective genetic perturbations proving the contact mechanism. The separate amino-acid-origin discussion remains open.
+
+
Attaches to: ecological_interactions#Direct-contact S. cerevisiae growth advantage, ecological_interactions#Indirect-contact Torulaspora growth shift, ecological_interactions#Contact-dependent amino acid profile shift
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
T. delbrueckii likely suppresses growth of L. thermotolerans through a medium-mediated mechanism.
+
+
+
+
@@ -1217,7 +1265,7 @@ Evidence
var processes = [];
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
diff --git a/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html b/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html
index e9b3c2e08..16dcfccda 100644
--- a/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html
+++ b/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html
@@ -738,7 +738,7 @@ Ecological Interactions
Ecological interaction network for Wolffia Mankai Endosphere Cobamide Guild
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding, niche partitioning.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -746,13 +746,8 @@
Ecological Interactions
-
-
@@ -760,10 +755,9 @@ Ecological Interactions
-
Bacterial assemblages from cultivation medium, washed fronds, and surface-sterilized tissue clustered separately; the endosphere retained a lower-diversity, distinct subset of the broader plant-associated and medium-associated pool.
+
Bacterial DNA profiles from cultivation medium, washed fronds and surface-sterilized tissue differed in composition and diversity. Environmental and host filtering is an interpretation of these compartment associations, not a selectively perturbed host mechanism or demonstrated microbial niche partitioning. Endosphere denotes the operational sterilized-tissue fraction; washed whole fronds are not a strictly epiphytic sample.
@@ -785,7 +779,7 @@
Evidence
PMID:42304541
- - SUPPORT (IN_VIVO)
+ - PARTIAL (IN_VIVO)
"The pronounced differences in richness and composition between the medium, phyllosphere and endosphere (Fig. 2 ) indicate strong environmental and host filtering along the plant-water interface"
@@ -799,9 +793,8 @@ Evidence
-
Genome-resolved endosphere analysis predicted an uneven cobamide pathway architecture: Hyphomicrobium zavarzinii, Methylobacterium, Devosia, Labrys, Ferrovibrionaceae, and other Alphaproteobacteria encoded most biosynthetic steps, while many Gammaproteobacteria and Bacteroidota lineages had incomplete pathways and were inferred to salvage or remodel exogenous intermediates. The network edges represent MAG-derived metabolic compatibility, not direct metabolite-flux or abundance-correlation evidence.
+
Genome-resolved endosphere analysis predicted an uneven cobamide pathway architecture: Hyphomicrobium zavarzinii, Methylobacterium, Devosia, Labrys, Ferrovibrionaceae, and other Alphaproteobacteria encoded most biosynthetic steps, while many Gammaproteobacteria and Bacteroidota lineages had incomplete pathways and were inferred to salvage or remodel exogenous intermediates. The network edges represent MAG-derived metabolic compatibility, not direct metabolite-flux or abundance-correlation evidence. HYPOTHESIZED cross-feeding is not established by gene presence or pathway gaps. Missing genes in individual MAGs can reflect reconstruction limitations. Cultured species-level comparators were not strain-matched endophytes, so their cobalamin production does not validate exchange in this guild or adaptive gene loss. The host is not established as a B12-dependent recipient.
@@ -883,7 +876,7 @@
Evidence
PMID:42304541
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"many Gammaproteobacteria and Bacteroidota lineages harbored incomplete pathways, implying reliance on exogenous cobamide intermediates"
@@ -948,7 +941,7 @@ Associated Datasets
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -994,6 +987,21 @@
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Do compartment profiles and comparator genomes establish host-selected cobamide dependence?
+
+
Operational fractions and possible carryover limit localization claims. Only endosphere MAGs were reconstructed, so pathway architecture was not compared across all compartments. Non-strain-matched culture-collection representatives cannot establish endophyte-specific gene loss or validate metabolite exchange. The existing direct-flux knowledge gap remains open.
+
+
Attaches to: ecological_interactions#Mankai Compartment-Associated Community Differentiation, ecological_interactions#MAG-Inferred Cobamide Producer-Salvager Guild
+
+
+
+
@@ -1249,7 +1257,7 @@ Environmental Factors
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1258,7 +1266,7 @@ Environmental Factors
nodes.push({
id: intId,
- label: "Mankai Compartment Host Filtering",
+ label: "Mankai Compartment-Associated Community Differentiation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1273,7 +1281,7 @@ Environmental Factors
(function() {
var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
diff --git a/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html b/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html
index fbf7e7b11..cf20b129f 100644
--- a/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html
+++ b/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html
@@ -567,7 +567,7 @@ Ecological Interactions
Ecological interaction network for Wollastonite Ramichloridium-Talaromyces Fungal Consortium
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding, niche partitioning.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -575,13 +575,8 @@
Ecological Interactions
-
-
@@ -589,10 +584,9 @@ Ecological Interactions
-
R. apiculatum CMS-1 synthesized extracellular polysaccharides and proteins during mixed cultivation; T. pseudofuniculosus hzt-3′ utilized these extracellular products, which was associated with increased hzt-3′ gluconic-acid, isocitric-acid, L-glutamine, and L-tyrosine production.
+
HYPOTHESIZED: CMS-1 extracellular products may support hzt-3′ metabolism in the mixed fungal culture. The source proposes this direction from bulk polysaccharide, protein and metabolite patterns; it does not trace CMS-1-derived material into hzt-3′. Medium sucrose consumption also contributes to the measured carbohydrate decline. Retain the proposed interaction without presenting direct transfer or recipient-specific production as demonstrated.
Source Taxon: Ramichloridium apiculatum CMS-1
@@ -635,7 +629,7 @@
CMS-1 Extracellular Polymer Cross-Feeding
→ Mixed-Culture Organic-Acid and Amino-Acid Upregulation
-
Cross-feeding of CMS-1 extracellular polymers and protein was linked to increased hzt-3′ acid and amino-acid production in the mixed culture.
+
HYPOTHESIZED: consumption of CMS-1 products could enable greater hzt-3′ acid and amino-acid production. Bulk culture comparisons support metabolic changes but do not isolate this transfer as their necessary cause or distinguish it from consumption of supplied sucrose.
Evidence
PMID:42478817
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"In mixed culture, CMS-1 synthesized extracellular polysaccharides and proteins that were utilized by hzt-3′"
@@ -665,9 +659,8 @@ Evidence
-
The 20% CMS-1 plus 80% hzt-3′ mixed culture had elevated organic acids and amino acids relative to pure cultures; CMS-1 chiefly produced oxalic acid, while hzt-3′ chiefly generated gluconic acid and increased secretion of gluconic acid, isocitric acid, L-glutamine, and L-tyrosine after receiving CMS-1 extracellular products.
+
The tested 20% CMS-1 plus 80% hzt-3′ culture showed increased total organic acids and selected amino acids relative to pure cultures. Pure CMS-1 chiefly produced oxalic acid, while pure hzt-3′ chiefly produced gluconic acid. These are bulk concentrations, not gene-expression measurements or proof of recipient-specific synthesis after cross-feeding. Individual compounds did not all increase: mixed-culture oxalic acid was much lower.
@@ -707,7 +700,7 @@
Mixed-Culture Organic-Acid and Amino-Acid Upregulation
→ Optimized Wollastonite Calcium and Silicon Leaching
-
Increased acids and amino acids lowered pH and intensified the chemical dissolution of wollastonite by the mixed fungal culture.
+
PARTIAL: increased acidic metabolites and lower pH are consistent with enhanced acid dissolution and complexation driving wollastonite leaching. The culture-ratio comparison supports this mechanism but does not selectively establish which acid or amino acid is necessary, or partition chemical dissolution from physical disruption.
Evidence
PMID:42478817
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"hzt-3′, which upregulated the production of gluconic acid, isocitric acid, L-glutamine, and L-tyrosine"
+
+
+
+ "The total organic acid production ranked as follows: 20% CMS-1 + 80% hzt-3′ > 100% hzt-3′ > 100% CMS-1."
+
+
+
@@ -750,9 +756,8 @@ Evidence
-
The 20% CMS-1 plus 80% hzt-3′ inoculation ratio produced the strongest wollastonite dissolution among the tested ratios, reaching 79.95% calcium leaching and 18.59% silicon leaching and visibly disrupting wollastonite residue structure.
+
The 20% CMS-1 plus 80% hzt-3′ input ratio gave the greatest wollastonite leaching among the tested ratios: 79.95% +/- 6.37% calcium and 18.59% +/- 0.11% silicon at day 12. Residue analyses support altered mineral structure. These positive outcomes do not demonstrate niche partitioning, quantify a separate hyphal-force contribution or measure net CO2 sequestration.
@@ -795,7 +800,7 @@
Evidence
PMID:42478817
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"surface cracks and grooves on leaching residues indicated additional biophysical disruption"
@@ -811,6 +816,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which processes mediate the mixed-culture leaching improvement?
+
+
The source demonstrates culture-ratio effects and bulk chemical changes. Direct CMS-1-to-hzt-3′ transfer, cell-specific synthesis, necessary individual metabolites and a separately quantified hyphal-force contribution remain unresolved. The proposed cross-feeding-to-acid-to-leaching chain is retained as qualified existing topology, not a traced flux pathway or a net-carbon-removal measurement.
+
+
Attaches to: ecological_interactions#Hypothesized CMS-1 Extracellular Polymer Cross-Feeding, ecological_interactions#Mixed-Culture Organic-Acid and Amino-Acid Upregulation, ecological_interactions#Optimized Wollastonite Calcium and Silicon Leaching
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
In mixed culture, CMS-1 synthesized extracellular polysaccharides and proteins that were utilized by hzt-3′
+
+
+
+
+
@@ -1165,7 +1209,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1184,7 +1228,7 @@ Evidence
nodes.push({
id: intId,
- label: "CMS-1 Extracellular Polymer Cross-Feeding",
+ label: "Hypothesized CMS-1 Extracellular Polymer Cross-Feeding",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1209,7 +1253,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1222,7 +1266,7 @@ Evidence
var processes = [];
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1254,7 +1298,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
diff --git a/history/records/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium/2026-10-08T164943Z-codex-71bcd5.yaml b/history/records/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium/2026-10-08T164943Z-codex-71bcd5.yaml
new file mode 100644
index 000000000..dfc0fd0e7
--- /dev/null
+++ b/history/records/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium/2026-10-08T164943Z-codex-71bcd5.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml
+ slug: Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium
+session:
+ id: 2026-10-08T164943Z-codex-71bcd5
+ timestamp: '2026-10-08T16:49:43Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1954
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve positive composition perturbations while distinguishing kinetics from
+ completion and molecular mechanism.; Retain competition as a qualified phenotypic inference
+ without absolute viability or every-pair causality.; Bound the broader non-Saccharomyces
+ metabolic effect to the tested panel and retain detectable S. cerevisiae effects.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
diff --git a/history/records/Wine_Yeast_ThreeSpecies_Contact_Consortium/2026-10-08T164944Z-codex-cf55bb.yaml b/history/records/Wine_Yeast_ThreeSpecies_Contact_Consortium/2026-10-08T164944Z-codex-cf55bb.yaml
new file mode 100644
index 000000000..5460defc4
--- /dev/null
+++ b/history/records/Wine_Yeast_ThreeSpecies_Contact_Consortium/2026-10-08T164944Z-codex-cf55bb.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml
+ slug: Wine_Yeast_ThreeSpecies_Contact_Consortium
+session:
+ id: 2026-10-08T164944Z-codex-cf55bb
+ timestamp: '2026-10-08T16:49:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1955
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain the positive contact-treatment growth phenotype without necessary-gene attribution.;
+ Mark proposed Torulaspora-mediated suppression as partial and hypothetical, not a demonstrated
+ toxin mechanism.; Preserve the 5 h amino-acid difference and 9 h null without inferring
+ transfer, secretion or uptake direction.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
diff --git a/history/records/Wolffia_Mankai_Endosphere_Cobamide_Guild/2026-10-08T164944Z-codex-638dc2.yaml b/history/records/Wolffia_Mankai_Endosphere_Cobamide_Guild/2026-10-08T164944Z-codex-638dc2.yaml
new file mode 100644
index 000000000..71c5f6203
--- /dev/null
+++ b/history/records/Wolffia_Mankai_Endosphere_Cobamide_Guild/2026-10-08T164944Z-codex-638dc2.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml
+ slug: Wolffia_Mankai_Endosphere_Cobamide_Guild
+session:
+ id: 2026-10-08T164944Z-codex-638dc2
+ timestamp: '2026-10-08T16:49:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1956
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Keep observed compartment differences separate from selectively demonstrated host
+ filtering and niche partitioning.; Retain annotated producer-salvager potential with computational
+ provenance, not observed cross-feeding or strain-matched validation.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
diff --git a/history/records/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium/2026-10-08T164944Z-codex-c1ca0f.yaml b/history/records/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium/2026-10-08T164944Z-codex-c1ca0f.yaml
new file mode 100644
index 000000000..fddee6b4e
--- /dev/null
+++ b/history/records/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium/2026-10-08T164944Z-codex-c1ca0f.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml
+ slug: Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium
+session:
+ id: 2026-10-08T164944Z-codex-c1ca0f
+ timestamp: '2026-10-08T16:49:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1957
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Qualify the proposed polymer handoff; bulk carbohydrate decline also includes medium-sucrose
+ consumption.; Preserve bulk metabolite changes without niche partitioning, uniform acid
+ increases or recipient-specific synthesis.; Keep measured day-12 calcium/silicon leaching
+ and residue changes distinct from isolated physical causality and CO2 sequestration.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
diff --git a/kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml b/kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml
index c727b880d..05c482a27 100644
--- a/kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml
+++ b/kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml
@@ -139,9 +139,10 @@ taxonomy:
explanation: Names T. delbrueckii as one of the five defined consortium species.
ecological_interactions:
- name: Species drop-out and strain-substitution output shifts
- description: Removing a species or substituting one of the two strains representing a species
- significantly changed population dynamics, growth behavior, and metabolic output across the
- five-species wine yeast consortium.
+ description: Species drop-out and strain substitution changed population succession, fermentation kinetics and
+ metabolic outputs in the defined five-species synthetic-must panel. These are positive composition-perturbation
+ effects, not identified molecular mechanisms. All tested consortia completed fermentation within the observation
+ period; changed kinetics should not be equated with failure to finish fermentation.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: fermentation
@@ -152,13 +153,22 @@ ecological_interactions:
- reference: PMID:42784437
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Both species drop-out and strain substitution produced significant impacts on population
- dynamics, growth behaviors, and metabolic outputs.
- explanation: Supports both perturbation classes affecting consortium composition, growth, and
- metabolite outputs.
-- name: Interspecies sugar-utilization competition
- description: Fermentation sugar utilization and population measurements together supported
- competitive interactions among the wine yeast species.
+ snippet: Both species drop-out and strain substitution produced significant impacts on population dynamics,
+ growth behaviors, and metabolic outputs.
+ explanation: Supports both perturbation classes affecting consortium composition, growth, and metabolite outputs.
+ - reference: PMID:42784437
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: the molecular mechanisms underlying the observed species- and strain-dependent effects were not addressed
+ in the present work.
+ explanation: The full-text Discussion explicitly limits mechanistic attribution.
+- name: Inferred interspecies sugar-utilization competition
+ description: 'PARTIAL: drop-out-associated sugar-preference shifts and compensatory relative-abundance changes
+ support the authors'' competition interpretation, principally among L. thermotolerans, S. bacillaris and T.
+ delbrueckii. These consortium-level observations do not resolve a direct inhibitory agent or establish every
+ pairwise relationship. ARISA measures relative DNA-based succession, not absolute viable population size; viable
+ plating provides complementary evidence. Contact, toxins and nitrogen preferences remain candidate mechanisms,
+ not demonstrated causes here.'
interaction_type: COMPETITION
scope: COMMUNITY_LEVEL
biological_processes:
@@ -168,15 +178,16 @@ ecological_interactions:
label: fermentation
evidence:
- reference: PMID:42784437
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: Sugar utilization and population data jointly revealed competitive interactions among species
- explanation: Links measured sugar consumption and population dynamics to competitive
- interspecies interactions in the five-species consortium.
+ explanation: Supports the authors' competition inference from phenotypic perturbations, not a resolved molecular
+ or complete pairwise mechanism.
- name: Non-Saccharomyces strain-dependent metabolic tuning
- description: Strain substitutions in the non-Saccharomyces members shifted metabolic output more
- broadly than the S. cerevisiae strain, while chemical profiles tracked the species and strain
- identities assembled into each consortium.
+ description: Among the particular strains tested, non-Saccharomyces substitutions affected a broader range of
+ final metabolites than switching the S. cerevisiae strain. The latter still had detectable effects and was not
+ metabolically silent. This result is panel- and synthetic-must-specific, not a universal ordering of species
+ importance or a demonstration that strain effects share one mechanism.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: fermentation
@@ -187,15 +198,14 @@ ecological_interactions:
- reference: PMID:42784437
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Two-way analysis confirmed that the non-Saccharomyces substitutions affected the metabolic
- output more broadly than the S. cerevisiae strain.
+ snippet: Two-way analysis confirmed that the non-Saccharomyces substitutions affected the metabolic output more
+ broadly than the S. cerevisiae strain.
explanation: Supports a broader metabolite effect for non-Saccharomyces strain substitutions.
- reference: PMID:42784437
supports: SUPPORT
evidence_source: IN_VITRO
snippet: chemical outputs tracked the identity of each consortium comprising different species and strains
- explanation: Supports consortium-specific chemical outputs across the species and strain
- perturbation panel.
+ explanation: Supports consortium-specific chemical outputs across the species and strain perturbation panel.
environmental_factors:
- name: five-species strain-substitution panel
value: Two phenotypically diverging strains represented each of five spontaneous-wine-fermentation
@@ -237,10 +247,8 @@ external_resources:
publication.
discussions:
- discussion_id: wine_yeast_five_species_strain_accessions
- prompt: Which exact strain names or culture-collection accessions correspond to the two
- Saccharomyces cerevisiae, Lachancea thermotolerans, Hanseniaspora uvarum, Starmerella
- bacillaris, and Torulaspora delbrueckii isolates used in the five-species strain-substitution
- panel, and which medium and incubation parameters were used for the fermentation assays?
