Geotrichum nitrogen supply to lactic acid bacteria
CROSS_FEEDING
-
Metabolomics and amino-acid perturbation assays linked G. candidum to nitrogen-source supply, including valine, that enhanced lactic-acid-bacterial growth, biofilm formation, and EPS production.
+
G. candidum Y1 supplies nitrogen sources, including valine, to L. lactis V9 and L. paracasei V21. Metabolomics and amino-acid depletion/supplementation support nutrient provision associated with increased bacterial growth, biofilm formation and EPS production. These assays do not by themselves isolate a valine-specific signaling mechanism independent of growth.
@@ -677,8 +677,8 @@
Geotrichum nitrogen supply to lactic acid bacteria
Downstream Effects:
- → G. candidum activation of AI-2-linked EPS production
-
The fungus-associated nitrogen supply was coupled with stronger lactic-acid-bacterial growth, quorum-sensing activity, and EPS production.
+ → AI-2 regulation of Viili bacterial EPS production
+
PARTIAL: fungal nitrogen provision supports bacterial growth and is accompanied by stronger quorum-sensing activity. It may contribute to activation of the AI-2 regulatory node, but the abstract does not isolate valine-specific mediation from growth effects.
@@ -720,10 +720,9 @@
Evidence
-
G. candidum activation of AI-2-linked EPS production
- CROSS_FEEDING
+
AI-2 regulation of Viili bacterial EPS production
-
Co-culture with G. candidum increased AI-2 production and luxS transcription in the lactic acid bacteria; AI-2 activation and inhibition assays linked this quorum-sensing response to EPS synthesis.
+
Fungal co-culture increases bacterial AI-2 production and luxS transcription. AI-2 activation and inhibition assays support positive regulation of EPS synthesis. This is signaling regulation, not evidence that G. candidum supplies AI-2 as an exchanged nutrient; the abstract describes fungal-metabolite activation of signaling as a possible contribution.
@@ -772,7 +771,7 @@
G. candidum activation of AI-2-linked EPS production
→ Three-species Viili EPS maximum
-
AI-2-mediated quorum sensing positively regulated EPS synthesis in the three-member Viili consortium.
+
AI-2 activation and inhibition support positive regulation of bacterial EPS synthesis and thus a contribution to the three-member output. They do not establish AI-2 as the sole explanation of the tested consortium maximum.
+ KNOWLEDGE_GAP
+ OPEN
+ Does fungal valine activate AI-2 signaling independently of its effect on bacterial growth?
+
+
The abstract reports nutrient depletion/supplementation and AI-2 perturbation assays, but the inspected source does not isolate the full nitrogen-to-signaling mediation chain. Full methods and growth-matched signaling perturbations are needed to resolve this link. The measured nutrient, AI-2 and EPS responses remain supported.
+
+
Attaches to: ecological_interactions#Geotrichum nitrogen supply to lactic acid bacteria, ecological_interactions#AI-2 regulation of Viili bacterial EPS production, ecological_interactions#Three-species Viili EPS maximum
Niche partitioning
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -712,7 +712,7 @@
Ecological Interactions
Biofilm-Suspension Spatial Division of Labor
NICHE_PARTITIONING
-
Electrode biofilms perform reductive debromination while planktonic suspensions perform acidogenesis, partitioning contaminant degradation from carbon recovery.
+
Multi-omics supports a spatial division of labor in the waste-sludge reactor: electrode biofilms are primarily associated with reductive debromination and planktonic suspensions with acidogenesis. The five listed genera are representative enrichments, not an exhaustive membership or a defined five-strain consortium.
@@ -785,12 +785,21 @@
Evidence
Biofilm Electroactivity and Dehalogenation
- NICHE_PARTITIONING
-
Syntrophomonas and Geobacter are enriched as electroactive biofilm members, while Hydrogenophaga is enriched as a dehalogenator.
+
Biofilm enrichment associates Syntrophomonas and Geobacter with electroactivity and Hydrogenophaga with dehalogenation. These are representative genus-level roles inferred from enrichment and multi-omics, not separately measured electron or dehalogenation fluxes for every genus or evidence of niche partitioning within this fraction.