+ prompt: How should the ten reported strains and synthetic-must assay context be represented in the canonical species-level
+ record?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
@@ -249,11 +257,29 @@ discussions:
- taxonomy#Hanseniaspora uvarum
- taxonomy#Starmerella bacillaris
- taxonomy#Torulaspora delbrueckii
- rationale: The PubMed abstract for PMID:42784437 identifies the five species and states that each
- was represented by two phenotypically diverging strains, but it does not name the ten strains,
- their accessions, the exact fermentation medium, temperature, or timing.
+ rationale: The primary article Table 1 names the ten strains, and Methods supplies the synthetic-must assay conditions.
+ The earlier abstract-only gap therefore concerns canonical strain and methods curation rather than missing source
+ information. These non-graph fields require a separate evidence-backed update; species identities and the existing
+ engineering-design block are preserved in this graph repair.
posed_by: codex
posed_date: '2026-09-28'
+- discussion_id: five_causal_scope_batch123
+ prompt: Which mechanisms account for the composition-dependent fermentation phenotypes?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Species drop-out and strain-substitution output shifts
+ - ecological_interactions#Inferred interspecies sugar-utilization competition
+ - ecological_interactions#Non-Saccharomyces strain-dependent metabolic tuning
+ rationale: Drop-outs and substitutions establish composition effects but not their molecular mediators. Relative
+ succession is not a complete pairwise interaction matrix, and non-significant statistical interactions are not
+ proof of absence. Do not transfer contact or toxin mechanisms from other systems to this panel.
+ posed_by: codex
+ posed_date: '2026-10-08'
+ evidence:
+ - reference: PMID:42784437
+ snippet: the molecular mechanisms underlying the observed species- and strain-dependent effects were not addressed
+ in the present work.
metals_present: []
rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
@@ -263,16 +289,24 @@ curation_history:
- timestamp: '2026-09-28T16:14:13Z'
curator: codex
action: CREATE_COMMUNITY
- changes: Created CommunityMech:000465 for PMID:42784437 / doi:10.1128/spectrum.02819-26,
- a defined five-species wine yeast consortium with two phenotypically diverging strains
- representing each species, species drop-out and strain-substitution perturbations, competitive
- sugar-utilization evidence, non-Saccharomyces strain-dependent metabolic-output tuning, PubMed
- and DOI resources, and an open discussion for exact strain identities and cultivation details.
+ changes: Created CommunityMech:000465 for PMID:42784437 / doi:10.1128/spectrum.02819-26, a defined five-species
+ wine yeast consortium with two phenotypically diverging strains representing each species, species drop-out
+ and strain-substitution perturbations, competitive sugar-utilization evidence, non-Saccharomyces strain-dependent
+ metabolic-output tuning, PubMed and DOI resources, and an open discussion for exact strain identities and cultivation
+ details.
llm_assisted: true
- timestamp: '2026-09-28T16:28:21Z'
curator: codex
action: FIX_ADVERSARIAL_REVIEW_FINDINGS
- changes: Addressed issue 1204 by rewriting the wine yeast abstract-backed knowledge-gap notes
- to remove transient publisher-access wording while keeping exact strain identities, medium, and
- incubation parameters explicitly unresolved.
+ changes: Addressed issue 1204 by rewriting the wine yeast abstract-backed knowledge-gap notes to remove transient
+ publisher-access wording while keeping exact strain identities, medium, and incubation parameters explicitly
+ unresolved.
+ llm_assisted: true
+- timestamp: '2026-10-08T16:49:42Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Preserve positive composition perturbations while distinguishing kinetics from completion and molecular
+ mechanism.; Retain competition as a qualified phenotypic inference without absolute viability or every-pair
+ causality.; Bound the broader non-Saccharomyces metabolic effect to the tested panel and retain detectable S.
+ cerevisiae effects. Issue#1954; reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
llm_assisted: true
diff --git a/kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml b/kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml
index b7132d8a9..45406387c 100644
--- a/kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml
+++ b/kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml
@@ -117,8 +117,10 @@ taxonomy:
explanation: Identifies the T. delbrueckii LO544 member, its CRBO accession, and its fluorescent marker.
ecological_interactions:
- name: Direct-contact S. cerevisiae growth advantage
- description: When all three yeasts shared the same YNB vessel, direct contact favored S. cerevisiae growth and S. cerevisiae
- established numerical dominance by the end of the 12 h observation period.
+ description: In the direct-contact treatment, the three yeast strains shared each YNB vessel while the membrane
+ and recirculation system was retained. S. cerevisiae growth was favored and it established numerical dominance
+ by the end of the 12 h observation period. This positive treatment effect does not identify a necessary contact-sensing
+ gene or demonstrate that the same mechanism operates in every strain.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: growth
@@ -137,8 +139,10 @@ ecological_interactions:
snippet: In direct contact, S. cerevisiae established rapid dominance
explanation: Explicitly reports S. cerevisiae dominance in the direct-contact condition.
- name: Indirect-contact Torulaspora growth shift
- description: When the three yeasts were physically separated but shared filtered medium, T. delbrueckii dominated early
- biomass growth while L. thermotolerans growth was lower than in the direct-contact mixed culture.
+ description: 'Physical separation with shared filtered medium favored early T. delbrueckii growth while L. thermotolerans
+ declined more than in direct contact. HYPOTHESIZED: medium-mediated suppression of L. thermotolerans by T. delbrueckii
+ could explain the pattern. Neither a killer toxin nor a specific inhibitory metabolite was established as its
+ cause, and indirect pairwise confirmation was still needed. No pairwise causal arrow is inferred from this comparison.'
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: growth
@@ -152,26 +156,35 @@ ecological_interactions:
snippet: indirect (metabolic) contact favored T. delbrueckii growth at the expense of L. theromotolerans
explanation: Supports the indirect-contact growth shift toward T. delbrueckii.
- reference: PMID:42176030
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: T. delbrueckii likely suppresses growth of L. thermotolerans through a medium-mediated mechanism.
- explanation: Captures the authors' mechanistic interpretation for the no-contact L. thermotolerans decline.
+ explanation: 'The source says likely: this is a mechanistic interpretation of growth patterns, not a tested
+ inhibitory agent.'
- name: Contact-dependent amino acid profile shift
- description: Extracellular amino acid concentrations differed between direct and indirect contact fermentations after 5 h;
- the measured serine, glycine, valine, aspartic acid, and arginine concentrations were higher in the indirect-contact
- condition, with no significant difference after 9 h.
+ description: Extracellular amino acid concentrations differed between direct and indirect contact fermentations
+ after 5 h; the measured serine, glycine, valine, aspartic acid, and arginine concentrations were higher in the
+ indirect-contact condition, with no significant difference after 9 h. The difference does not by itself demonstrate
+ increased secretion, reduced uptake or cross-feeding; secretion, cell death and partial lysis remain possible
+ contributors. YNB already supplied histidine, methionine and tryptophan.
scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:42176030
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Direct cell contact favored S. cerevisiae growth and resulted in significantly different amino acid profiles
+ snippet: Direct cell contact favored S. cerevisiae growth and resulted in significantly different amino acid
+ profiles
explanation: Supports direct contact changing the amino-acid profile.
- reference: PMID:42176030
supports: SUPPORT
evidence_source: IN_VITRO
snippet: serine, glycine, valine, aspartic acid, and arginine
explanation: Names the amino acids that differed significantly between contact treatments at the 5 h time point.
+ - reference: PMID:42176030
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: No statistically significant differences between these conditions were observed after 9 h
+ explanation: Retains the later null result instead of generalizing the early amino-acid difference.
growth_media:
- name: YNB with amino acids, ammonium sulfate, and glucose
composition:
@@ -302,19 +315,37 @@ external_resources:
explanation: Lists the DOI for the wine yeast membrane-bioreactor publication.
discussions:
- discussion_id: wine_yeast_indirect_contact_amino_acid_source
- prompt: Which yeasts, export processes, or lysis processes produced the non-supplemented amino acids and the higher 5 h
- extracellular amino-acid concentrations in the indirect-contact three-species wine yeast membrane-bioreactor setup?
+ prompt: Which yeasts, export processes, or lysis processes produced the non-supplemented amino acids and the higher
+ 5 h extracellular amino-acid concentrations in the indirect-contact three-species wine yeast membrane-bioreactor
+ setup?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- ecological_interactions#Contact-dependent amino acid profile shift
- growth_media#YNB with amino acids, ammonium sulfate, and glucose
- rationale: YNB with amino acids supplied histidine, methionine, and tryptophan, but other amino acids appeared in
- fermentation supernatants and several were significantly higher in the indirect-contact treatment after 5 h. The article
- lists active secretion, species-specific cell death, and partial cell lysis as possible sources and states that further
- experiments are required to explain the concentration differences.
+ rationale: YNB with amino acids supplied histidine, methionine, and tryptophan, but other amino acids appeared
+ in fermentation supernatants and several were significantly higher in the indirect-contact treatment after 5
+ h. The article lists active secretion, species-specific cell death, and partial cell lysis as possible sources
+ and states that further experiments are required to explain the concentration differences.
posed_by: codex
posed_date: '2026-09-26'
+- discussion_id: three_causal_scope_batch123
+ prompt: Which medium-mediated process explains the indirect-contact growth shift?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Direct-contact S. cerevisiae growth advantage
+ - ecological_interactions#Indirect-contact Torulaspora growth shift
+ - ecological_interactions#Contact-dependent amino acid profile shift
+ rationale: The three-species treatment comparison supports contrasting growth patterns. It does not isolate a
+ T. delbrueckii inhibitor, and the paper explicitly requires indirect pairwise confirmation. Transcriptional
+ differences, including HXT and HPF1 responses, are not selective genetic perturbations proving the contact mechanism.
+ The separate amino-acid-origin discussion remains open.
+ posed_by: codex
+ posed_date: '2026-10-08'
+ evidence:
+ - reference: PMID:42176030
+ snippet: T. delbrueckii likely suppresses growth of L. thermotolerans through a medium-mediated mechanism.
metals_present: []
rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
@@ -324,14 +355,23 @@ curation_history:
- timestamp: '2026-09-26T15:23:43Z'
curator: codex
action: CREATE_COMMUNITY
- changes: Created CommunityMech:000438 for PMID:42176030 / doi:10.1007/s00253-026-13856-4, a defined three-species wine
- yeast consortium with strain-level membership, direct-versus-indirect cell-contact growth effects, YNB membrane-bioreactor
- cultivation details, an S. cerevisiae RNA-seq BioProject, and an open amino-acid-source discussion.
+ changes: Created CommunityMech:000438 for PMID:42176030 / doi:10.1007/s00253-026-13856-4, a defined three-species
+ wine yeast consortium with strain-level membership, direct-versus-indirect cell-contact growth effects, YNB
+ membrane-bioreactor cultivation details, an S. cerevisiae RNA-seq BioProject, and an open amino-acid-source
+ discussion.
llm_assisted: true
- timestamp: '2026-09-26T15:30:38Z'
curator: codex
action: UPDATE_COMMUNITY
- changes: Addressed adversarial review issues 1111, 1112, and 1113 by narrowing the amino-acid-source knowledge gap,
- dropping an unsupported aerobic atmosphere assignment, and replacing weak direct-contact dominance evidence with an
- explicit source quote.
+ changes: Addressed adversarial review issues 1111, 1112, and 1113 by narrowing the amino-acid-source knowledge
+ gap, dropping an unsupported aerobic atmosphere assignment, and replacing weak direct-contact dominance evidence
+ with an explicit source quote.
+ llm_assisted: true
+- timestamp: '2026-10-08T16:49:42Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain the positive contact-treatment growth phenotype without necessary-gene attribution.; Mark proposed
+ Torulaspora-mediated suppression as partial and hypothetical, not a demonstrated toxin mechanism.; Preserve
+ the 5 h amino-acid difference and 9 h null without inferring transfer, secretion or uptake direction. Issue#1955;
+ reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
llm_assisted: true
diff --git a/kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml b/kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml
index f99461147..a0edb9b8e 100644
--- a/kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml
+++ b/kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml
@@ -187,25 +187,29 @@ taxonomy:
cobamide intermediates
explanation: Supports Bacteroidota cobamide salvagers as a member of the Mankai endosphere cobamide network.
ecological_interactions:
-- name: Mankai Compartment Host Filtering
- description: Bacterial assemblages from cultivation medium, washed fronds, and surface-sterilized tissue clustered separately;
- the endosphere retained a lower-diversity, distinct subset of the broader plant-associated and medium-associated pool.
- interaction_type: NICHE_PARTITIONING
+- name: Mankai Compartment-Associated Community Differentiation
+ description: Bacterial DNA profiles from cultivation medium, washed fronds and surface-sterilized tissue differed
+ in composition and diversity. Environmental and host filtering is an interpretation of these compartment associations,
+ not a selectively perturbed host mechanism or demonstrated microbial niche partitioning. Endosphere denotes
+ the operational sterilized-tissue fraction; washed whole fronds are not a strictly epiphytic sample.
scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:42304541
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: The pronounced differences in richness and composition between the medium, phyllosphere and endosphere (Fig.
- 2 ) indicate strong environmental and host filtering along the plant-water interface
- explanation: Supports compartment filtering across medium, phyllosphere, and endosphere fractions.
+ snippet: The pronounced differences in richness and composition between the medium, phyllosphere and endosphere
+ (Fig. 2 ) indicate strong environmental and host filtering along the plant-water interface
+ explanation: Supports compartment differentiation and the authors' filtering interpretation, not an isolated
+ host-filtering mechanism.
- name: MAG-Inferred Cobamide Producer-Salvager Guild
- description: 'Genome-resolved endosphere analysis predicted an uneven cobamide pathway architecture: Hyphomicrobium zavarzinii,
- Methylobacterium, Devosia, Labrys, Ferrovibrionaceae, and other Alphaproteobacteria encoded most biosynthetic steps, while
- many Gammaproteobacteria and Bacteroidota lineages had incomplete pathways and were inferred to salvage or remodel exogenous
- intermediates. The network edges represent MAG-derived metabolic compatibility, not direct metabolite-flux or abundance-correlation
- evidence.'
- interaction_type: CROSS_FEEDING
+ description: 'Genome-resolved endosphere analysis predicted an uneven cobamide pathway architecture: Hyphomicrobium
+ zavarzinii, Methylobacterium, Devosia, Labrys, Ferrovibrionaceae, and other Alphaproteobacteria encoded most
+ biosynthetic steps, while many Gammaproteobacteria and Bacteroidota lineages had incomplete pathways and were
+ inferred to salvage or remodel exogenous intermediates. The network edges represent MAG-derived metabolic compatibility,
+ not direct metabolite-flux or abundance-correlation evidence. HYPOTHESIZED cross-feeding is not established
+ by gene presence or pathway gaps. Missing genes in individual MAGs can reflect reconstruction limitations. Cultured
+ species-level comparators were not strain-matched endophytes, so their cobalamin production does not validate
+ exchange in this guild or adaptive gene loss. The host is not established as a B12-dependent recipient.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Hyphomicrobium zavarzinii
@@ -264,19 +268,33 @@ ecological_interactions:
capacity as highly connected hub nodes
explanation: Supports the MAG-inferred hub structure of the cobamide network.
- reference: PMID:42304541
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: many Gammaproteobacteria and Bacteroidota lineages harbored incomplete pathways, implying reliance on exogenous
- cobamide intermediates
- explanation: Supports the broad salvager clades in the inferred network.
+ snippet: many Gammaproteobacteria and Bacteroidota lineages harbored incomplete pathways, implying reliance
+ on exogenous cobamide intermediates
+ explanation: Pathway incompleteness supports predicted salvage potential, not demonstrated dependence or metabolite
+ uptake.
- reference: PMID:42304541
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: edges represent the number of cobamide pathway intermediates that could be supplied by one taxon and utilized by
- another based on complementary gene content, thereby capturing putative exchange relationships inferred from pathway annotation
- rather than abundance correlations
- explanation: Documents that the network edges are inferred from MAG-derived pathway complementarity rather than direct
- exchange or abundance-correlation evidence.
+ snippet: edges represent the number of cobamide pathway intermediates that could be supplied by one taxon and
+ utilized by another based on complementary gene content, thereby capturing putative exchange relationships
+ inferred from pathway annotation rather than abundance correlations
+ explanation: Documents that the network edges are inferred from MAG-derived pathway complementarity rather than
+ direct exchange or abundance-correlation evidence.
+ computational_provenance:
+ prediction_type: OTHER
+ tools:
+ - tool_name: MetaBat2
+ role: MAG reconstruction
+ - tool_name: MetaErg
+ role: MAG annotation
+ - tool_name: igraph
+ role: Functional complementarity network construction in R
+ model_source: Cobamide biosynthesis, salvage and remodeling functions annotated in endosphere MAGs.
+ input_accession: PRJNA1356720; SRP645794
+ parameters: At least three compatible cobamide intermediates per edge; gene-content complementarity, not FBA,
+ direct flux or abundance correlation.
environmental_factors:
- name: industrial rotating greenhouse raceway
value: Mankai from Hinoman rotating raceway basins
@@ -351,14 +369,14 @@ external_resources:
explanation: Identifies the seed paper curated into this record.
discussions:
- discussion_id: direct_cobamide_exchange_not_measured
- prompt: The cobamide producer-salvager structure is inferred from MAG annotations and network complementarity; direct exchange
- of cobamide intermediates among endosphere members remains unmeasured.
+ prompt: The cobamide producer-salvager structure is inferred from MAG annotations and network complementarity;
+ direct exchange of cobamide intermediates among endosphere members remains unmeasured.
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- ecological_interactions#MAG-Inferred Cobamide Producer-Salvager Guild
- rationale: Resolving this would distinguish true metabolite handoff from shared niche preference or correlated cobamide
- pathway potential.
+ rationale: Resolving this would distinguish true metabolite handoff from shared niche preference or correlated
+ cobamide pathway potential.
proposed_experiments:
- experiment_id: mankai_cobamide_flux
name: Trace cobamide exchange in controlled Mankai endosphere microcosms
@@ -377,17 +395,30 @@ discussions:
- reference: PMID:42304541
supports: SUPPORT
evidence_source: OTHER
- snippet: Future work integrating transcriptomics, metabolite flux measurements, and controlled manipulation of key producer
- and salvager taxa will be essential to move from genomic potential and inferred interactions to directly measured cobamide
- exchange
+ snippet: Future work integrating transcriptomics, metabolite flux measurements, and controlled manipulation
+ of key producer and salvager taxa will be essential to move from genomic potential and inferred interactions
+ to directly measured cobamide exchange
explanation: The primary source explicitly frames direct cobamide exchange as a future measurement need.
+- discussion_id: wolffia_causal_scope_batch123
+ prompt: Do compartment profiles and comparator genomes establish host-selected cobamide dependence?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Mankai Compartment-Associated Community Differentiation
+ - ecological_interactions#MAG-Inferred Cobamide Producer-Salvager Guild
+ rationale: Operational fractions and possible carryover limit localization claims. Only endosphere MAGs were reconstructed,
+ so pathway architecture was not compared across all compartments. Non-strain-matched culture-collection representatives
+ cannot establish endophyte-specific gene loss or validate metabolite exchange. The existing direct-flux knowledge
+ gap remains open.
+ posed_by: codex
+ posed_date: '2026-10-08'
curation_history:
- timestamp: '2026-09-13T10:27:13Z'
curator: claude
action: ADD_MANKAI_ENDOSPHERE_RECORD
- changes: Added a new Mankai endosphere cobamide-guild community from PMID:42304541, including seven evidence-backed taxa
- and clades, MAG-inferred cobamide interactions, the BioProject accession, industrial raceway context, and an open discussion
- for unmeasured direct cobamide exchange.
+ changes: Added a new Mankai endosphere cobamide-guild community from PMID:42304541, including seven evidence-backed
+ taxa and clades, MAG-inferred cobamide interactions, the BioProject accession, industrial raceway context, and
+ an open discussion for unmeasured direct cobamide exchange.
llm_assisted: true
- timestamp: '2026-09-13T11:09:33Z'
curator: gtdb_ground.py
@@ -397,3 +428,10 @@ curation_history:
curator: gtdb_ground.py
action: GTDB_SET_STATUS
changes: 'Wrote gtdb_grounding_status on 7 taxonomy entries (#294, #395).'
+- timestamp: '2026-10-08T16:49:43Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Keep observed compartment differences separate from selectively demonstrated host filtering and niche
+ partitioning.; Retain annotated producer-salvager potential with computational provenance, not observed cross-feeding
+ or strain-matched validation. Issue#1956; reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
+ llm_assisted: true
diff --git a/kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml b/kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml
index 2cce83f73..ad3f418c4 100644
--- a/kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml
+++ b/kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml
@@ -82,11 +82,12 @@ taxonomy:
snippet: Ramichloridium apiculatum CMS-1 and Talaromyces pseudofuniculosus hzt-3′ in different ratios
explanation: Identifies T. pseudofuniculosus hzt-3′ as a member of the defined fungal mixed culture.
ecological_interactions:
-- name: CMS-1 Extracellular Polymer Cross-Feeding
- description: R. apiculatum CMS-1 synthesized extracellular polysaccharides and proteins during mixed cultivation; T. pseudofuniculosus
- hzt-3′ utilized these extracellular products, which was associated with increased hzt-3′ gluconic-acid, isocitric-acid,
- L-glutamine, and L-tyrosine production.
- interaction_type: CROSS_FEEDING
+- name: Hypothesized CMS-1 Extracellular Polymer Cross-Feeding
+ description: 'HYPOTHESIZED: CMS-1 extracellular products may support hzt-3′ metabolism in the mixed fungal culture.
+ The source proposes this direction from bulk polysaccharide, protein and metabolite patterns; it does not trace
+ CMS-1-derived material into hzt-3′. Medium sucrose consumption also contributes to the measured carbohydrate
+ decline. Retain the proposed interaction without presenting direct transfer or recipient-specific production
+ as demonstrated.'
scope: PAIRWISE
source_taxon:
preferred_term: Ramichloridium apiculatum CMS-1
@@ -114,19 +115,23 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
- description: Cross-feeding of CMS-1 extracellular polymers and protein was linked to increased hzt-3′ acid and amino-acid
- production in the mixed culture.
+ description: 'HYPOTHESIZED: consumption of CMS-1 products could enable greater hzt-3′ acid and amino-acid production.
+ Bulk culture comparisons support metabolic changes but do not isolate this transfer as their necessary cause
+ or distinguish it from consumption of supplied sucrose.'
evidence:
- reference: PMID:42478817
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: In mixed culture, CMS-1 synthesized extracellular polysaccharides and proteins that were utilized by hzt-3′
- explanation: Supports the directed extracellular-polysaccharide and protein cross-feeding edge from CMS-1 to hzt-3′.
+ snippet: In mixed culture, CMS-1 synthesized extracellular polysaccharides and proteins that were utilized by
+ hzt-3′
+ explanation: An author-proposed transfer mechanism inferred from bulk measurements, not direct donor-to-recipient
+ tracing.
- name: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
- description: The 20% CMS-1 plus 80% hzt-3′ mixed culture had elevated organic acids and amino acids relative to pure cultures;
- CMS-1 chiefly produced oxalic acid, while hzt-3′ chiefly generated gluconic acid and increased secretion of gluconic acid,
- isocitric acid, L-glutamine, and L-tyrosine after receiving CMS-1 extracellular products.
- interaction_type: NICHE_PARTITIONING
+ description: 'The tested 20% CMS-1 plus 80% hzt-3′ culture showed increased total organic acids and selected amino
+ acids relative to pure cultures. Pure CMS-1 chiefly produced oxalic acid, while pure hzt-3′ chiefly produced
+ gluconic acid. These are bulk concentrations, not gene-expression measurements or proof of recipient-specific
+ synthesis after cross-feeding. Individual compounds did not all increase: mixed-culture oxalic acid was much
+ lower.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Ramichloridium apiculatum CMS-1
@@ -152,24 +157,33 @@ ecological_interactions:
label: amino acid
downstream:
- target: Optimized Wollastonite Calcium and Silicon Leaching
- description: Increased acids and amino acids lowered pH and intensified the chemical dissolution of wollastonite by the
- mixed fungal culture.
+ description: 'PARTIAL: increased acidic metabolites and lower pH are consistent with enhanced acid dissolution
+ and complexation driving wollastonite leaching. The culture-ratio comparison supports this mechanism but does
+ not selectively establish which acid or amino acid is necessary, or partition chemical dissolution from physical
+ disruption.'
evidence:
- reference: PMID:42478817
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The strain CMS-1 primarily produced oxalic acid (0.66 ± 0.033 mg/mL), while strain hzt-3′ mainly generated gluconic
- acid (1.60 ± 0.0798 mg/mL).
+ snippet: The strain CMS-1 primarily produced oxalic acid (0.66 ± 0.033 mg/mL), while strain hzt-3′ mainly generated
+ gluconic acid (1.60 ± 0.0798 mg/mL).
explanation: Supports the distinct dominant organic acids measured for each fungal strain.
- reference: PMID:42478817
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: hzt-3′, which upregulated the production of gluconic acid, isocitric acid, L-glutamine, and L-tyrosine
- explanation: Supports increased hzt-3′ acid and amino-acid production in the mixed system.
+ explanation: The abstract assigns the mixed-culture change to hzt-3′; bulk assays do not independently establish
+ cell-specific flux.
+ - reference: PMID:42478817
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 'The total organic acid production ranked as follows: 20% CMS-1 + 80% hzt-3′ > 100% hzt-3′ > 100% CMS-1.'
+ explanation: Results reports the mixed culture above both pure cultures; individual acids need not all increase.
- name: Optimized Wollastonite Calcium and Silicon Leaching
- description: The 20% CMS-1 plus 80% hzt-3′ inoculation ratio produced the strongest wollastonite dissolution among the tested
- ratios, reaching 79.95% calcium leaching and 18.59% silicon leaching and visibly disrupting wollastonite residue structure.
- interaction_type: NICHE_PARTITIONING
+ description: 'The 20% CMS-1 plus 80% hzt-3′ input ratio gave the greatest wollastonite leaching among the tested
+ ratios: 79.95% +/- 6.37% calcium and 18.59% +/- 0.11% silicon at day 12. Residue analyses support altered mineral
+ structure. These positive outcomes do not demonstrate niche partitioning, quantify a separate hyphal-force contribution
+ or measure net CO2 sequestration.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Ramichloridium apiculatum CMS-1
@@ -184,14 +198,14 @@ ecological_interactions:
- reference: PMID:42478817
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The 20% CMS-1 + 80% hzt-3′ ratio achieved leaching efficiency of 79.95% ± 6.37% for Ca2+ and 18.59% ± 0.11% for
- Si4+
+ snippet: The 20% CMS-1 + 80% hzt-3′ ratio achieved leaching efficiency of 79.95% ± 6.37% for Ca2+ and 18.59%
+ ± 0.11% for Si4+
explanation: Supports the optimum mixed-culture ratio and Ca/Si leaching efficiencies.
- reference: PMID:42478817
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: surface cracks and grooves on leaching residues indicated additional biophysical disruption
- explanation: Supports fungal physical disruption of wollastonite residues as an additional leaching mechanism.
+ explanation: Residue morphology is consistent with disruption but does not isolate a causal hyphal-force contribution.
environmental_factors:
- name: Optimum CMS-1:hzt-3′ inoculation ratio
value: 20% Ramichloridium apiculatum CMS-1 plus 80% Talaromyces pseudofuniculosus hzt-3′
@@ -296,27 +310,27 @@ curation_history:
- timestamp: '2026-09-21T07:22:13Z'
curator: claude
action: CREATE_RECORD
- changes: Created CommunityMech:000404 for the Ramichloridium apiculatum CMS-1 / Talaromyces pseudofuniculosus hzt-3′ wollastonite
- fungal mixed-culture consortium from PMID:42478817, including taxonomy, cross-feeding and bioleaching interactions, cultivation
- conditions, and claim-level evidence snippets.
+ changes: Created CommunityMech:000404 for the Ramichloridium apiculatum CMS-1 / Talaromyces pseudofuniculosus
+ hzt-3′ wollastonite fungal mixed-culture consortium from PMID:42478817, including taxonomy, cross-feeding and
+ bioleaching interactions, cultivation conditions, and claim-level evidence snippets.
llm_assisted: true
- timestamp: '2026-09-21T07:39:56Z'
curator: claude
action: FIX_REFERENCE_SNIPPETS
- changes: Split the modified-Czapek method evidence around the bracketed pH clause stripped by reference validation, removed
- the unsupported pH field, and tightened the hzt-3′ organic-acid upregulation quote.
+ changes: Split the modified-Czapek method evidence around the bracketed pH clause stripped by reference validation,
+ removed the unsupported pH field, and tightened the hzt-3′ organic-acid upregulation quote.
llm_assisted: true
- timestamp: '2026-09-21T07:40:33Z'
curator: claude
action: FIX_ONTOLOGY_LABEL
- changes: Updated the GO:0044419 label on the extracellular polymer cross-feeding interaction to the canonical term-validator
- label.
+ changes: Updated the GO:0044419 label on the extracellular polymer cross-feeding interaction to the canonical
+ term-validator label.
llm_assisted: true
- timestamp: '2026-09-21T07:45:20Z'
curator: claude
action: FIX_STRAIN_DESIGNATION
- changes: Restored the prime mark in the Talaromyces pseudofuniculosus hzt-3′ strain designation and member references so
- the record preserves the strain identifier reported by PMID:42478817.
+ changes: Restored the prime mark in the Talaromyces pseudofuniculosus hzt-3′ strain designation and member references
+ so the record preserves the strain identifier reported by PMID:42478817.
llm_assisted: true
- timestamp: '2026-09-21T07:46:24Z'
curator: claude
@@ -332,7 +346,34 @@ curation_history:
curator: codex
action: REPAIR_OBSOLETE_GO_PROCESS
llm_assisted: true
- changes: Removed the optional obsolete GO:0016053 descriptor. Its only explicit GO replacement is GO:0008152
- (metabolic process), which the existing no-vacuous-annotations policy rejects. Retained the specific
- biological meaning in the unchanged interaction prose, metabolites, downstream links, and evidence
- without inventing a narrower ontology mapping.
+ changes: Removed the optional obsolete GO:0016053 descriptor. Its only explicit GO replacement is GO:0008152 (metabolic
+ process), which the existing no-vacuous-annotations policy rejects. Retained the specific biological meaning
+ in the unchanged interaction prose, metabolites, downstream links, and evidence without inventing a narrower
+ ontology mapping.
+- timestamp: '2026-10-08T16:49:43Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Qualify the proposed polymer handoff; bulk carbohydrate decline also includes medium-sucrose consumption.;
+ Preserve bulk metabolite changes without niche partitioning, uniform acid increases or recipient-specific synthesis.;
+ Keep measured day-12 calcium/silicon leaching and residue changes distinct from isolated physical causality
+ and CO2 sequestration. Issue#1957; reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
+ llm_assisted: true
+discussions:
+- discussion_id: woll_causal_scope_batch123
+ prompt: Which processes mediate the mixed-culture leaching improvement?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Hypothesized CMS-1 Extracellular Polymer Cross-Feeding
+ - ecological_interactions#Mixed-Culture Organic-Acid and Amino-Acid Upregulation
+ - ecological_interactions#Optimized Wollastonite Calcium and Silicon Leaching
+ rationale: The source demonstrates culture-ratio effects and bulk chemical changes. Direct CMS-1-to-hzt-3′ transfer,
+ cell-specific synthesis, necessary individual metabolites and a separately quantified hyphal-force contribution
+ remain unresolved. The proposed cross-feeding-to-acid-to-leaching chain is retained as qualified existing topology,
+ not a traced flux pathway or a net-carbon-removal measurement.
+ posed_by: codex
+ posed_date: '2026-10-08'
+ evidence:
+ - reference: PMID:42478817
+ snippet: In mixed culture, CMS-1 synthesized extracellular polysaccharides and proteins that were utilized by
+ hzt-3′
diff --git a/references_cache/PMID_42784437.txt b/references_cache/PMID_42784437.txt
index 06dd03fa9..a8d0453c0 100644
--- a/references_cache/PMID_42784437.txt
+++ b/references_cache/PMID_42784437.txt
@@ -47,4 +47,11 @@ differences must be accounted for when engineering predictable microbial
fermentations.
DOI: 10.1128/spectrum.02819-26
-PMID: 42784437
\ No newline at end of file
+PMID: 42784437
+
+## Primary full-text excerpt
+Source: https://journals.asm.org/doi/10.1128/spectrum.02819-26
+Section: Discussion. Retrieved 2026-10-08 through publisher web-rendered text.
+License: CC BY 4.0. This is a literal excerpt, not the full article or a supplement.
+
+the molecular mechanisms underlying the observed species- and strain-dependent effects were not addressed in the present work.
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index b7a97d4cc..d82b1e97d 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,35 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch123: Phenotypes And Inferred Mechanisms
+
+[Decisions](decisions/20261008-four-records-batch123.yaml),
+[provenance](cache-provenance-20261008-batch123.json),
+[validation](validation-20261008-batch123.json), and
+[self-adversarial review](adversarial-review-20261008-batch123.yaml) cover
+the five- and three-species wine yeast consortia, Mankai cobamide guild and
+wollastonite fungal pair. All eleven nodes and both existing arrows remain,
+with three renames and no new topology.
+
+Wine perturbation outcomes remain positive, with competition and proposed
+suppression mechanisms qualified. The early amino-acid difference and later
+null remain distinct. Mankai compartment profiles and annotated pathway
+compatibility are not demonstrated host filtering or metabolite transfer;
+computational provenance records the gene-content method. Fungal bulk
+metabolite and leaching outcomes remain positive, while the proposed transfer
+and acid-to-leaching links are explicitly qualified.
+
+Fresh primary sources support all 26 graph/discussion quotations. Three open
+main bodies and the five-species publisher Results, Discussion, Methods and
+Table 1 were inspected. Original figure pixels, external supplements, raw
+data and analysis code were not audited. One 17-word CC BY 4.0 excerpt was
+appended with provenance; the other 922 caches and 456 records are unchanged.
+Four append-only histories record the repairs. No Edison submission or spend.
+
+Repairs #1954-#1957 await protected-main merge. Non-graph metadata follow-ups
+#1958-#1961 remain open. This is source-based self-review, not independent
+approval or completion of the overall review and protected merge.
+
## Batch122: Treatment Outcomes And Mechanism Limits
[Decisions](decisions/20261008-four-records-batch122.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch123.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch123.yaml
new file mode 100644
index 000000000..b2a82f6b5
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch123.yaml
@@ -0,0 +1,437 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: a8eb38f28e262f5a6f6c804f68d782a6a6eb1d64
+scope:
+- kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml
+- kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml
+- kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml
+- kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch123.json
+findings:
+- issue: 1954
+ severity: P2
+ finding: Bound five-species wine competition and strain-output interpretation
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1955
+ severity: P2
+ finding: Qualify three-species wine suppression mechanism and preserve later amino-acid null
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1956
+ severity: P2
+ finding: Separate Mankai compartment associations and MAG potential from demonstrated interactions
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1957
+ severity: P2
+ finding: Bound wollastonite fungal cross-feeding and acid-to-leaching causal chain
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1958
+ severity: P2
+ finding: Curate available ten-strain identities and assay context for five-species wine panel
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1959
+ severity: P2
+ finding: Represent wine membrane-bioreactor recirculation separately from feed or dilution
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1960
+ severity: P2
+ finding: Qualify non-graph Mankai cross-feeder roles as genomic predictions
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1961
+ severity: P2
+ finding: Align non-graph wollastonite fungal role claims with inferred transfer evidence
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+adversarial_checks:
+- All11nodes and2arrows retained,three coherent renames,no new topology. All four canonical diffs and the narrow
+ cache append read after guarded writes. No dangling targets or anchors; unrelated fields and prior history artifacts
+ preserved.
+- Five-species drop-outs/substitutions retain positive treatment effects and completion. Competition remains qualified,not
+ an identified molecular cause or complete pairwise matrix. ARISA is not absolute viable abundance. Non-Saccharomyces
+ breadth is panel-specific and S.cerevisiae effects remain detectable. Available Table1/Methods metadata is separate1958,not
+ a renewed inaccessible-source claim.
+- Three-species contact-dependent growth retained,with hypothesized medium-mediated suppression PARTIAL. Early amino-acid
+ difference and9h null retained with supplied-medium amino acids distinguished. No toxin identity,necessary gene
+ or secretion/uptake direction inferred. Prior1111-1113 remain intact; recirculation metadata1959 separate.