Sedimentibacter and Petrimonas are enriched in the planktonic suspension associated with hydrolysis, fatty-acid biosynthesis, and acidogenesis.
+
Suspension enrichment associates Sedimentibacter and Petrimonas with fermentation, hydrolysis, fatty-acid biosynthesis and acidogenesis. These representative roles do not assign all activities to each genus or establish niche partitioning between the two genera.
Modeled EET support for biofilm-suspension cooperation
-
Extracellular electron transfer reinforces cooperation between the spatial fractions and contributes to dehalogenation and acidogenesis.
+
PARTIAL: partial least squares path modeling identifies extracellular electron transfer as a factor supporting cooperation between the biofilm and suspension and their dehalogenation and acidogenesis outputs. The authors call this syntrophy, but the abstract does not resolve a product-removal thermodynamic dependency, obligatory reciprocal growth or a direct EET interruption/rescue experiment.
@@ -912,12 +927,12 @@
EET-Reinforced Biofilm-Suspension Syntrophy
→ Biofilm Electroactivity and Dehalogenation
-
EET reinforces the electrode-biofilm side of the syntrophy, where electroactive Syntrophomonas and Geobacter and dehalogenating Hydrogenophaga are enriched.
+
PARTIAL: the path model links EET to biofilm-associated dehalogenation. Retain this inferred contribution, not a directly perturbed EET-to-output mechanism or a flux assigned to each representative genus.
→ Suspension Acidogenesis
-
EET also contributes to the suspension side of the syntrophy, where Sedimentibacter and Petrimonas are enriched with hydrolysis, fatty-acid biosynthesis, and acidogenesis.
+
PARTIAL: the path model links EET to suspension-associated acidogenesis. Retain this inferred contribution, not a directly perturbed EET-to-output mechanism or a flux assigned to each representative genus.
@@ -933,10 +948,10 @@
Evidence
PMID:41793807
- - SUPPORT (IN_VITRO)
+ - PARTIAL (COMPUTATIONAL)
-
"extracellular electron transfer as the key factor reinforcing this biofilm-suspension syntrophy, significantly contributing to both dehalogenation and acidogenesis"
+
"Partial least squares path modeling identified extracellular electron transfer as the key factor"
@@ -949,6 +964,45 @@
Evidence
+
+
Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which electron-transfer route causally links the biofilm and suspension outputs?
+
+
The accessible abstract identifies a partial least squares path model, not the route-resolved inhibition/rescue or partner-fitness controls needed to isolate EET mediation and thermodynamic dependence. Full methods and relevant perturbation data are needed; compartment enrichment and reactor-level removal/carbon recovery remain supported.
+
+
Attaches to: ecological_interactions#Biofilm-Suspension Spatial Division of Labor, ecological_interactions#Biofilm Electroactivity and Dehalogenation, ecological_interactions#Suspension Acidogenesis, ecological_interactions#Modeled EET support for biofilm-suspension cooperation
Colonization facilitation
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -581,47 +581,18 @@
Ecological Interactions
Pseudomonas-Centered Metabolic Facilitation
- MUTUALISM
+ CROSS_FEEDING
-
Seven simplified-SynCom partners with low substrate-use overlap promote Pseudomonas aeruginosa Q6 growth through spent-medium metabolites, including N-acetyl-L-serine among compounds enriched in mutually interacting strains.
+
Seven selected helper strains promote P. aeruginosa Q6 growth in spent-medium assays; only three of those pairs show bilateral positive effects. PARTIAL: differential substrate depletion and candidate secreted/consumed compounds, including N-acetyl serine, support potential cross-feeding, not compound-specific rescue, resolved stereochemistry or measured transfer in the rhizosphere. MUTUALISM cannot describe all seven helper pairs.
Metabolic facilitation by the seven helper strains supports the Pseudomonas-centered simplified community whose inoculation enriches Pseudomonas biofilm-formation functions in the rhizosphere.
-
-
@@ -637,7 +608,7 @@
Evidence
- SUPPORT (IN_VITRO)
-
"Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained from the rhizosphere of grafted watermelon plants."
+
"We identified that seven strains enhanced Pseudomonas aeruginosa Q6"
@@ -650,7 +621,7 @@
Evidence
- SUPPORT (IN_VITRO)
-
"We identified compounds such as n-acetyl serine and lysine-hydroxyproline"
+
"Among these, three strains engaged in mutualistic interactions"
@@ -660,10 +631,10 @@
Evidence
PMID:38840214
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (IN_VITRO)
-
"increase in the relative abundance and biofilm-forming pathways of Pseudomonas post-SynCom inoculation"
+
"indicating metabolic cross-feeding potential among these species"
@@ -673,40 +644,18 @@
Evidence
-
Pseudomonas Biofilm Pathway Enrichment
- COLONIZATION_FACILITATION
+
SSC8 watermelon growth promotion without added pathogen
-
SynCom inoculation increases Pseudomonas abundance and enriches Pseudomonas biofilm-synthesis pathway genes in the watermelon rhizosphere.
-
-
-
-
+
The eight-member SSC8 improved ungrafted-watermelon growth in non-sterile greenhouse soil, with height, root weight and dry weight comparable to the parent16-member SBC. This simplified-consortium experiment had no added pathogen. The55.6% disease-index reduction and biofilm-pathway enrichment were measured for SBC and must not be assigned to SSC8; neither plant protection nor biofilm mediation is established by this growth assay.
- → Watermelon Growth and Disease-Resistance Increase
-
Pseudomonas biofilm-formation enrichment and rhizosphere colonization are linked to the SynCom's improved watermelon growth and Fusarium oxysporum resistance.
-
-
-
@@ -719,10 +668,10 @@
Evidence
PMID:38840214
- - SUPPORT (COMPUTATIONAL)
+ - SUPPORT (IN_VIVO)
-
"SynCom inoculation was found to substantially increase the abundance of rhizosphere Pseudomonas"
+
"none of the treatments in this potting experiment were supplemented with pathogen"
@@ -732,10 +681,10 @@
Evidence
PMID:38840214
- - SUPPORT (COMPUTATIONAL)
+ - SUPPORT (IN_VIVO)
-
"metagenomics analysis highlighted a significant enrichment of the Pseudomonas biofilm synthesis pathway in SynCom-treated groups"
+
"the growth parameters of the SSC8 group plants, including plant height, root weight, and dry weight, were comparable to the initial SynCom (SBC) group"
@@ -743,74 +692,51 @@
Evidence
-
-
-
Watermelon Growth and Disease-Resistance Increase
- COLONIZATION_FACILITATION
-
-
The grafted-rhizosphere SynCom increases ungrafted-watermelon growth and reduces Fusarium oxysporum disease pressure in non-sterile greenhouse soil.
+ KNOWLEDGE_GAP
+ OPEN
+ Does SSC8 itself suppress Fusarium disease, and do its candidate metabolites or biofilms mediate that effect?
+
+
The paper tests pathogen challenge and metagenomic biofilm-pathway enrichment for the parent16-member SBC, whereas the simplified SSC8 experiment measures growth without added pathogen. Spent-medium benefit and metabolomic candidates do not close that cross-experiment causal chain. An SSC8 pathogen challenge and mechanism-specific controls would be required. The broad canonical membership placeholders also need separate supplement-grounded curation under issue1919.
+
Attaches to: ecological_interactions#Pseudomonas-Centered Metabolic Facilitation, ecological_interactions#SSC8 watermelon growth promotion without added pathogen
none of the treatments in this potting experiment were supplemented with pathogen
-
"significantly lower disease index (with a 55.6% reduction) and F. oxysporum abundance"
+
-
+
-
-
-
-
-
@@ -1042,19 +968,11 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "MUTUALISM";
+ var intType = "CROSS_FEEDING";
var metabolites = [];
-
- metabolites.push("N-acetyl-L-serine");
-
-
var processes = [];
-
- processes.push("biofilm formation");
-
-
var evidenceCount = 3;
nodes.push({
@@ -1074,48 +992,16 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("biofilm formation");
-
-
- var evidenceCount = 2;
-
- nodes.push({
- id: intId,
- label: "Pseudomonas Biofilm Pathway Enrichment",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("defense response to fungus");
-
-
var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Watermelon Growth and Disease-Resistance Increase",
+ label: "SSC8 watermelon growth promotion without added pathogen",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1147,7 +1033,7 @@
Evidence
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
- var nodeCount = 5;
+ var nodeCount = 4;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html b/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html
index 69dfa3f4f..1c9a47d88 100644
--- a/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html
+++ b/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html
@@ -644,17 +644,12 @@
Ecological Interactions
Taxon
-
- Cross-feeding
-
Niche partitioning
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -674,7 +669,7 @@
Ecological Interactions
Sulfate Suppression Of Methanogenesis
COMPETITION
-
Elevated sulfate reduced methane emissions, with hydrogenotrophic methanogenesis more strongly suppressed than acetoclastic methanogenesis, consistent with competition between sulfate-linked respiratory guilds and methanogenic carbon flow.