+- Wolffia compartment differentiation retained without microbial niche partitioning or selectively tested host filtering.
+ Predicted guild retains seven participants and gene-complementarity provenance,not FBA or measured transfer. Operational
+ fractions,MAG gaps and non-strain-matched comparators constrain localization and adaptation. Prior839/840 and
+ direct-flux gap preserved; non-graph roles1960 separate.
+- Wollastonite bulk metabolites and positive day12Ca/Si leaching retained. Both existing arrows qualified; polymer
+ transfer not traced,medium sucrose contributes to carbohydrate loss,individual acids need not all rise. Residue
+ morphology does not isolate hyphal force; no measured net carbon sequestration inferred. Non-graph roles1961 separate.
+- Thirteen focused tests and twelve targeted in-memory control/mutation/restored-control probes pass. Earlier broader
+ probe receipt retained in scratch; targeted rerun improves isolation of completion,Saccharomyces-effect,acid-pattern
+ and leaching-value mutations. These guard specified assertions,not arbitrary semantic equivalence or every possible
+ textual regression.
+- All22graph and4discussion quotes match fresh primary artifacts and caches. One17-word CC BY4 excerpt appended;922othercaches
+ unchanged. Complete local primary main bodies plus publisher Results/Discussion/Methods/Table1 inspected; no figure-pixel,external
+ supplement,raw-data or code audit. Literal matches are not entailment proof.
+- Four focused schema/strict/terms/references/snippets/rank/history gates pass.1174selected tests,lint,mypy and
+ deterministic rendering pass.57existing network warnings remain and zero structural defects. Exact descriptions
+ on456pages,1359nodes,522arrows verified,not screenshot QA or full Linux CI certification.
+- 456otherrecords,unrelated raw fields and all prior history/decision files unchanged. Participant lists/scopes
+ unchanged;299participant-list users and census414community-level,136mixed,278community-only,1568taxa,1281sole-credit
+ preserved. Scope credit is not participant-coverage certification. No schema,connectivity or threshold changes.
+- 1954-1957 addressed pending protected-main merge;1958-1961 remain non-graph follow-ups. Source-based self-review
+ is not independent approval. No Edison invocation or spend; Ruegeria1883 unchanged authentication blocker not
+ retried. Protected-root1836,actual exact-head CI,merge and branch deletion remain separate requirements.
+- Corpus400reviewed,6pending,54needs_research across460records. Overall goal incomplete. Postcommit docs-current
+ and publication must be checked separately,not preasserted.
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Erase fermentation completion
+ test: test_five_positive_perturbations_do_not_imply_failed_completion
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 22
+ assertion: assert "All tested consortia completed fermentation" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/description
+ before: Species drop-out and strain substitution changed population succession, fermentation kinetics and
+ metabolic outputs in the defined five-species synthetic-must panel. These are positive composition-perturbation
+ effects, not identified molecular mechanisms. All tested consortia completed fermentation within the observation
+ period; changed kinetics should not be equated with failure to finish fermentation.
+ after: Species drop-out and strain substitution changed population succession, fermentation kinetics and
+ metabolic outputs in the defined five-species synthetic-must panel. These are positive composition-perturbation
+ effects, not identified molecular mechanisms. Some consortia failed fermentation within the observation
+ period; changed kinetics should not be equated with failure to finish fermentation.
+ - mutation: Promote competition certainty
+ test: test_five_competition_remains_a_qualified_inference
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 32
+ assertion: assert node["evidence"][0]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/1/evidence/0/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Erase detectable Saccharomyces effect
+ test: test_five_strain_effects_are_panel_specific_and_not_saccharomyces_silence
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 41
+ assertion: assert "still had detectable effects" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/2/description
+ before: Among the particular strains tested, non-Saccharomyces substitutions affected a broader range of
+ final metabolites than switching the S. cerevisiae strain. The latter still had detectable effects and
+ was not metabolically silent. This result is panel- and synthetic-must-specific, not a universal ordering
+ of species importance or a demonstration that strain effects share one mechanism.
+ after: Among the particular strains tested, non-Saccharomyces substitutions affected a broader range of
+ final metabolites than switching the S. cerevisiae strain. The latter had no detectable effects and was
+ not metabolically silent. This result is panel- and synthetic-must-specific, not a universal ordering
+ of species importance or a demonstration that strain effects share one mechanism.
+ - mutation: Promote hypothetical inhibitor
+ test: test_three_keeps_growth_and_qualifies_suppression
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 51
+ assertion: assert b["evidence"][1]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/1/evidence/1/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Erase late amino-acid null
+ test: test_three_keeps_amino_acid_early_effect_late_null_and_source_limits
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 61
+ assertion: assert "after 9 h" in node["evidence"][-1]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/2/evidence/2/snippet
+ before: No statistically significant differences between these conditions were observed after 9 h
+ after: All timepoints differed.
+ - mutation: Reassert demonstrated niche partitioning
+ test: test_wolffia_compartments_are_not_selectively_demonstrated_filtering
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 73
+ assertion: assert "interaction_type" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/0/interaction_type
+ before: null
+ after: NICHE_PARTITIONING
+ - mutation: Reassert demonstrated cobamide exchange
+ test: test_wolffia_potential_is_not_exchange_or_strain_matched_validation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 82
+ assertion: assert "interaction_type" not in node and not node.get("downstream")
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/1/interaction_type
+ before: null
+ after: CROSS_FEEDING
+ - mutation: Misclassify gene complementarity as FBA
+ test: test_wolffia_provenance_is_gene_content_not_flux_simulation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 95
+ assertion: assert provenance["prediction_type"] == "OTHER"
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/1/evidence/2/computational_provenance/prediction_type
+ before: OTHER
+ after: FLUX_BALANCE_ANALYSIS
+ - mutation: Promote fungal transfer certainty
+ test: test_woll_transfer_is_hypothesized_and_carbohydrate_loss_is_not_tracing
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 109
+ assertion: assert node["evidence"][0]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/0/evidence/0/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Erase nonuniform acid behavior
+ test: test_woll_metabolite_changes_are_bulk_and_not_uniform
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 117
+ assertion: assert "mixed-culture oxalic acid was much lower" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/1/description
+ before: "The tested 20% CMS-1 plus 80% hzt-3\u2032 culture showed increased total organic acids and selected\
+ \ amino acids relative to pure cultures. Pure CMS-1 chiefly produced oxalic acid, while pure hzt-3\u2032\
+ \ chiefly produced gluconic acid. These are bulk concentrations, not gene-expression measurements or proof\
+ \ of recipient-specific synthesis after cross-feeding. Individual compounds did not all increase: mixed-culture\
+ \ oxalic acid was much lower."
+ after: "The tested 20% CMS-1 plus 80% hzt-3\u2032 culture showed increased total organic acids and selected\
+ \ amino acids relative to pure cultures. Pure CMS-1 chiefly produced oxalic acid, while pure hzt-3\u2032\
+ \ chiefly produced gluconic acid. These are bulk concentrations, not gene-expression measurements or proof\
+ \ of recipient-specific synthesis after cross-feeding. Individual compounds did not all increase: all\
+ \ mixed-culture acids were higher."
+ - mutation: Drop existing acid-to-leaching direction
+ test: test_woll_retains_both_qualified_directions
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 125
+ assertion: assert len(a["downstream"]) == len(b["downstream"]) == 1
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/1/downstream
+ before:
+ - target: Optimized Wollastonite Calcium and Silicon Leaching
+ description: 'PARTIAL: increased acidic metabolites and lower pH are consistent with enhanced acid dissolution
+ and complexation driving wollastonite leaching. The culture-ratio comparison supports this mechanism
+ but does not selectively establish which acid or amino acid is necessary, or partition chemical dissolution
+ from physical disruption.'
+ after: []
+ - mutation: Erase positive leaching endpoint
+ test: test_woll_positive_leaching_is_not_carbon_sequestration
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 136
+ assertion: assert all(s in node["description"] for s in ["79.95%", "18.59%", "day 12"])
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/2/description
+ before: "The 20% CMS-1 plus 80% hzt-3\u2032 input ratio gave the greatest wollastonite leaching among the\
+ \ tested ratios: 79.95% +/- 6.37% calcium and 18.59% +/- 0.11% silicon at day 12. Residue analyses support\
+ \ altered mineral structure. These positive outcomes do not demonstrate niche partitioning, quantify a\
+ \ separate hyphal-force contribution or measure net CO2 sequestration."
+ after: "The 20% CMS-1 plus 80% hzt-3\u2032 input ratio gave the greatest wollastonite leaching among the\
+ \ tested ratios: 0% +/- 6.37% calcium and 18.59% +/- 0.11% silicon at day 12. Residue analyses support\
+ \ altered mineral structure. These positive outcomes do not demonstrate niche partitioning, quantify a\
+ \ separate hyphal-force contribution or measure net CO2 sequestration."
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml: 2df1d32db9dc666dbb93f9b7ae103d5c80f43c7e19e01450024dc416f31d3b2b
+ kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml: ba42e79fb1133d49ce6280562566ffedd6bcf37306ce42b97473e7cfdc1b017f
+ kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml: 829d29dcebcb9ba30483df9d1ec71eafb945a6a3bf966539ee6a16d9abd9077d
+ kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml: 06d15492c6e358b75deffe722b5299d7b5f86bf15090276db87fda690c6e639e
+ tests/test_causal_review_batch123.py: e319d885faf398047c0afb6f22ddf36723d30e5ffa375db0653d6eae3f9d6253
+ probe_script_sha256: 6c200fb6c9750e44bd80dc1b792ce830b21eba6a676846e1d8fac7a9bff6389d
+ scope: In-memory control/mutation/restored-control; no canonical writes and not additional pytest tests.
+ artifact: /private/tmp/communitymech-batch123/adversarial-regression-proof-targeted.json
+ sha256: b120061453e14621815c0881b26bc4c2da27b174be6cd9461f79d4524c7ad373
+verification:
+ combined_regressions: 1174 passed in 372.38s (0:06:12)
+ new_regression_tests: 13
+ total_recorded_gate_outputs: 41
+ primary_graph_snippet_proof:
+ graph_quotations: 22
+ discussion_quotations: 4
+ fresh_primary_literal_matches: 26
+ all_cached_literal_matches: 26
+ retained_nodes: 11
+ removed_nodes: 0
+ renamed_nodes: 3
+ retained_arrows: 2
+ removed_arrows: 0
+ new_nodes_or_directions: 0
+ references: Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment.
+ Total checks in the reference CLI counts issues, not examined snippets.
+ snippet_counts_by_record:
+ kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml:
+ MATCH: 17
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml:
+ MATCH: 24
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml:
+ MATCH: 17
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml:
+ MATCH: 20
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9090
+ categories:
+ MATCH: 8942
+ RENDERING: 31
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 76
+ caveat: Informational audit exit0 is not clean-corpus or entailment certification.
+ network:
+ existing_findings_preserved: 57
+ added_findings: {}
+ removed_findings: {}
+ structural_defects: 0
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml: 67f38c6539251cd8960e66af9b998bb4c038a984b4a018c826226615673779f8
+ tests/test_causal_review_batch123.py: e319d885faf398047c0afb6f22ddf36723d30e5ffa375db0653d6eae3f9d6253
+ tests/test_participating_taxa.py: f438815b4a028c0f38a077df53c95f685f98b3c2b523593896a124b544269db1
+ tests/test_community_level_connectivity_credit.py: 996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a
+ tests/test_causal_review_batch109.py: ff8e9e26771545e1ace22b3c1d42076789c99cc4bc83e588b6a4b9ad698d3d73
+ tests/test_datamodel.py: f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25
+ reports/causal_graph_review/cache-provenance-20261008-batch123.json: 88edcdd069da742f9b7a2318d960ae7133628d1d403966e8d3f16e0f082751a6
+ kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml: 2df1d32db9dc666dbb93f9b7ae103d5c80f43c7e19e01450024dc416f31d3b2b
+ kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml: ba42e79fb1133d49ce6280562566ffedd6bcf37306ce42b97473e7cfdc1b017f
+ kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml: 829d29dcebcb9ba30483df9d1ec71eafb945a6a3bf966539ee6a16d9abd9077d
+ kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml: 06d15492c6e358b75deffe722b5299d7b5f86bf15090276db87fda690c6e639e
+ history_sha256:
+ history/records/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium/2026-10-08T164943Z-codex-71bcd5.yaml: 123b54b5c732e2b51626fa158dcd3008bc1e42df90dafc47695824401dd0af8f
+ history/records/Wine_Yeast_ThreeSpecies_Contact_Consortium/2026-10-08T164944Z-codex-cf55bb.yaml: 662352e0473c72723c061b6543c56834e5b1e940848013f625281b37c5b31212
+ history/records/Wolffia_Mankai_Endosphere_Cobamide_Guild/2026-10-08T164944Z-codex-638dc2.yaml: 707d9c4ae34c750e4101294aed6111a7740a468b160895e8f7b3c5c7bd884f12
+ history/records/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium/2026-10-08T164944Z-codex-c1ca0f.yaml: bfc8c9abc9bacd9fad4a950cf4b9dcb6fe59eaa97136758244ca9d8f12336b77
+ unchanged_records: 456
+ unchanged_caches: 922
+ immutable_prior_history_and_decision_files: 904
+ cache_changes:
+ - path: references_cache/PMID_42784437.txt
+ before_sha256: 73c149edcbb34439981d8d5b8cb5a6f9f0003963f8f458149c62a8063fbc598d
+ after_sha256: 712ca54ab2fb5d865c15918a9283810912a0fb34c0d817fd229f4493c0e80036
+ action: Append a17-word literal primary Discussion limitation with URL,section,date and license; preserve original
+ cache prefix.
+ edison:
+ required_for_this_repair: false
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior approved invocation;
+ no unchanged-state retry.'
+ post_commit_docs_current: Separate publication gate, not preasserted.
+participant_census:
+ current:
+ records: 460
+ with_community_level: 414
+ mixed: 136
+ community_level_only: 278
+ taxa: 1568
+ credited_solely_by_the_rule: 1281
+ delta_from_batch122:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ explanation: All participant lists and scopes are unchanged;299participant-list users. Scope credit is not certification
+ of actual participant coverage. Connectivity logic and thresholds are unchanged.
+corpus:
+ records: 460
+ nodes: 1373
+ edges: 530
+ review_status_counts:
+ needs_research: 54
+ pending: 6
+ reviewed: 400
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary established Python3.13 lint environment; project dependencies unchanged.
+limitations:
+- Both-root pre-source baseline covers460records and923caches,57existing warnings and zero structural defects. Four
+ whole records and11nodes/two arrows reviewed; all retained,three renames,no new topology.
+- Fresh EuropePMC metadata/abstracts and Crossref identities checked for all four papers. Three complete OA main
+ bodies and five-species publisher Results/Discussion/Methods/Table1 plus captions inspected. Publisher web access
+ succeeded despite independent direct-HTTP403. Original figure pixels,external supplements,raw data and analysis
+ code not audited.
+- Five-species positive drop-out and strain-substitution effects retained. Competition is a phenotypic inference,not
+ resolved molecular or complete pairwise causality; ARISA is relative DNA-based succession. All consortia complete
+ fermentation and S.cerevisiae effects remain detectable. Table1/Methods information is available; separate metadata1958
+ remains.
+- Three-species direct-contact growth and indirect-contact Torulaspora shifts retained. Medium-mediated suppression
+ and toxin identity remain untested; expression differences are not necessary-gene perturbations. Preserve the5h
+ amino-acid effect,the9h null and supplied histidine/methionine/tryptophan. Recirculation-versus-feed metadata1959
+ remains.
+- Wolffia compartment associations do not establish selectively tested host filtering or microbial niche partitioning.
+ MAG gene-content complementarity and minimum-three-intermediate edges are potential,not flux/FBA/abundance correlation.
+ Operational endosphere fractions and non-strain-matched cultured comparators limit localization and adaptive-loss
+ claims; cross-feeder role metadata1960 remains.
+- Wollastonite positive day12Ca/Si leaching and bulk metabolite changes retained. CMS-1-to-hzt transfer is hypothesized;
+ medium sucrose also explains carbohydrate consumption. Selected metabolites increase,not every acid. Both existing
+ arrows remain qualified; no necessary individual mediator,isolated hyphal force or measured net CO2 sequestration
+ inferred. Non-graph role metadata1961 remains.
+- All22graph and4discussion quotes matched to fresh primary artifacts and caches. One17-word CC BY4 publisher Discussion
+ excerpt appended with provenance to the five-species cache;922othercaches unchanged. No full-body cache import.
+ Wolffia is CC BY-NC-ND4; no new verbatim excerpts added from that source.
+- Expanded all-state1188issue titles/bodies and hidden/ignored local paths searched;141matchinglocalpaths,sixpriorissue
+ bodies and onepriorfive-speciesreviewreport read. Credentials,.git,generateddocs/site and reference caches excluded
+ from local issue-dedup search; caches separately inspected for evidence. No historical PR-comment audit.
+- Four guarded writes preserve456otherrecords,unrelated raw YAML fields,all prior history/decision artifacts and
+ existing taxonomy/participant/scopes. Four append-only histories and curation events. Neighbor cobalamin-coculture
+ and mineral-SOM records inspected as conventions only,not transferred scientific evidence.
+- No Edison submission or spend,new nodes or directions. Prior authorized Ruegeria1883 configured-authentication
+ blocker not retried unchanged; no credentials inspected. Source-based self-adversarial review is not independent
+ approval. Overall objective,protected merge and branch deletion remain incomplete.
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch123.json b/reports/causal_graph_review/cache-provenance-20261008-batch123.json
new file mode 100644
index 000000000..b3bff26b3
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch123.json
@@ -0,0 +1,318 @@
+{
+ "changes": [
+ {
+ "path": "references_cache/PMID_42784437.txt",
+ "before_sha256": "73c149edcbb34439981d8d5b8cb5a6f9f0003963f8f458149c62a8063fbc598d",
+ "after_sha256": "712ca54ab2fb5d865c15918a9283810912a0fb34c0d817fd229f4493c0e80036",
+ "action": "Append a17-word literal primary Discussion limitation with URL,section,date and license; preserve original cache prefix."