+
Sulfate addition reduced methane accumulation in the wetland microcosms. PARTIAL: metaproteomic markers and fitted fluxes support stronger suppression of hydrogenotrophic than acetoclastic methanogenesis and competition between sulfate-reducing bacterial and methanogenic guilds. This does not measure a universal Bacteria-to-Archaea antagonism or establish direct acetate competition with acetoclastic methanogens.
- → Lactate-Sulfate Carbon And Sulfur Subnetwork
-
Sulfate addition both suppresses methane emissions and provides the electron acceptor routed through the lactate-to-acetate, hydrogen sulfide, and carbon dioxide subnetwork.
-
-
-
-
-
Evidence
@@ -753,13 +745,26 @@
Evidence
PMID:38961111
- - SUPPORT (IN_VITRO)
+ - PARTIAL (COMPUTATIONAL)
"hydrogenotrophic methanogenesis more suppressed than acetoclastic"
Oxygen exposure shifted greenhouse gas emissions from CH4 toward CO2, reflecting redox-driven restructuring of carbon flow in the wetland soil community.
+
Oxygen-treated soil microcosms accumulated less methane and more carbon dioxide than the anoxic baseline. The combined oxygen-plus-sulfate treatment showed a similar overall gas pattern to oxygen alone, not identity of all microbial responses. This abiotic treatment effect is not an organism-to-organism niche-partitioning interaction; residual methane in the measurements must not be equated with zero production.
@@ -807,17 +811,6 @@
Oxygen Shift From Methane To Carbon Dioxide
-
- Downstream Effects:
-
-
- → Lactate-Sulfate Carbon And Sulfur Subnetwork
-
Oxygen exposure redirects wetland carbon flow from methane toward carbon dioxide and, under elevated sulfate, participates in the oxic sulfate condition that revealed the lactate-centered sulfur subnetwork.
-
-
-
-
-
Evidence
@@ -855,16 +848,21 @@
Evidence
-
Lactate-Sulfate Carbon And Sulfur Subnetwork
- CROSS_FEEDING
+
Modeled lactate-sulfate carbon and sulfur subnetwork
-
Under elevated sulfate and oxic conditions, metaproteomics and stoichiometric modeling resolved a subnetwork that converts lactate and sulfate into acetate, hydrogen sulfide, and carbon dioxide.
+
PARTIAL: a nine-reaction stoichiometric model fitted to measured metabolite amounts supports sulfidogenic lactate oxidation producing acetate, H2S and CO2 in the oxic sulfate treatment. Fitted fluxes and concordant protein abundances are not directly measured interspecies transfer or unique donor-recipient cross-feeding. Oxygen also suppressed sulfate-reduction activity relative to anoxic sulfate treatment, so this subnetwork is not evidence of universally enhanced sulfate reduction under oxygen.
"The fluxes of these reactions were fitted to the cumulative amounts of acetate, lactate, butyrate, H2, CO2, CH4, and H2S produced or consumed over the 30 days of incubation."
+
+
+
@@ -1003,6 +1014,45 @@
Associated Datasets
+
+
Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which guild-resolved transfers and causal dependencies are uniquely established beyond the fitted wetland model?
+
+
Measured standing metabolites and endpoint metaproteomes constrain a nine-reaction model but do not isolate donor-recipient fluxes or establish the two removed response-to-model arrows. Source results/discussion also differ in statements about additivity and some oxygen-linked routes, so no stronger route-specific or universal-zero conclusion is added. Model-code, raw-data and perturbation review would be needed to resolve those dependencies.
+
+
Attaches to: ecological_interactions#Sulfate Suppression Of Methanogenesis, ecological_interactions#Oxygen Shift From Methane To Carbon Dioxide, ecological_interactions#Modeled lactate-sulfate carbon and sulfur subnetwork
The fluxes of these reactions were fitted to the cumulative amounts of acetate, lactate, butyrate, H2, CO2, CH4, and H2S produced or consumed over the 30 days of incubation.
+
+
+
+
+
+
+
+
+
@@ -1462,7 +1512,7 @@
Evidence
processes.push("methanogenesis");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1491,7 +1541,7 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1527,7 +1577,7 @@
Evidence
(function() {
var intId = "interaction:2";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1547,14 +1597,14 @@
Evidence
processes.push("sulfate reduction");
- processes.push("organic substance catabolic process");
+ processes.push("catabolic process");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
- label: "Lactate-Sulfate Carbon And Sulfur Subnetwork",
+ label: "Modeled lactate-sulfate carbon and sulfur subnetwork",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/history/records/Viili_Fungus_Bacterium_EPS_SynCom/2026-10-08T124721Z-codex-2774fb.yaml b/history/records/Viili_Fungus_Bacterium_EPS_SynCom/2026-10-08T124721Z-codex-2774fb.yaml
new file mode 100644
index 000000000..b31ceb10e
--- /dev/null
+++ b/history/records/Viili_Fungus_Bacterium_EPS_SynCom/2026-10-08T124721Z-codex-2774fb.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml
+ slug: Viili_Fungus_Bacterium_EPS_SynCom
+session:
+ id: 2026-10-08T124721Z-codex-2774fb
+ timestamp: '2026-10-08T12:47:21Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1915
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain experimental nitrogen cross-feeding while bounding the signaling bridge.;
+ Keep AI-2 perturbation support without typing regulation as nutrient transfer.; Retain
+ the three-member EPS maximum only among tested combinations with explicit participants.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
diff --git a/history/records/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community/2026-10-08T124721Z-codex-ba3224.yaml b/history/records/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community/2026-10-08T124721Z-codex-ba3224.yaml
new file mode 100644
index 000000000..7bef1ddf3
--- /dev/null
+++ b/history/records/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community/2026-10-08T124721Z-codex-ba3224.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml
+ slug: Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community
+session:
+ id: 2026-10-08T124721Z-codex-ba3224
+ timestamp: '2026-10-08T12:47:21Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1916
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain observed spatial differentiation without exhaustive five-genus membership.;
+ Limit biofilm roles to its three representative genera and omit unsupported within-fraction
+ partitioning.; Limit suspension roles to its two representative genera without assigning
+ each all pathways.; Qualify both EET arrows as computational inference and leave unspecified
+ dependency untyped.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
diff --git a/history/records/Watermelon_Rhizosphere_Fusarium_SynCom8/2026-10-08T124721Z-codex-4fbc8e.yaml b/history/records/Watermelon_Rhizosphere_Fusarium_SynCom8/2026-10-08T124721Z-codex-4fbc8e.yaml
new file mode 100644
index 000000000..09d1d77b0
--- /dev/null
+++ b/history/records/Watermelon_Rhizosphere_Fusarium_SynCom8/2026-10-08T124721Z-codex-4fbc8e.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml
+ slug: Watermelon_Rhizosphere_Fusarium_SynCom8
+session:
+ id: 2026-10-08T124721Z-codex-4fbc8e
+ timestamp: '2026-10-08T12:47:21Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1917
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve seven positive spent-medium responses and three bilateral pairs with only
+ potential cross-feeding.; Restrict the SSC8 outcome to measured growth without added pathogen.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
diff --git a/history/records/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community/2026-10-08T124721Z-codex-37eb64.yaml b/history/records/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community/2026-10-08T124721Z-codex-37eb64.yaml
new file mode 100644
index 000000000..350fbe9d4
--- /dev/null
+++ b/history/records/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community/2026-10-08T124721Z-codex-37eb64.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml
+ slug: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+session:
+ id: 2026-10-08T124721Z-codex-37eb64
+ timestamp: '2026-10-08T12:47:21Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1918
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain measured sulfate effect with guild-level, pathway-inferred competition.;
+ Keep the measured oxygen response untyped and do not convert residual methane to zero.;
+ Qualify the fitted subnetwork without assigning directly measured cross-feeding or universal
+ oxygen stimulation.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
diff --git a/kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml b/kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml
index fb12d0503..f84103510 100644
--- a/kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml
+++ b/kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml
@@ -104,8 +104,10 @@ taxonomy:
explanation: Names the three Viili-derived strains assembled into the top-down synthetic microbial consortium.