+ }
+ ],
+ "unchanged_cache_files": 922,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch123/baseline.json": "69cb401d7f613e0f6dde181e3a41bf820520328c9107bb2a541b3b38702da1a3",
+ "/private/tmp/communitymech-batch123/five-abstract.txt": "128dd013622fc111a1edd118a7bf85efee8f53aa9a5a53c01c88efb8f017d16e",
+ "/private/tmp/communitymech-batch123/five-crossref.json": "340f2fbd2aa60c1eb983c03c8787956d5e1f8e512770372a533f090b6e35e3b9",
+ "/private/tmp/communitymech-batch123/five-metadata.json": "c8fcfe4d8c87e0ace63a202835687093fbfb23da3c6ea6233c3caf9cced288a1",
+ "/private/tmp/communitymech-batch123/five-primary.txt": "829fd52c51329da5db0c3ec13d59e55d965a5ad66800cafbdc6bc5d73cc0946a",
+ "/private/tmp/communitymech-batch123/five-publisher-results1.txt": "a3cb7fc46e01ab2b2a88badd41001d591b6fafe60c02f80ddce0a7536ca2a6f3",
+ "/private/tmp/communitymech-batch123/five-publisher-results2.txt": "e14a1b2495c6d31a0d6ca8e7360a679fafe4ca6c65423897a8830dd4f389f99e",
+ "/private/tmp/communitymech-batch123/five-publisher-retrieval.json": "c6e91d5fe50f284719b66fbe78941d5f7a6254b22aa080883a3cd6b3d6d203a1",
+ "/private/tmp/communitymech-batch123/issue-dedup-current.json": "7d4960e490effddd7f8dfdf81b9bfc39c20db19dc58c8f5ee6476ded5c7f024a",
+ "/private/tmp/communitymech-batch123/local-matches-expanded.txt": "9ba8577ee6bcff84f09530c0e303e9d5631e22bd8cf6874ff76c772107a38960",
+ "/private/tmp/communitymech-batch123/local-matches.txt": "48a9b81e2a103a7fbf8f803d5e3eef99a5987395009a196d7e8fef4a6d594060",
+ "/private/tmp/communitymech-batch123/primary-manifest.json": "ea39984f6645b072023511a74ba9874f11e77b00eb5501b736b72509e61d59c2",
+ "/private/tmp/communitymech-batch123/target-baseline.json": "8fb2c59e5dfd5c82da6d87ff7abc52b4158ccc0200cd31e378bd69d43866ac94",
+ "/private/tmp/communitymech-batch123/three-abstract.txt": "ca05e5cd6e7a5e5035d2ae40b3faee063d94e8767a8b0b6516f449b38837306c",
+ "/private/tmp/communitymech-batch123/three-crossref.json": "6a147abd574ab80afde6153f5e09c9b41bfc4e02f2380c8491b39cccddf74d5f",
+ "/private/tmp/communitymech-batch123/three-metadata.json": "e429674e87c84c5dbf1c948d2c26bb725751d4e8e257776cbd90ee21074886e3",
+ "/private/tmp/communitymech-batch123/three-primary.txt": "f82c06da25c53c255d66cd219451cbe9bbff117aa80b57a5ff1b4bac5c3be846",
+ "/private/tmp/communitymech-batch123/three-primary.xml": "6be5199a52d4ada845c08ab2b7f179e49684c4c9c2548aae7db43edde816e4ed",
+ "/private/tmp/communitymech-batch123/wolffia-abstract.txt": "f144e020f47b9c07b7502fa6be13b5b23891717a5b5288a35495a7bd52970c94",
+ "/private/tmp/communitymech-batch123/wolffia-crossref.json": "1b2b911549316223f66a1a0b7d81ad438bdc7360e1d67ce2d4512bcaf2518e52",
+ "/private/tmp/communitymech-batch123/wolffia-metadata.json": "0bacaac05748a3518d22afc62a68fed53f886a6a18d9262366b18552fb6b8a4f",
+ "/private/tmp/communitymech-batch123/wolffia-primary.txt": "8a156084ee5a70d9d3c5e02763ca0974cce3f3c12e4fe3c2bf00570fdb56e0a0",
+ "/private/tmp/communitymech-batch123/wolffia-primary.xml": "f94e26d64a7dff99fc9b0e4d5a97b2fb44d45f120a8b3e7a2968402eabd1cf07",
+ "/private/tmp/communitymech-batch123/woll-abstract.txt": "db01a6fb05f8b55c0d200f3bb57dbf8be5c9edee77c6a8549cf9165434f11ae7",
+ "/private/tmp/communitymech-batch123/woll-crossref.json": "938523e0e243d2cfe8379995ca50c88055448f3320c68c35b5defb837ecbaf7d",
+ "/private/tmp/communitymech-batch123/woll-metadata.json": "6e69f2b54938592fd889b4a3b1853a742025bef93e933a48b7963653e86daa81",
+ "/private/tmp/communitymech-batch123/woll-primary.txt": "1108a4ecfbb2b9ab4e27e2f15c78f7b147006ee07ac5db3cb4460e065649f610",
+ "/private/tmp/communitymech-batch123/woll-primary.xml": "a5fd72d224d836636b73dc00fa62402bf6c63454a1413c4659e24ffeb2522a5a",
+ "references_cache/PMID_42176030.txt": "00f49c79569200a4a591bad07ccea19f9cabd96ec9728c10820e30e68647c1fd",
+ "references_cache/PMID_42304541.txt": "79d8cd5d1bb724484d8d5c3bd11349a8a6f03043a159ee79446ee375cf6bba7b",
+ "references_cache/PMID_42478817.txt": "a16fc2b369d4bab42a84959c670d1b6e1306e5959731af305e964cf2e6d7d0d9",
+ "references_cache/PMID_42784437.txt": "712ca54ab2fb5d865c15918a9283810912a0fb34c0d817fd229f4493c0e80036"
+ },
+ "source_access": {
+ "retrieval_manifest": {
+ "five": {
+ "pmid": "42784437",
+ "doi": "10.1128/spectrum.02819-26",
+ "pmcid": null,
+ "title": "Species and strain-specific phenotypes shape performance and output of a five-species yeast consortium.",
+ "metadata": "/private/tmp/communitymech-batch123/five-metadata.json",
+ "metadata_sha256": "c8fcfe4d8c87e0ace63a202835687093fbfb23da3c6ea6233c3caf9cced288a1",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42784437+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch123/five-abstract.txt",
+ "abstract_sha256": "128dd013622fc111a1edd118a7bf85efee8f53aa9a5a53c01c88efb8f017d16e",
+ "crossref": "/private/tmp/communitymech-batch123/five-crossref.json",
+ "crossref_sha256": "340f2fbd2aa60c1eb983c03c8787956d5e1f8e512770372a533f090b6e35e3b9",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2026,
+ 9,
+ 24
+ ]
+ ],
+ "date-time": "2026-09-24T00:00:00Z",
+ "timestamp": 1790208000000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0/"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2026,
+ 9,
+ 24
+ ]
+ ],
+ "date-time": "2026-09-24T00:00:00Z",
+ "timestamp": 1790208000000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://journals.asm.org/non-commercial-tdm-license"
+ }
+ ],
+ "primary_text": "/private/tmp/communitymech-batch123/five-primary.txt",
+ "primary_sha256": "829fd52c51329da5db0c3ec13d59e55d965a5ad66800cafbdc6bc5d73cc0946a",
+ "web_body_artifacts": [
+ "/private/tmp/communitymech-batch123/five-publisher-results1.txt",
+ "/private/tmp/communitymech-batch123/five-publisher-results2.txt"
+ ],
+ "primary_scope": "Fresh abstract plus publisher web-rendered lines93-299 covering Results, Discussion, Methods, Table1 and captions. No original figure pixels or supplements.",
+ "direct_http": "403 receipt retained separately; web retrieval succeeded."
+ },
+ "three": {
+ "pmid": "42176030",
+ "doi": "10.1007/s00253-026-13856-4",
+ "pmcid": "PMC13375760",
+ "title": "Impact of direct cell-cell contact in a three-species wine yeast consortium.",
+ "metadata": "/private/tmp/communitymech-batch123/three-metadata.json",
+ "metadata_sha256": "e429674e87c84c5dbf1c948d2c26bb725751d4e8e257776cbd90ee21074886e3",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42176030+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved"
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13375760/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch123/three-abstract.txt",
+ "abstract_sha256": "ca05e5cd6e7a5e5035d2ae40b3faee063d94e8767a8b0b6516f449b38837306c",
+ "xml": "/private/tmp/communitymech-batch123/three-primary.xml",
+ "xml_sha256": "6be5199a52d4ada845c08ab2b7f179e49684c4c9c2548aae7db43edde816e4ed",
+ "primary_text": "/private/tmp/communitymech-batch123/three-primary.txt",
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+ "actual_read_scope": [
+ "Fresh EuropePMC metadata/abstracts and Crossref identities checked for all four papers. Three complete OA main bodies and five-species publisher Results/Discussion/Methods/Table1 plus captions inspected. Publisher web access succeeded despite independent direct-HTTP403. Original figure pixels,external supplements,raw data and analysis code not audited.",
+ "Five-species positive drop-out and strain-substitution effects retained. Competition is a phenotypic inference,not resolved molecular or complete pairwise causality; ARISA is relative DNA-based succession. All consortia complete fermentation and S.cerevisiae effects remain detectable. Table1/Methods information is available; separate metadata1958 remains.",
+ "Three-species direct-contact growth and indirect-contact Torulaspora shifts retained. Medium-mediated suppression and toxin identity remain untested; expression differences are not necessary-gene perturbations. Preserve the5h amino-acid effect,the9h null and supplied histidine/methionine/tryptophan. Recirculation-versus-feed metadata1959 remains.",
+ "Wolffia compartment associations do not establish selectively tested host filtering or microbial niche partitioning. MAG gene-content complementarity and minimum-three-intermediate edges are potential,not flux/FBA/abundance correlation. Operational endosphere fractions and non-strain-matched cultured comparators limit localization and adaptive-loss claims; cross-feeder role metadata1960 remains.",
+ "Wollastonite positive day12Ca/Si leaching and bulk metabolite changes retained. CMS-1-to-hzt transfer is hypothesized; medium sucrose also explains carbohydrate consumption. Selected metabolites increase,not every acid. Both existing arrows remain qualified; no necessary individual mediator,isolated hyphal force or measured net CO2 sequestration inferred. Non-graph role metadata1961 remains.",
+ "All22graph and4discussion quotes matched to fresh primary artifacts and caches. One17-word CC BY4 publisher Discussion excerpt appended with provenance to the five-species cache;922othercaches unchanged. No full-body cache import. Wolffia is CC BY-NC-ND4; no new verbatim excerpts added from that source."
+ ]
+ },
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+ "Five-species positive drop-out and strain-substitution effects retained. Competition is a phenotypic inference,not resolved molecular or complete pairwise causality; ARISA is relative DNA-based succession. All consortia complete fermentation and S.cerevisiae effects remain detectable. Table1/Methods information is available; separate metadata1958 remains.",
+ "Three-species direct-contact growth and indirect-contact Torulaspora shifts retained. Medium-mediated suppression and toxin identity remain untested; expression differences are not necessary-gene perturbations. Preserve the5h amino-acid effect,the9h null and supplied histidine/methionine/tryptophan. Recirculation-versus-feed metadata1959 remains.",
+ "Wolffia compartment associations do not establish selectively tested host filtering or microbial niche partitioning. MAG gene-content complementarity and minimum-three-intermediate edges are potential,not flux/FBA/abundance correlation. Operational endosphere fractions and non-strain-matched cultured comparators limit localization and adaptive-loss claims; cross-feeder role metadata1960 remains.",
+ "Wollastonite positive day12Ca/Si leaching and bulk metabolite changes retained. CMS-1-to-hzt transfer is hypothesized; medium sucrose also explains carbohydrate consumption. Selected metabolites increase,not every acid. Both existing arrows remain qualified; no necessary individual mediator,isolated hyphal force or measured net CO2 sequestration inferred. Non-graph role metadata1961 remains.",
+ "All22graph and4discussion quotes matched to fresh primary artifacts and caches. One17-word CC BY4 publisher Discussion excerpt appended with provenance to the five-species cache;922othercaches unchanged. No full-body cache import. Wolffia is CC BY-NC-ND4; no new verbatim excerpts added from that source.",
+ "Expanded all-state1188issue titles/bodies and hidden/ignored local paths searched;141matchinglocalpaths,sixpriorissue bodies and onepriorfive-speciesreviewreport read. Credentials,.git,generateddocs/site and reference caches excluded from local issue-dedup search; caches separately inspected for evidence. No historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,unrelated raw YAML fields,all prior history/decision artifacts and existing taxonomy/participant/scopes. Four append-only histories and curation events. Neighbor cobalamin-coculture and mineral-SOM records inspected as conventions only,not transferred scientific evidence.",
+ "No Edison submission or spend,new nodes or directions. Prior authorized Ruegeria1883 configured-authentication blocker not retried unchanged; no credentials inspected. Source-based self-adversarial review is not independent approval. Overall objective,protected merge and branch deletion remain incomplete."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
new file mode 100644
index 000000000..8c63aa938
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
@@ -0,0 +1,754 @@
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+issues:
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+- 1955
+- 1956
+- 1957
+unresolved_research_issues: []
+unresolved_non_graph_issues:
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+- 1960
+- 1961
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+ pmcid: null
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+ provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third
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+ otherwise in a credit line to the material. If material is not included in the article's Creative Commons
+ licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you
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+ \ of it. The images or other third party material in this article are included in the article\u2019s Creative\
+ \ Commons licence, unless indicated otherwise in a credit line to the material. If material is not included\
+ \ in the article\u2019s Creative Commons licence and your intended use is not permitted by statutory regulation\
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+ - Three-species direct-contact growth and indirect-contact Torulaspora shifts retained. Medium-mediated suppression
+ and toxin identity remain untested; expression differences are not necessary-gene perturbations. Preserve the5h
+ amino-acid effect,the9h null and supplied histidine/methionine/tryptophan. Recirculation-versus-feed metadata1959
+ remains.
+ - Wolffia compartment associations do not establish selectively tested host filtering or microbial niche partitioning.
+ MAG gene-content complementarity and minimum-three-intermediate edges are potential,not flux/FBA/abundance correlation.
+ Operational endosphere fractions and non-strain-matched cultured comparators limit localization and adaptive-loss
+ claims; cross-feeder role metadata1960 remains.
+ - Wollastonite positive day12Ca/Si leaching and bulk metabolite changes retained. CMS-1-to-hzt transfer is hypothesized;
+ medium sucrose also explains carbohydrate consumption. Selected metabolites increase,not every acid. Both existing
+ arrows remain qualified; no necessary individual mediator,isolated hyphal force or measured net CO2 sequestration
+ inferred. Non-graph role metadata1961 remains.
+ - All22graph and4discussion quotes matched to fresh primary artifacts and caches. One17-word CC BY4 publisher
+ Discussion excerpt appended with provenance to the five-species cache;922othercaches unchanged. No full-body
+ cache import. Wolffia is CC BY-NC-ND4; no new verbatim excerpts added from that source.