ecological_interactions:
- name: Geotrichum nitrogen supply to lactic acid bacteria
- description: Metabolomics and amino-acid perturbation assays linked G. candidum to nitrogen-source supply, including valine,
- that enhanced lactic-acid-bacterial growth, biofilm formation, and EPS production.
+ description: G. candidum Y1 supplies nitrogen sources, including valine, to L. lactis V9 and L. paracasei V21.
+ Metabolomics and amino-acid depletion/supplementation support nutrient provision associated with increased bacterial
+ growth, biofilm formation and EPS production. These assays do not by themselves isolate a valine-specific signaling
+ mechanism independent of growth.
interaction_type: CROSS_FEEDING
scope: COMMUNITY_LEVEL
participating_taxa:
@@ -131,27 +133,30 @@ ecological_interactions:
id: CHEBI:33709
label: amino acid
downstream:
- - target: G. candidum activation of AI-2-linked EPS production
- description: The fungus-associated nitrogen supply was coupled with stronger lactic-acid-bacterial growth, quorum-sensing
- activity, and EPS production.
+ - target: AI-2 regulation of Viili bacterial EPS production
+ description: 'PARTIAL: fungal nitrogen provision supports bacterial growth and is accompanied by stronger quorum-sensing
+ activity. It may contribute to activation of the AI-2 regulatory node, but the abstract does not isolate valine-specific
+ mediation from growth effects.'
evidence:
- reference: PMID:42372608
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Untargeted metabolomics combined with validation experiments revealed that G. candidum supplied lactic acid bacteria
- with nitrogen sources, including valine.
- explanation: Supports G. candidum as a nitrogen-source supplier to the lactic acid bacteria and names valine as one implicated
- amino acid.
+ snippet: Untargeted metabolomics combined with validation experiments revealed that G. candidum supplied lactic
+ acid bacteria with nitrogen sources, including valine.
+ explanation: Supports G. candidum as a nitrogen-source supplier to the lactic acid bacteria and names valine
+ as one implicated amino acid.
- reference: PMID:42372608
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Amino acid depletion and supplementation experiments indicated that valine, as a key amino acid, is closely associated
- with enhanced growth, biofilm formation, and EPS production in lactic acid bacteria.
- explanation: Connects valine availability to growth, biofilm formation, and EPS production in the bacterial partners.
-- name: G. candidum activation of AI-2-linked EPS production
- description: Co-culture with G. candidum increased AI-2 production and luxS transcription in the lactic acid bacteria; AI-2
- activation and inhibition assays linked this quorum-sensing response to EPS synthesis.
- interaction_type: CROSS_FEEDING
+ snippet: Amino acid depletion and supplementation experiments indicated that valine, as a key amino acid, is
+ closely associated with enhanced growth, biofilm formation, and EPS production in lactic acid bacteria.
+ explanation: Connects valine availability to growth, biofilm formation, and EPS production in the bacterial
+ partners.
+- name: AI-2 regulation of Viili bacterial EPS production
+ description: Fungal co-culture increases bacterial AI-2 production and luxS transcription. AI-2 activation and
+ inhibition assays support positive regulation of EPS synthesis. This is signaling regulation, not evidence that
+ G. candidum supplies AI-2 as an exchanged nutrient; the abstract describes fungal-metabolite activation of signaling
+ as a possible contribution.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Geotrichum candidum Y1
@@ -182,23 +187,32 @@ ecological_interactions:
label: quorum sensing
downstream:
- target: Three-species Viili EPS maximum
- description: AI-2-mediated quorum sensing positively regulated EPS synthesis in the three-member Viili consortium.