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+ retained_nodes: 11
+ removed_nodes: 0
+ original_arrows: 2
+ retained_arrows: 2
+ removed_arrows: 0
+ renamed_nodes: 3
+ graph_quotations: 22
+ discussion_quotations: 4
+ new_discussions: 4
+primary_graph_snippet_count: 22
+snippet_checks:
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+ node: Species drop-out and strain-substitution output shifts
+ evidence_index: 0
+ reference: PMID:42784437
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/five-primary.txt
+ cache_artifact: references_cache/PMID_42784437.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium
+ node: Species drop-out and strain-substitution output shifts
+ evidence_index: 1
+ reference: PMID:42784437
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/five-primary.txt
+ cache_artifact: references_cache/PMID_42784437.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium
+ node: Inferred interspecies sugar-utilization competition
+ evidence_index: 0
+ reference: PMID:42784437
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/five-primary.txt
+ cache_artifact: references_cache/PMID_42784437.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium
+ node: Non-Saccharomyces strain-dependent metabolic tuning
+ evidence_index: 0
+ reference: PMID:42784437
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/five-primary.txt
+ cache_artifact: references_cache/PMID_42784437.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium
+ node: Non-Saccharomyces strain-dependent metabolic tuning
+ evidence_index: 1
+ reference: PMID:42784437
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/five-primary.txt
+ cache_artifact: references_cache/PMID_42784437.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_ThreeSpecies_Contact_Consortium
+ node: Direct-contact S. cerevisiae growth advantage
+ evidence_index: 0
+ reference: PMID:42176030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/three-primary.txt
+ cache_artifact: references_cache/PMID_42176030.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_ThreeSpecies_Contact_Consortium
+ node: Direct-contact S. cerevisiae growth advantage
+ evidence_index: 1
+ reference: PMID:42176030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/three-primary.txt
+ cache_artifact: references_cache/PMID_42176030.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_ThreeSpecies_Contact_Consortium
+ node: Indirect-contact Torulaspora growth shift
+ evidence_index: 0
+ reference: PMID:42176030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/three-primary.txt
+ cache_artifact: references_cache/PMID_42176030.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_ThreeSpecies_Contact_Consortium
+ node: Indirect-contact Torulaspora growth shift
+ evidence_index: 1
+ reference: PMID:42176030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/three-primary.txt
+ cache_artifact: references_cache/PMID_42176030.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_ThreeSpecies_Contact_Consortium
+ node: Contact-dependent amino acid profile shift
+ evidence_index: 0
+ reference: PMID:42176030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/three-primary.txt
+ cache_artifact: references_cache/PMID_42176030.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_ThreeSpecies_Contact_Consortium
+ node: Contact-dependent amino acid profile shift
+ evidence_index: 1
+ reference: PMID:42176030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/three-primary.txt
+ cache_artifact: references_cache/PMID_42176030.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_ThreeSpecies_Contact_Consortium
+ node: Contact-dependent amino acid profile shift
+ evidence_index: 2
+ reference: PMID:42176030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/three-primary.txt
+ cache_artifact: references_cache/PMID_42176030.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wolffia_Mankai_Endosphere_Cobamide_Guild
+ node: Mankai Compartment-Associated Community Differentiation
+ evidence_index: 0
+ reference: PMID:42304541
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/wolffia-primary.txt
+ cache_artifact: references_cache/PMID_42304541.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wolffia_Mankai_Endosphere_Cobamide_Guild
+ node: MAG-Inferred Cobamide Producer-Salvager Guild
+ evidence_index: 0
+ reference: PMID:42304541
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/wolffia-primary.txt
+ cache_artifact: references_cache/PMID_42304541.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wolffia_Mankai_Endosphere_Cobamide_Guild
+ node: MAG-Inferred Cobamide Producer-Salvager Guild
+ evidence_index: 1
+ reference: PMID:42304541
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/wolffia-primary.txt
+ cache_artifact: references_cache/PMID_42304541.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wolffia_Mankai_Endosphere_Cobamide_Guild
+ node: MAG-Inferred Cobamide Producer-Salvager Guild
+ evidence_index: 2
+ reference: PMID:42304541
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/wolffia-primary.txt
+ cache_artifact: references_cache/PMID_42304541.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium
+ node: Hypothesized CMS-1 Extracellular Polymer Cross-Feeding
+ evidence_index: 0
+ reference: PMID:42478817
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/woll-primary.txt
+ cache_artifact: references_cache/PMID_42478817.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium
+ node: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
+ evidence_index: 0
+ reference: PMID:42478817
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/woll-primary.txt
+ cache_artifact: references_cache/PMID_42478817.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium
+ node: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
+ evidence_index: 1
+ reference: PMID:42478817
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/woll-primary.txt
+ cache_artifact: references_cache/PMID_42478817.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium
+ node: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
+ evidence_index: 2
+ reference: PMID:42478817
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/woll-primary.txt
+ cache_artifact: references_cache/PMID_42478817.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium
+ node: Optimized Wollastonite Calcium and Silicon Leaching
+ evidence_index: 0
+ reference: PMID:42478817
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/woll-primary.txt
+ cache_artifact: references_cache/PMID_42478817.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium
+ node: Optimized Wollastonite Calcium and Silicon Leaching
+ evidence_index: 1
+ reference: PMID:42478817
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/woll-primary.txt
+ cache_artifact: references_cache/PMID_42478817.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+discussion_snippet_checks:
+- record: Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium
+ node: five_causal_scope_batch123
+ evidence_index: 0
+ reference: PMID:42784437
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/five-primary.txt
+ cache_artifact: references_cache/PMID_42784437.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wine_Yeast_ThreeSpecies_Contact_Consortium
+ node: three_causal_scope_batch123
+ evidence_index: 0
+ reference: PMID:42176030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/three-primary.txt
+ cache_artifact: references_cache/PMID_42176030.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wolffia_Mankai_Endosphere_Cobamide_Guild
+ node: direct_cobamide_exchange_not_measured
+ evidence_index: 0
+ reference: PMID:42304541
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/wolffia-primary.txt
+ cache_artifact: references_cache/PMID_42304541.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium
+ node: woll_causal_scope_batch123
+ evidence_index: 0
+ reference: PMID:42478817
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch123/woll-primary.txt
+ cache_artifact: references_cache/PMID_42478817.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+cache_changes:
+- path: references_cache/PMID_42784437.txt
+ before_sha256: 73c149edcbb34439981d8d5b8cb5a6f9f0003963f8f458149c62a8063fbc598d
+ after_sha256: 712ca54ab2fb5d865c15918a9283810912a0fb34c0d817fd229f4493c0e80036
+ action: Append a17-word literal primary Discussion limitation with URL,section,date and license; preserve original
+ cache prefix.
+edison:
+ required_for_this_repair: false
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior approved invocation; no
+ unchanged-state retry.'
+limitations:
+- Both-root pre-source baseline covers460records and923caches,57existing warnings and zero structural defects. Four
+ whole records and11nodes/two arrows reviewed; all retained,three renames,no new topology.
+- Fresh EuropePMC metadata/abstracts and Crossref identities checked for all four papers. Three complete OA main
+ bodies and five-species publisher Results/Discussion/Methods/Table1 plus captions inspected. Publisher web access
+ succeeded despite independent direct-HTTP403. Original figure pixels,external supplements,raw data and analysis
+ code not audited.
+- Five-species positive drop-out and strain-substitution effects retained. Competition is a phenotypic inference,not
+ resolved molecular or complete pairwise causality; ARISA is relative DNA-based succession. All consortia complete
+ fermentation and S.cerevisiae effects remain detectable. Table1/Methods information is available; separate metadata1958
+ remains.
+- Three-species direct-contact growth and indirect-contact Torulaspora shifts retained. Medium-mediated suppression
+ and toxin identity remain untested; expression differences are not necessary-gene perturbations. Preserve the5h
+ amino-acid effect,the9h null and supplied histidine/methionine/tryptophan. Recirculation-versus-feed metadata1959
+ remains.
+- Wolffia compartment associations do not establish selectively tested host filtering or microbial niche partitioning.
+ MAG gene-content complementarity and minimum-three-intermediate edges are potential,not flux/FBA/abundance correlation.
+ Operational endosphere fractions and non-strain-matched cultured comparators limit localization and adaptive-loss
+ claims; cross-feeder role metadata1960 remains.
+- Wollastonite positive day12Ca/Si leaching and bulk metabolite changes retained. CMS-1-to-hzt transfer is hypothesized;
+ medium sucrose also explains carbohydrate consumption. Selected metabolites increase,not every acid. Both existing
+ arrows remain qualified; no necessary individual mediator,isolated hyphal force or measured net CO2 sequestration
+ inferred. Non-graph role metadata1961 remains.
+- All22graph and4discussion quotes matched to fresh primary artifacts and caches. One17-word CC BY4 publisher Discussion
+ excerpt appended with provenance to the five-species cache;922othercaches unchanged. No full-body cache import.
+ Wolffia is CC BY-NC-ND4; no new verbatim excerpts added from that source.
+- Expanded all-state1188issue titles/bodies and hidden/ignored local paths searched;141matchinglocalpaths,sixpriorissue
+ bodies and onepriorfive-speciesreviewreport read. Credentials,.git,generateddocs/site and reference caches excluded
+ from local issue-dedup search; caches separately inspected for evidence. No historical PR-comment audit.
+- Four guarded writes preserve456otherrecords,unrelated raw YAML fields,all prior history/decision artifacts and
+ existing taxonomy/participant/scopes. Four append-only histories and curation events. Neighbor cobalamin-coculture
+ and mineral-SOM records inspected as conventions only,not transferred scientific evidence.
+- No Edison submission or spend,new nodes or directions. Prior authorized Ruegeria1883 configured-authentication
+ blocker not retried unchanged; no credentials inspected. Source-based self-adversarial review is not independent
+ approval. Overall objective,protected merge and branch deletion remain incomplete.
+records:
+- path: kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml
+ id: CommunityMech:000465
+ original_sha256: 29c5ffbc44052dbaf61fdeffa2ba7c0495f4c37cd1f9a246834d1bee9ed07e16
+ record_sha256: 2df1d32db9dc666dbb93f9b7ae103d5c80f43c7e19e01450024dc416f31d3b2b
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Preserve positive composition perturbations while distinguishing kinetics from completion and molecular
+ mechanism.; Retain competition as a qualified phenotypic inference without absolute viability or every-pair
+ causality.; Bound the broader non-Saccharomyces metabolic effect to the tested panel and retain detectable S.
+ cerevisiae effects.
+ node_decisions:
+ - node: Species drop-out and strain-substitution output shifts
+ rationale: Preserve positive composition perturbations while distinguishing kinetics from completion and molecular
+ mechanism.
+ - node: Inferred interspecies sugar-utilization competition
+ rationale: Retain competition as a qualified phenotypic inference without absolute viability or every-pair causality.
+ - node: Non-Saccharomyces strain-dependent metabolic tuning
+ rationale: Bound the broader non-Saccharomyces metabolic effect to the tested panel and retain detectable S.
+ cerevisiae effects.
+ removed_node_decisions: []
+ renamed_nodes:
+ Interspecies sugar-utilization competition: Inferred interspecies sugar-utilization competition
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42784437
+ issues:
+ - 1954
+ - 1958
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium/2026-10-08T164943Z-codex-71bcd5.yaml
+- path: kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml
+ id: CommunityMech:000438
+ original_sha256: ff36b0a04edec258678a5f4d0ba1e640469d034fdc190621f02a7a311b9ecfcc
+ record_sha256: ba42e79fb1133d49ce6280562566ffedd6bcf37306ce42b97473e7cfdc1b017f
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain the positive contact-treatment growth phenotype without necessary-gene attribution.; Mark proposed
+ Torulaspora-mediated suppression as partial and hypothetical, not a demonstrated toxin mechanism.; Preserve
+ the 5 h amino-acid difference and 9 h null without inferring transfer, secretion or uptake direction.
+ node_decisions:
+ - node: Direct-contact S. cerevisiae growth advantage
+ rationale: Retain the positive contact-treatment growth phenotype without necessary-gene attribution.
+ - node: Indirect-contact Torulaspora growth shift
+ rationale: Mark proposed Torulaspora-mediated suppression as partial and hypothetical, not a demonstrated toxin
+ mechanism.
+ - node: Contact-dependent amino acid profile shift
+ rationale: Preserve the 5 h amino-acid difference and 9 h null without inferring transfer, secretion or uptake
+ direction.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42176030
+ issues:
+ - 1955
+ - 1959
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wine_Yeast_ThreeSpecies_Contact_Consortium/2026-10-08T164944Z-codex-cf55bb.yaml
+- path: kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml
+ id: CommunityMech:000360
+ original_sha256: 9f793b34cca134cc17f6d4919f37e56336b155b1a9423f22973f4cd701cd4be9
+ record_sha256: 829d29dcebcb9ba30483df9d1ec71eafb945a6a3bf966539ee6a16d9abd9077d
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Keep observed compartment differences separate from selectively demonstrated host filtering and niche
+ partitioning.; Retain annotated producer-salvager potential with computational provenance, not observed cross-feeding
+ or strain-matched validation.
+ node_decisions:
+ - node: Mankai Compartment-Associated Community Differentiation
+ rationale: Keep observed compartment differences separate from selectively demonstrated host filtering and niche
+ partitioning.
+ - node: MAG-Inferred Cobamide Producer-Salvager Guild
+ rationale: Retain annotated producer-salvager potential with computational provenance, not observed cross-feeding
+ or strain-matched validation.
+ removed_node_decisions: []
+ renamed_nodes:
+ Mankai Compartment Host Filtering: Mankai Compartment-Associated Community Differentiation
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42304541
+ issues:
+ - 1956
+ - 1960
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wolffia_Mankai_Endosphere_Cobamide_Guild/2026-10-08T164944Z-codex-638dc2.yaml
+- path: kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml
+ id: CommunityMech:000404
+ original_sha256: 13963fab699a08f782adfabbadeff9a09c1b891ac8c0714a99cc0f07079a883e
+ record_sha256: 06d15492c6e358b75deffe722b5299d7b5f86bf15090276db87fda690c6e639e
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Qualify the proposed polymer handoff; bulk carbohydrate decline also includes medium-sucrose consumption.;
+ Preserve bulk metabolite changes without niche partitioning, uniform acid increases or recipient-specific synthesis.;
+ Keep measured day-12 calcium/silicon leaching and residue changes distinct from isolated physical causality
+ and CO2 sequestration.
+ node_decisions:
+ - node: Hypothesized CMS-1 Extracellular Polymer Cross-Feeding
+ rationale: Qualify the proposed polymer handoff; bulk carbohydrate decline also includes medium-sucrose consumption.
+ - node: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
+ rationale: Preserve bulk metabolite changes without niche partitioning, uniform acid increases or recipient-specific
+ synthesis.
+ - node: Optimized Wollastonite Calcium and Silicon Leaching
+ rationale: Keep measured day-12 calcium/silicon leaching and residue changes distinct from isolated physical
+ causality and CO2 sequestration.
+ removed_node_decisions: []
+ renamed_nodes:
+ CMS-1 Extracellular Polymer Cross-Feeding: Hypothesized CMS-1 Extracellular Polymer Cross-Feeding
+ edges_before:
+ - &id001
+ source: CMS-1 Extracellular Polymer Cross-Feeding
+ target: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
+ description: "Cross-feeding of CMS-1 extracellular polymers and protein was linked to increased hzt-3\u2032\
+ \ acid and amino-acid production in the mixed culture."
+ - &id003
+ source: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
+ target: Optimized Wollastonite Calcium and Silicon Leaching
+ description: Increased acids and amino acids lowered pH and intensified the chemical dissolution of wollastonite
+ by the mixed fungal culture.
+ edges_after:
+ - &id002
+ source: Hypothesized CMS-1 Extracellular Polymer Cross-Feeding
+ target: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
+ description: "HYPOTHESIZED: consumption of CMS-1 products could enable greater hzt-3\u2032 acid and amino-acid\
+ \ production. Bulk culture comparisons support metabolic changes but do not isolate this transfer as their\
+ \ necessary cause or distinguish it from consumption of supplied sucrose."
+ - &id004
+ source: Mixed-Culture Organic-Acid and Amino-Acid Upregulation
+ target: Optimized Wollastonite Calcium and Silicon Leaching
+ description: 'PARTIAL: increased acidic metabolites and lower pH are consistent with enhanced acid dissolution
+ and complexation driving wollastonite leaching. The culture-ratio comparison supports this mechanism but does
+ not selectively establish which acid or amino acid is necessary, or partition chemical dissolution from physical
+ disruption.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: "HYPOTHESIZED: consumption of CMS-1 products could enable greater hzt-3\u2032 acid and amino-acid\
+ \ production. Bulk culture comparisons support metabolic changes but do not isolate this transfer as their\
+ \ necessary cause or distinguish it from consumption of supplied sucrose."
+ - before: *id003
+ after: *id004
+ rationale: 'PARTIAL: increased acidic metabolites and lower pH are consistent with enhanced acid dissolution
+ and complexation driving wollastonite leaching. The culture-ratio comparison supports this mechanism but does
+ not selectively establish which acid or amino acid is necessary, or partition chemical dissolution from physical
+ disruption.'
+ removed_edge_decisions: []
+ references:
+ - PMID:42478817
+ issues:
+ - 1957
+ - 1961
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium/2026-10-08T164944Z-codex-c1ca0f.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index a6b35e8ab..26c1823c4 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -450,10 +450,10 @@ kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml CommunityMech:000391 d
kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml CommunityMech:000429 ee5b482655aeb0d187e29cfe8b18016b247b355f3d63dbba2db3b591c84f05ef 2 0 55.0 reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml reviewed
kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml CommunityMech:000118 f7eb74b6868f91109757655407c0934a7e1971e9692283f52c51ecbf329c9df4 3 2 88.3 reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml reviewed
kb/communities/Wheat_SynCom_SASW01_Drought_Inoculant.yaml CommunityMech:000409 613f8b97efa732c213fae320935a4f8cafa8cb899718e6c18a7c1f47f9ba0420 2 0 55.0 reports/causal_graph_review/decisions/20261008-four-records-batch122.yaml reviewed
-kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml CommunityMech:000465 29c5ffbc44052dbaf61fdeffa2ba7c0495f4c37cd1f9a246834d1bee9ed07e16 3 0 68.3 pending
-kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml CommunityMech:000438 ff36b0a04edec258678a5f4d0ba1e640469d034fdc190621f02a7a311b9ecfcc 3 0 63.3 pending
-kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml CommunityMech:000360 9f793b34cca134cc17f6d4919f37e56336b155b1a9423f22973f4cd701cd4be9 2 0 67.5 pending
-kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml CommunityMech:000404 13963fab699a08f782adfabbadeff9a09c1b891ac8c0714a99cc0f07079a883e 3 2 98.3 pending
+kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml CommunityMech:000465 2df1d32db9dc666dbb93f9b7ae103d5c80f43c7e19e01450024dc416f31d3b2b 3 0 68.3 reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml reviewed
+kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml CommunityMech:000438 ba42e79fb1133d49ce6280562566ffedd6bcf37306ce42b97473e7cfdc1b017f 3 0 63.3 reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml reviewed
+kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml CommunityMech:000360 829d29dcebcb9ba30483df9d1ec71eafb945a6a3bf966539ee6a16d9abd9077d 2 0 57.5 reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml reviewed
+kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml CommunityMech:000404 06d15492c6e358b75deffe722b5299d7b5f86bf15090276db87fda690c6e639e 3 2 88.3 reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml reviewed
kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml CommunityMech:000354 3f48f2b903eec6f6ac2e93c952821980eb066df571ec4e1a5519ac7c47293e7c 3 2 100.0 pending
kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml CommunityMech:000164 49f5a5749a60d2f6b314cd487f84c5c6c609d23657faf7342daad53833dc9ec2 4 2 100.0 pending
kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml CommunityMech:000210 5640166eed0e15b269178e292e4e63066adb88cd20d82e65b3dd05938ae49be3 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 9c6e6586e..d8094565b 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -8,8 +8,8 @@
"records_without_edges": 189,
"review_status_counts": {
"needs_research": 54,
- "pending": 10,
- "reviewed": 396
+ "pending": 6,
+ "reviewed": 400
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch123.json b/reports/causal_graph_review/validation-20261008-batch123.json
new file mode 100644
index 000000000..e7d09d58e
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch123.json
@@ -0,0 +1,1105 @@
+{
+ "base_commit": "a8eb38f28e262f5a6f6c804f68d782a6a6eb1d64",
+ "scope": [
+ "kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml",
+ "kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml",
+ "kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml",
+ "kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch123.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/focused.log",
+ "log_sha256": "6574f1e7fc17d6ac373aeec44f92a650ba5a7e1abb23870f79e7c846fe132dc8",
+ "output_tail": "............. [100%]\n13 passed in 2.44s\n"
+ },
+ {
+ "check": "Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch123/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-strict.tsv",
+ "kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-strict.log",
+ "log_sha256": "29241dfacb590aad5c5fdc56216f821d520c40f6d9664c06b5f70beef26d3b74",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch123/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch123/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-references.log",
+ "log_sha256": "2bb53bfc43f1a1449555a81643faa2bf521af605b344da9c4b83c408346e5c2b",
+ "output_tail": "Validating kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-snippets.log",
+ "log_sha256": "5f0e8a5be45b94195ee5599498c60e06ff8db089c85d0bf23969aa37351ca96e",
+ "output_tail": "# 17 evidence snippets scanned across 1 files\n MATCH 17\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-rank.log",
+ "log_sha256": "c7f710df063f38fbd2eac067ce01c0471fed2f8d27cdd586be0f4ea762cdb393",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000465\",\n \"name\": \"Wine Yeast Five-Species Strain-Substitution Consortium\",\n \"score\": 68.3,\n \"taxonomy\": 5,\n \"connected_taxa\": 5,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium/2026-10-08T164943Z-codex-71bcd5.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wine_Yeast_ThreeSpecies_Contact_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_ThreeSpecies_Contact_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wine_Yeast_ThreeSpecies_Contact_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch123/Wine_Yeast_ThreeSpecies_Contact_Consortium-strict.tsv",
+ "kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_ThreeSpecies_Contact_Consortium-strict.log",
+ "log_sha256": "12bc36af3bd3df2d74d47523718534dbf9cc0e3992010e816f23f7776192c13a",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch123/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch123/Wine_Yeast_ThreeSpecies_Contact_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Wine_Yeast_ThreeSpecies_Contact_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_ThreeSpecies_Contact_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wine_Yeast_ThreeSpecies_Contact_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_ThreeSpecies_Contact_Consortium-references.log",
+ "log_sha256": "e5fb01d879b537d744250a4c56cb2afdb1d3310f52d9b81f7a1277ed8def7789",
+ "output_tail": "Validating kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Wine_Yeast_ThreeSpecies_Contact_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_ThreeSpecies_Contact_Consortium-snippets.log",
+ "log_sha256": "2ffa6e242265b4c1c2eb555bd8bd14abb6cc63ed4d5a8a818da9b515db44daff",
+ "output_tail": "# 24 evidence snippets scanned across 1 files\n MATCH 24\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Wine_Yeast_ThreeSpecies_Contact_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_ThreeSpecies_Contact_Consortium-rank.log",
+ "log_sha256": "4410d4581bc191d452e6dbcdf55f2db04f85067eef27526813862e07209baed9",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000438\",\n \"name\": \"Wine Yeast Three-Species Contact Consortium\",\n \"score\": 63.3,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 7,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Wine_Yeast_ThreeSpecies_Contact_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wine_Yeast_ThreeSpecies_Contact_Consortium/2026-10-08T164944Z-codex-cf55bb.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wine_Yeast_ThreeSpecies_Contact_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wolffia_Mankai_Endosphere_Cobamide_Guild-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wolffia_Mankai_Endosphere_Cobamide_Guild-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wolffia_Mankai_Endosphere_Cobamide_Guild-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch123/Wolffia_Mankai_Endosphere_Cobamide_Guild-strict.tsv",
+ "kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wolffia_Mankai_Endosphere_Cobamide_Guild-strict.log",
+ "log_sha256": "2a153c794c8084238d0be4ffa31d889a92fe5f5ac73d707baedda1923da9cbde",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch123/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch123/Wolffia_Mankai_Endosphere_Cobamide_Guild-strict.tsv\n"
+ },
+ {
+ "check": "Wolffia_Mankai_Endosphere_Cobamide_Guild-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wolffia_Mankai_Endosphere_Cobamide_Guild-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wolffia_Mankai_Endosphere_Cobamide_Guild-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wolffia_Mankai_Endosphere_Cobamide_Guild-references.log",
+ "log_sha256": "4cfe2807f8f9fbac11fccdc1ef349aee51df202e386df52a04c5eefc7aa493af",
+ "output_tail": "Validating kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Wolffia_Mankai_Endosphere_Cobamide_Guild-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wolffia_Mankai_Endosphere_Cobamide_Guild-snippets.log",
+ "log_sha256": "5f0e8a5be45b94195ee5599498c60e06ff8db089c85d0bf23969aa37351ca96e",
+ "output_tail": "# 17 evidence snippets scanned across 1 files\n MATCH 17\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Wolffia_Mankai_Endosphere_Cobamide_Guild-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wolffia_Mankai_Endosphere_Cobamide_Guild-rank.log",
+ "log_sha256": "ab6b28921a68adb7ea88234db10142d9e9406d1a5855955df0e234fda6812a03",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000360\",\n \"name\": \"Wolffia Mankai Endosphere Cobamide Guild\",\n \"score\": 57.5,\n \"taxonomy\": 7,\n \"connected_taxa\": 7,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Wolffia_Mankai_Endosphere_Cobamide_Guild-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wolffia_Mankai_Endosphere_Cobamide_Guild/2026-10-08T164944Z-codex-638dc2.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wolffia_Mankai_Endosphere_Cobamide_Guild-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch123/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-strict.tsv",
+ "kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-strict.log",
+ "log_sha256": "b1d476c188fe3c39e0a01ebca58db74676b36fe18a9c675f269f93c869ddac98",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch123/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch123/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-references.log",
+ "log_sha256": "61291f5701946a9f8186afab32920efc697ea60829549e8f9d498048b4c1e28c",
+ "output_tail": "Validating kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-snippets.log",
+ "log_sha256": "32d5c17677a000100a0b22db07734e7af95b7e2b40f82a74ed21b581b1a6d4f5",
+ "output_tail": "# 20 evidence snippets scanned across 1 files\n MATCH 20\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-rank.log",
+ "log_sha256": "8f2cc571e789f5de25d16945b5647e77e1703ee67f56539aea107d52c12ab08e",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000404\",\n \"name\": \"Wollastonite Ramichloridium-Talaromyces Fungal Consortium\",\n \"score\": 88.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium/2026-10-08T164944Z-codex-c1ca0f.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "inventory",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "reports/causal_graph_review/build_inventory.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/inventory.log",
+ "log_sha256": "c222dcef305d3b2b861dd533219b658a1f63cbcbb46e52cff56aff2561769ba8",
+ "output_tail": "{\n \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n \"records\": 460,\n \"nodes\": 1373,\n \"edges\": 530,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 189,\n \"review_status_counts\": {\n \"needs_research\": 54,\n \"pending\": 6,\n \"reviewed\": 400\n },\n \"structural_defects\": []\n}\n"
+ },
+ {
+ "check": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
+ 1
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/network.log",
+ "log_sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9",
+ "output_tail": "\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ],\n \"Tinto_River_Iron_Cycling_Community\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Basidiomycota\",\n \"taxon_id\": \"NCBITaxon:5204\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Basidiomycota\",\n \"term\": {\n \"id\": \"NCBITaxon:5204\",\n \"label\": \"Basidiomycota\"\n },\n \"gtdb_grounding_status\": \"NO_GTDB_EQUIVALENT\",\n \"notes\": \"Acidophilic fungi including Hortaea werneckii (black yeast) detected in Rio Tinto sediments and water. Fungi contribute to organic matter degradation, biofilm formation, and nutrient cycling through extracellular enzyme secretion.\\n\"\n },\n \"functional_role\": [\n \"PRIMARY_DEGRADER\"\n ],\n \"abundance_level\": \"RARE\",\n \"evidence\": [\n {\n \"reference\": \"PMID:25369810\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons\",\n \"explanation\": \"Documents fungal presence\"\n }\n ]\n },\n \"message\": \"Taxon 'Basidiomycota' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/just-network-json.log",
+ "log_sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/rank-all.log",
+ "log_sha256": "3d040a2d8d4bcec43c8cffb25fc997ce03f11f9e8837fe19840d612d6bd45e74",
+ "output_tail": "\t8\tinteraction_type\t0\t0\n405\t96.7\tkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml\tCommunityMech:000266\tClostridium carboxidivorans-Clostridium kluyveri CO Chain-Elongation Coculture\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n406\t96.7\tkb/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.yaml\tCommunityMech:000174\tClostridium cellulovorans-Methanosarcina barkeri Cellulose Methane Coculture\t2\t2\t0\t3\t2\t8\tinteraction_type\t0\t0\n407\t96.7\tkb/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.yaml\tCommunityMech:000206\tClostridium-Saccharomyces Cellulose Ethanol Coculture\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n408\t96.7\tkb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml\tCommunityMech:000297\tDIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n409\t96.7\tkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml\tCommunityMech:000023\tDesulfovibrio-Methanococcus Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n410\t96.7\tkb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml\tCommunityMech:000340\tPelagerythrobacter-Salinicola PES Pyrene-Degradation SynCom\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n411\t96.7\tkb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml\tCommunityMech:000291\tPseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium\t2\t2\t0\t3\t2\t3\tinteraction_type\t0\t0\n412\t96.7\tkb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml\tCommunityMech:000083\tStreptococcus mutans - Candida albicans ECC Biofilm Model\t2\t2\t0\t3\t2\t4\tinteraction_type\t0\t0\n413\t96.7\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n414\t96.7\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n415\t96.7\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\tinteraction_type\t0\t0\n416\t96.7\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t9\tinteraction_type\t0\t0\n417\t96.7\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t9\tinteraction_type\t0\t0\n418\t96.7\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\tinteraction_type\t0\t0\n419\t96.7\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n420\t96.7\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n421\t96.7\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n422\t97.5\tkb/communities/Anammox_Granule_Metabolic_Interaction_Community.yaml\tCommunityMech:000146\tAnammox Granule Metabolic Interaction Community\t3\t3\t0\t4\t3\t5\tinteraction_type\t0\t0\n423\t97.5\tkb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml\tCommunityMech:000176\tORNL Clostridium-Desulfovibrio-Geobacter Trophic Model Community\t3\t3\t0\t4\t2\t8\tinteraction_type\t0\t0\n424\t97.5\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t8\tinteraction_type\t0\t0\n425\t97.5\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t8\tinteraction_type\t0\t0\n426\t97.9\tkb/communities/Maize_Drought_Response_SynCom.yaml\tCommunityMech:000103\tMaize Drought Response SynCom\t1\t1\t0\t7\t7\t8\tmetabolites_or_biological_processes\t0\t0\n427\t98.3\tkb/communities/Populus_Salt_Tolerant_SynComs.yaml\tCommunityMech:000090\tPopulus Salt-Tolerant Rhizosphere SynComs\t1\t1\t0\t3\t2\t3\tmetabolites_or_biological_processes\t0\t0\n428\t98.8\tdata/isolates/Chromobacterium_Gold_Biocyanidation.yaml\tCommunityMech:000273\tChromobacterium Gold Biocyanidation Platform\t1\t1\t0\t4\t2\t7\tmetabolites_or_biological_processes\t0\t0\n429\t100.0\tdata/isolates/Aspergillus_Indium_LED_Recovery.yaml\tCommunityMech:000320\tAspergillus Indium LCD Recovery Platform\t1\t1\t0\t5\t4\t6\t\t0\t0\n430\t100.0\tdata/isolates/Methylobacterium_REE_Ewaste_Platform.yaml\tCommunityMech:000322\tMethylobacterium REE E-waste Platform\t1\t1\t0\t4\t2\t6\t\t0\t0\n431\t100.0\tkb/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.yaml\tCommunityMech:000276\tANME/SRB Anaerobic Methanotrophic Syntrophic Consortia\t6\t6\t0\t3\t2\t7\t\t0\t0\n432\t100.0\tkb/communities/Anabaena_MGS1_Anaerobic_Digestion_Methanogen_Consortium.yaml\tCommunityMech:000307\tAnabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium\t1\t1\t0\t5\t2\t7\t\t0\t0\n433\t100.0\tkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml\tCommunityMech:000245\tAvena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds\t1\t1\t0\t5\t2\t7\t\t0\t0\n434\t100.0\tkb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml\tCommunityMech:000142\tBacteroides-Methanobrevibacter Gnotobiotic Mouse Mutualism\t2\t2\t0\t3\t2\t3\t\t0\t0\n435\t100.0\tkb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml\tCommunityMech:000012\tBioModels MODEL2405300001 Infant Gut HMO SynCom\t13\t13\t0\t3\t2\t6\t\t0\t0\n436\t100.0\tkb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml\tCommunityMech:000215\tCalifornia Grassland Precipitation Legacy Soil Community\t1\t1\t0\t3\t2\t6\t\t0\t0\n437\t100.0\tkb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml\tCommunityMech:000089\tCellulose-to-Methane Quad-Culture SynCom\t4\t4\t0\t6\t5\t9\t\t0\t0\n438\t100.0\tkb/communities/DVM_Triculture.yaml\tCommunityMech:000021\tDVM Tri-culture\t3\t3\t0\t4\t2\t7\t\t0\t0\n439\t100.0\tkb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml\tCommunityMech:000301\tDehalococcoides mccartyi CWV2 Dechlorinating Consortium\t1\t1\t0\t5\t2\t6\t\t0\t0\n440\t100.0\tkb/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.yaml\tCommunityMech:000296\tEscherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture\t2\t2\t0\t3\t2\t6\t\t0\t0\n441\t100.0\tkb/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.yaml\tCommunityMech:000350\tHigh-Ammonia Biogas 0B Butyrate-Oxidizing Enrichment\t4\t4\t0\t3\t2\t6\t\t0\t0\n442\t100.0\tkb/communities/Honeybee_Core20_Defined_Microbiota.yaml\tCommunityMech:000124\tHoneybee Core-20 Defined Microbiota\t1\t1\t0\t3\t2\t3\t\t0\t0\n443\t100.0\tkb/communities/Microbacterium_Terrabacter_Sulfadiazine_CrossFeeding_Coculture.yaml\tCommunityMech:000462\tMicrobacterium-Terrabacter Sulfadiazine Cross-Feeding Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n444\t100.0\tkb/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.yaml\tCommunityMech:000157\tMicrocoleus-Massilia Cyanosphere Urea Mutualism\t2\t2\t0\t3\t2\t5\t\t0\t0\n445\t100.0\tkb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml\tCommunityMech:000119\tMultiomics Corn Straw Degradation SynCom\t1\t1\t0\t4\t3\t9\t\t0\t0\n446\t100.0\tkb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml\tCommunityMech:000156\tNeocallimastix-Methanobrevibacter Xylanolytic Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n447\t100.0\tkb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml\tCommunityMech:000190\tPelotomaculum-Methanocella Propionate RNA-Seq Coculture\t2\t2\t0\t4\t2\t9\t\t0\t0\n448\t100.0\tkb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\tCommunityMech:000052\tPelotomaculum-Methanothermobacter Syntrophic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n449\t100.0\tkb/communities/Phenol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n450\t100.0\tkb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml\tCommunityMech:000290\tPhosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture\t2\t2\t0\t3\t2\t4\t\t0\t0\n451\t100.0\tkb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml\tCommunityMech:000289\tPseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml\tCommunityMech:000092\tRhodopseudomonas-E. coli Cross-Feeding Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n453\t100.0\tkb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml\tCommunityMech:000109\tRice Acid Soil Bioinoculant SynCom\t1\t1\t0\t4\t4\t4\t\t0\t0\n454\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t4\t2\t4\t\t0\t0\n455\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n456\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n457\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n458\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n459\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n460\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/render.log",
+ "log_sha256": "38eafe36855ce55c803f56f5debca8b6bdc0049b04bb1a92b58b2468cefe2915",
+ "output_tail": "unitymech-causal-batch123/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch123/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch123/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch123/docs/index.html\n"
+ },
+ {
+ "check": "render-repeat",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/render-repeat.log",
+ "log_sha256": "38eafe36855ce55c803f56f5debca8b6bdc0049b04bb1a92b58b2468cefe2915",
+ "output_tail": "unitymech-causal-batch123/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch123/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch123/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch123/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch123/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']()))"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/connectivity-survey.log",
+ "log_sha256": "6dba3d2251cf8431c1fc7f04f3c0806d8a8c166c0901fd6be1fcbc268a1730a4",
+ "output_tail": "{\"records\": 460, \"with_community_level\": 414, \"mixed\": 136, \"community_level_only\": 278, \"taxa\": 1568, \"credited_solely_by_the_rule\": 1281}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_batch107.py",
+ "tests/test_causal_review_batch108.py",
+ "tests/test_causal_review_batch109.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch110.py",
+ "tests/test_causal_review_batch111.py",
+ "tests/test_causal_review_batch112.py",
+ "tests/test_causal_review_batch113.py",
+ "tests/test_causal_review_batch114.py",
+ "tests/test_causal_review_batch115.py",
+ "tests/test_causal_review_batch116.py",
+ "tests/test_causal_review_batch117.py",
+ "tests/test_causal_review_batch118.py",
+ "tests/test_causal_review_batch119.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch120.py",
+ "tests/test_causal_review_batch121.py",
+ "tests/test_causal_review_batch122.py",
+ "tests/test_causal_review_batch123.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_network_palette.py",
+ "tests/test_datamodel.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/regressions.log",
+ "log_sha256": "5cd54c80cdc898e993ccf6015f53ba83bb35e89cd90c83ee76438bb266d57aef",
+ "output_tail": "........................................................................ [ 6%]\n........................................................................ [ 12%]\n........................................................................ [ 18%]\n........................................................................ [ 24%]\n........................................................................ [ 30%]\n........................................................................ [ 36%]\n........................................................................ [ 42%]\n........................................................................ [ 49%]\n........................................................................ [ 55%]\n........................................................................ [ 61%]\n........................................................................ [ 67%]\n........................................................................ [ 73%]\n........................................................................ [ 79%]\n........................................................................ [ 85%]\n........................................................................ [ 91%]\n........................................................................ [ 98%]\n...................... [100%]\n1174 passed in 372.38s (0:06:12)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/just-lint.log",
+ "log_sha256": "73a8b698a90352e36898243f2d38cf6fff8880fd2ee7962ecff7194ed40eae60",
+ "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n376 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n"
+ },
+ {
+ "check": "mypy-explicit-runtime",
+ "command": [
+ "/private/tmp/communitymech-batch100/lint-env/bin/mypy",
+ "--no-incremental",
+ "--python-executable",
+ "/private/tmp/communitymech-batch100/lint-env/bin/python",
+ "src/"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/mypy-explicit-runtime.log",
+ "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875",
+ "output_tail": "Success: no issues found in 49 source files\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/audit-snippets-all.log",
+ "log_sha256": "7eae2e4e1711a584433c722c08a98c92b6aefd2fd8fc04299639144bd4147e90",
+ "output_tail": "# 9090 evidence snippets scanned across 460 files\n MATCH 8942\n RENDERING 31\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch123/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Both-root pre-source baseline covers460records and923caches,57existing warnings and zero structural defects. Four whole records and11nodes/two arrows reviewed; all retained,three renames,no new topology.",
+ "Fresh EuropePMC metadata/abstracts and Crossref identities checked for all four papers. Three complete OA main bodies and five-species publisher Results/Discussion/Methods/Table1 plus captions inspected. Publisher web access succeeded despite independent direct-HTTP403. Original figure pixels,external supplements,raw data and analysis code not audited.",
+ "Five-species positive drop-out and strain-substitution effects retained. Competition is a phenotypic inference,not resolved molecular or complete pairwise causality; ARISA is relative DNA-based succession. All consortia complete fermentation and S.cerevisiae effects remain detectable. Table1/Methods information is available; separate metadata1958 remains.",
+ "Three-species direct-contact growth and indirect-contact Torulaspora shifts retained. Medium-mediated suppression and toxin identity remain untested; expression differences are not necessary-gene perturbations. Preserve the5h amino-acid effect,the9h null and supplied histidine/methionine/tryptophan. Recirculation-versus-feed metadata1959 remains.",
+ "Wolffia compartment associations do not establish selectively tested host filtering or microbial niche partitioning. MAG gene-content complementarity and minimum-three-intermediate edges are potential,not flux/FBA/abundance correlation. Operational endosphere fractions and non-strain-matched cultured comparators limit localization and adaptive-loss claims; cross-feeder role metadata1960 remains.",
+ "Wollastonite positive day12Ca/Si leaching and bulk metabolite changes retained. CMS-1-to-hzt transfer is hypothesized; medium sucrose also explains carbohydrate consumption. Selected metabolites increase,not every acid. Both existing arrows remain qualified; no necessary individual mediator,isolated hyphal force or measured net CO2 sequestration inferred. Non-graph role metadata1961 remains.",
+ "All22graph and4discussion quotes matched to fresh primary artifacts and caches. One17-word CC BY4 publisher Discussion excerpt appended with provenance to the five-species cache;922othercaches unchanged. No full-body cache import. Wolffia is CC BY-NC-ND4; no new verbatim excerpts added from that source.",
+ "Expanded all-state1188issue titles/bodies and hidden/ignored local paths searched;141matchinglocalpaths,sixpriorissue bodies and onepriorfive-speciesreviewreport read. Credentials,.git,generateddocs/site and reference caches excluded from local issue-dedup search; caches separately inspected for evidence. No historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,unrelated raw YAML fields,all prior history/decision artifacts and existing taxonomy/participant/scopes. Four append-only histories and curation events. Neighbor cobalamin-coculture and mineral-SOM records inspected as conventions only,not transferred scientific evidence.",
+ "No Edison submission or spend,new nodes or directions. Prior authorized Ruegeria1883 configured-authentication blocker not retried unchanged; no credentials inspected. Source-based self-adversarial review is not independent approval. Overall objective,protected merge and branch deletion remain incomplete."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml": {
+ "MATCH": 17,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml": {
+ "MATCH": 24,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml": {
+ "MATCH": 17,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml": {
+ "MATCH": 20,
+ "RENDERING": 0,
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+ }
+ },
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 922,
+ "unchanged_raw_blocks": 56,
+ "cache_changes": [
+ {
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+ "before_sha256": "73c149edcbb34439981d8d5b8cb5a6f9f0003963f8f458149c62a8063fbc598d",
+ "after_sha256": "712ca54ab2fb5d865c15918a9283810912a0fb34c0d817fd229f4493c0e80036",
+ "action": "Append a17-word literal primary Discussion limitation with URL,section,date and license; preserve original cache prefix."
+ }
+ ],
+ "edison": {
+ "required_for_this_repair": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "new_nodes_or_directions": 0,
+ "prior_extension_blocker": "Ruegeria1883: configured authentication unavailable in prior approved invocation; no unchanged-state retry."
+ },
+ "primary_artifacts": {
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+ "/private/tmp/communitymech-batch123/local-matches-expanded.txt": "9ba8577ee6bcff84f09530c0e303e9d5631e22bd8cf6874ff76c772107a38960",
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+ "/private/tmp/communitymech-batch123/primary-manifest.json": "ea39984f6645b072023511a74ba9874f11e77b00eb5501b736b72509e61d59c2",
+ "/private/tmp/communitymech-batch123/target-baseline.json": "8fb2c59e5dfd5c82da6d87ff7abc52b4158ccc0200cd31e378bd69d43866ac94",
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+ "/private/tmp/communitymech-batch123/three-crossref.json": "6a147abd574ab80afde6153f5e09c9b41bfc4e02f2380c8491b39cccddf74d5f",
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+ "/private/tmp/communitymech-batch123/three-primary.xml": "6be5199a52d4ada845c08ab2b7f179e49684c4c9c2548aae7db43edde816e4ed",
+ "/private/tmp/communitymech-batch123/wolffia-abstract.txt": "f144e020f47b9c07b7502fa6be13b5b23891717a5b5288a35495a7bd52970c94",
+ "/private/tmp/communitymech-batch123/wolffia-crossref.json": "1b2b911549316223f66a1a0b7d81ad438bdc7360e1d67ce2d4512bcaf2518e52",
+ "/private/tmp/communitymech-batch123/wolffia-metadata.json": "0bacaac05748a3518d22afc62a68fed53f886a6a18d9262366b18552fb6b8a4f",
+ "/private/tmp/communitymech-batch123/wolffia-primary.txt": "8a156084ee5a70d9d3c5e02763ca0974cce3f3c12e4fe3c2bf00570fdb56e0a0",
+ "/private/tmp/communitymech-batch123/wolffia-primary.xml": "f94e26d64a7dff99fc9b0e4d5a97b2fb44d45f120a8b3e7a2968402eabd1cf07",
+ "/private/tmp/communitymech-batch123/woll-abstract.txt": "db01a6fb05f8b55c0d200f3bb57dbf8be5c9edee77c6a8549cf9165434f11ae7",
+ "/private/tmp/communitymech-batch123/woll-crossref.json": "938523e0e243d2cfe8379995ca50c88055448f3320c68c35b5defb837ecbaf7d",
+ "/private/tmp/communitymech-batch123/woll-metadata.json": "6e69f2b54938592fd889b4a3b1853a742025bef93e933a48b7963653e86daa81",
+ "/private/tmp/communitymech-batch123/woll-primary.txt": "1108a4ecfbb2b9ab4e27e2f15c78f7b147006ee07ac5db3cb4460e065649f610",
+ "/private/tmp/communitymech-batch123/woll-primary.xml": "a5fd72d224d836636b73dc00fa62402bf6c63454a1413c4659e24ffeb2522a5a",
+ "references_cache/PMID_42176030.txt": "00f49c79569200a4a591bad07ccea19f9cabd96ec9728c10820e30e68647c1fd",
+ "references_cache/PMID_42304541.txt": "79d8cd5d1bb724484d8d5c3bd11349a8a6f03043a159ee79446ee375cf6bba7b",
+ "references_cache/PMID_42478817.txt": "a16fc2b369d4bab42a84959c670d1b6e1306e5959731af305e964cf2e6d7d0d9",
+ "references_cache/PMID_42784437.txt": "712ca54ab2fb5d865c15918a9283810912a0fb34c0d817fd229f4493c0e80036"
+ },
+ "immutable_prior_history_and_decision_files": 904,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 22,
+ "discussion_quotations": 4,
+ "fresh_primary_literal_matches": 26,
+ "all_cached_literal_matches": 26,
+ "retained_nodes": 11,
+ "removed_nodes": 0,
+ "renamed_nodes": 3,
+ "retained_arrows": 2,
+ "removed_arrows": 0,
+ "new_nodes_or_directions": 0
+ },
+ "network_delta": {
+ "existing_findings_preserved": 57,
+ "added_findings": {},
+ "removed_findings": {},
+ "structural_defects": 0
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1359,
+ "arrows": 522
+ },
+ "render_scope": "Deterministic rendering and exact HTML description parsing, not screenshots; postcommit docs-current still required.",
+ "participant_census": {
+ "current": {
+ "records": 460,
+ "with_community_level": 414,
+ "mixed": 136,
+ "community_level_only": 278,
+ "taxa": 1568,
+ "credited_solely_by_the_rule": 1281
+ },
+ "delta_from_batch122": {
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+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "explanation": "All participant lists and scopes are unchanged;299participant-list users. Scope credit is not certification of actual participant coverage. Connectivity logic and thresholds are unchanged."
+ },
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary established Python3.13 lint environment; project dependencies unchanged."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 9090,
+ "categories": {
+ "MATCH": 8942,
+ "RENDERING": 31,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 40,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Informational audit exit0 is not clean-corpus or entailment certification.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1373,
+ "edges": 530,
+ "records_without_nodes": 10,
+ "records_without_edges": 189,
+ "review_status_counts": {
+ "needs_research": 54,
+ "pending": 6,
+ "reviewed": 400
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml": "67f38c6539251cd8960e66af9b998bb4c038a984b4a018c826226615673779f8",
+ "tests/test_causal_review_batch123.py": "e319d885faf398047c0afb6f22ddf36723d30e5ffa375db0653d6eae3f9d6253",
+ "tests/test_participating_taxa.py": "f438815b4a028c0f38a077df53c95f685f98b3c2b523593896a124b544269db1",
+ "tests/test_community_level_connectivity_credit.py": "996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a",
+ "tests/test_causal_review_batch109.py": "ff8e9e26771545e1ace22b3c1d42076789c99cc4bc83e588b6a4b9ad698d3d73",
+ "tests/test_datamodel.py": "f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25",
+ "reports/causal_graph_review/cache-provenance-20261008-batch123.json": "88edcdd069da742f9b7a2318d960ae7133628d1d403966e8d3f16e0f082751a6",
+ "kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml": "2df1d32db9dc666dbb93f9b7ae103d5c80f43c7e19e01450024dc416f31d3b2b",
+ "kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml": "ba42e79fb1133d49ce6280562566ffedd6bcf37306ce42b97473e7cfdc1b017f",
+ "kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml": "829d29dcebcb9ba30483df9d1ec71eafb945a6a3bf966539ee6a16d9abd9077d",
+ "kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml": "06d15492c6e358b75deffe722b5299d7b5f86bf15090276db87fda690c6e639e"
+ },
+ "pre_research_baseline": {
+ "base_commit": "a8eb38f28e262f5a6f6c804f68d782a6a6eb1d64",
+ "base_tree": "8b26ed5f8364da0c76565678d7cf40111db9ab43",
+ "research_worktree": "/private/tmp/communitymech-causal-batch123",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch123/baseline-rank.log",
+ "sha256": "b2bca44c33343718910a23b42b9fa2df49ed350b20be9f5287877e8bac366024"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch123/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch123/baseline-network.log",
+ "sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch123/baseline-downstream.log",
+ "sha256": "d78ee0410d71fd8894f22db0ff3098785e3388160a53d8f819812718d2b97ab0"
+ }
+ ],
+ "baseline_sha256": "69cb401d7f613e0f6dde181e3a41bf820520328c9107bb2a541b3b38702da1a3"
+ },
+ "reference_validator_caveat": "Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment. Total checks in the reference CLI counts issues, not examined snippets.",
+ "status": "verified_existing_graph_repairs",
+ "total_recorded_gate_outputs": 41
+}
diff --git a/tests/test_causal_review_batch123.py b/tests/test_causal_review_batch123.py
new file mode 100644
index 000000000..88846ad15
--- /dev/null
+++ b/tests/test_causal_review_batch123.py
@@ -0,0 +1,176 @@
+"""Preserve observed endpoints and explicit inference limits in four graphs."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_five_positive_perturbations_do_not_imply_failed_completion():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][0]
+ assert "positive composition-perturbation effects" in node["description"]
+ assert "All tested consortia completed fermentation" in node["description"]
+ assert "produced significant impacts" in node["evidence"][0]["snippet"]
+ assert "were not addressed" in node["evidence"][1]["snippet"]
+
+
+def test_five_competition_remains_a_qualified_inference():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][1]
+ assert node["interaction_type"] == "COMPETITION"
+ assert node["name"].startswith("Inferred ")
+ assert node["evidence"][0]["supports"] == "PARTIAL"
+ assert "not absolute viable population size" in node["description"]
+ assert "candidate mechanisms" in node["description"]
+
+
+def test_five_strain_effects_are_panel_specific_and_not_saccharomyces_silence():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][2]
+ assert "particular strains tested" in node["description"]
+ assert "still had detectable effects" in node["description"]
+ assert "Table 1 names the ten strains" in docs[0]["discussions"][0]["rationale"]
+ assert not any(n.get("downstream") for n in docs[0]["ecological_interactions"])
+
+
+def test_three_keeps_growth_and_qualifies_suppression():
+ _, _, docs = records()
+ a, b, _ = docs[1]["ecological_interactions"]
+ assert "established numerical dominance" in a["description"]
+ assert "HYPOTHESIZED" in b["description"]
+ assert b["evidence"][1]["supports"] == "PARTIAL"
+ assert "indirect pairwise confirmation" in b["description"]
+ assert "interaction_type" not in b and not b.get("downstream")
+
+
+def test_three_keeps_amino_acid_early_effect_late_null_and_source_limits():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][2]
+ assert "higher in the indirect-contact condition" in node["description"]
+ assert "no significant difference after 9 h" in node["description"]
+ assert "after 9 h" in node["evidence"][-1]["snippet"]
+ assert "does not by itself demonstrate" in node["description"]
+ assert "histidine, methionine and tryptophan" in node["description"]
+ assert (
+ docs[1]["discussions"][0]["discussion_id"]
+ == "wine_yeast_indirect_contact_amino_acid_source"
+ )
+
+
+def test_wolffia_compartments_are_not_selectively_demonstrated_filtering():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][0]
+ assert "interaction_type" not in node
+ assert "operational sterilized-tissue fraction" in node["description"]
+ assert "not a strictly epiphytic sample" in node["description"]
+ assert node["evidence"][0]["supports"] == "PARTIAL"
+
+
+def test_wolffia_potential_is_not_exchange_or_strain_matched_validation():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][1]
+ assert "interaction_type" not in node and not node.get("downstream")
+ assert "HYPOTHESIZED cross-feeding" in node["description"]
+ assert "not strain-matched endophytes" in node["description"]
+ assert "reconstruction limitations" in node["description"]
+ assert len(node["participating_taxa"]) == 7
+ assert docs[2]["discussions"][0]["discussion_id"] == "direct_cobamide_exchange_not_measured"
+
+
+def test_wolffia_provenance_is_gene_content_not_flux_simulation():
+ _, _, docs = records()
+ evidence = docs[2]["ecological_interactions"][1]["evidence"][2]
+ provenance = evidence["computational_provenance"]
+ assert evidence["evidence_source"] == "COMPUTATIONAL"
+ assert provenance["prediction_type"] == "OTHER"
+ assert "At least three compatible" in provenance["parameters"]
+ assert "not FBA, direct flux or abundance correlation" in provenance["parameters"]
+ assert [t["tool_name"] for t in provenance["tools"]] == ["MetaBat2", "MetaErg", "igraph"]
+ assert not any(t.get("tool_version") for t in provenance["tools"])
+
+
+def test_woll_transfer_is_hypothesized_and_carbohydrate_loss_is_not_tracing():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][0]
+ assert node["name"].startswith("Hypothesized ")
+ assert "interaction_type" not in node
+ assert "Medium sucrose consumption" in node["description"]
+ assert "does not trace" in node["description"]
+ assert node["evidence"][0]["supports"] == "PARTIAL"
+
+
+def test_woll_metabolite_changes_are_bulk_and_not_uniform():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][1]
+ assert "interaction_type" not in node
+ assert "bulk concentrations, not gene-expression measurements" in node["description"]
+ assert "mixed-culture oxalic acid was much lower" in node["description"]
+ assert node["evidence"][1]["supports"] == "PARTIAL"
+ assert "100% CMS-1." in node["evidence"][2]["snippet"]
+
+
+def test_woll_retains_both_qualified_directions():
+ _, _, docs = records()
+ a, b, c = docs[3]["ecological_interactions"]
+ assert len(a["downstream"]) == len(b["downstream"]) == 1
+ assert a["downstream"][0]["target"] == b["name"]
+ assert b["downstream"][0]["target"] == c["name"]
+ assert a["downstream"][0]["description"].startswith("HYPOTHESIZED:")
+ assert b["downstream"][0]["description"].startswith("PARTIAL:")
+
+
+def test_woll_positive_leaching_is_not_carbon_sequestration():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][2]
+ assert "interaction_type" not in node
+ assert all(s in node["description"] for s in ["79.95%", "18.59%", "day 12"])
+ assert "measure net CO2 sequestration" in node["description"]
+ assert node["evidence"][0]["supports"] == "SUPPORT"
+ assert node["evidence"][1]["supports"] == "PARTIAL"
+
+
+def test_ledger_binds_topology_history_and_narrow_cache_append():
+ ledger, rows, docs = records()
+ counts = ledger["reviewed_counts"]
+ assert (counts["original_nodes"], counts["retained_nodes"], counts["removed_nodes"]) == (
+ 11,
+ 11,
+ 0,
+ )
+ assert (counts["original_arrows"], counts["retained_arrows"], counts["removed_arrows"]) == (
+ 2,
+ 2,
+ 0,
+ )
+ assert counts["renamed_nodes"] == 3
+ assert (counts["graph_quotations"], counts["discussion_quotations"]) == (22, 4)
+ assert len(ledger["cache_changes"]) == 1 and not ledger["independent_approval"]
+ cache = ledger["cache_changes"][0]
+ assert cache["path"] == "references_cache/PMID_42784437.txt"
+ assert hashlib.sha256((ROOT / cache["path"]).read_bytes()).hexdigest() == cache["after_sha256"]
+ assert ledger["edison"]["provider_submissions"] == 0
+ assert ledger["unresolved_non_graph_issues"] == [1958, 1959, 1960, 1961]
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert len(row["history_files"]) == 1 and doc["curation_history"][-1]["llm_assisted"]
+ names = [n["name"] for n in doc["ecological_interactions"]]
+ assert [n["node"] for n in row["node_decisions"]] == names
+ assert all(
+ a.removeprefix("ecological_interactions#") in names
+ for a in doc["discussions"][-1]["attaches_to"]
+ )
+ assert all(
+ e["target"] in names
+ for n in doc["ecological_interactions"]
+ for e in n.get("downstream", [])
+ )