+ description: AI-2 activation and inhibition support positive regulation of bacterial EPS synthesis and thus
+ a contribution to the three-member output. They do not establish AI-2 as the sole explanation of the tested
+ consortium maximum.
evidence:
- reference: PMID:42372608
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: co-culture with G. candidum significantly enhanced AI-2 production and luxS gene transcription in lactic acid
- bacteria.
- explanation: Supports stronger AI-2 production and luxS transcription when the fungal member was present with the lactic
+ snippet: co-culture with G. candidum significantly enhanced AI-2 production and luxS gene transcription in lactic
acid bacteria.
+ explanation: Supports stronger AI-2 production and luxS transcription when the fungal member was present with
+ the lactic acid bacteria.
- reference: PMID:42372608
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: AI-2 activation and inhibition assays confirmed that AI-2-mediated quorum sensing positively regulates EPS synthesis.
+ snippet: AI-2 activation and inhibition assays confirmed that AI-2-mediated quorum sensing positively regulates
+ EPS synthesis.
explanation: Supports the causal link from AI-2-mediated quorum sensing to EPS synthesis.
+ - reference: PMID:42372608
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: fungal metabolites may contribute to the activation of AI-2 signaling
+ explanation: Qualifies the fungal-metabolite-to-signaling mechanism; the separate AI-2 perturbations support
+ downstream regulation.
- name: Three-species Viili EPS maximum
- description: Among the microbial combinations tested in the Viili model, the complete L. lactis V9 plus L. paracasei V21
- plus G. candidum Y1 consortium had the highest measured exopolysaccharide concentration.
+ description: Among the microbial combinations tested in the Viili model, the complete L. lactis V9 plus L. paracasei
+ V21 plus G. candidum Y1 consortium had the highest measured exopolysaccharide concentration.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: exopolysaccharide
@@ -209,10 +223,23 @@ ecological_interactions:
- reference: PMID:42372608
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: the three-species consortium (L. lactis V9 + L. paracasei V21 + G. candidum Y1) exhibited the highest EPS concentration
- among all tested microbial combinations, reaching 1.09 mg/mL.
- explanation: Supports the highest-EPS output of the full three-strain Viili SynCom relative to the other tested microbial
- combinations.
+ snippet: the three-species consortium (L. lactis V9 + L. paracasei V21 + G. candidum Y1) exhibited the highest
+ EPS concentration among all tested microbial combinations, reaching 1.09 mg/mL.
+ explanation: Supports the highest-EPS output of the full three-strain Viili SynCom relative to the other tested
+ microbial combinations.
+ participating_taxa:
+ - preferred_term: Lactococcus lactis V9
+ term:
+ id: NCBITaxon:1358
+ label: Lactococcus lactis
+ - preferred_term: Lacticaseibacillus paracasei V21
+ term:
+ id: NCBITaxon:1597
+ label: Lacticaseibacillus paracasei
+ - preferred_term: Geotrichum candidum Y1
+ term:
+ id: NCBITaxon:1173061
+ label: Geotrichum candidum
related_ingredients:
- preferred_term: valine
chebi_term:
@@ -290,8 +317,8 @@ external_resources:
explanation: Names the DOI assigned to the primary Viili SynCom publication.
discussions:
- discussion_id: viili_syncom_methods_paywalled
- prompt: Which Viili media, incubation parameters, inoculation ratios, and original isolation details were used for strains
- V9, V21, and Y1?
+ prompt: Which Viili media, incubation parameters, inoculation ratios, and original isolation details were used
+ for strains V9, V21, and Y1?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
@@ -302,6 +329,22 @@ discussions:
and original isolate sources remain uncited.
posed_by: codex
posed_date: '2026-09-21'
+- discussion_id: viili_causal_graph_scope_batch118
+ prompt: Does fungal valine activate AI-2 signaling independently of its effect on bacterial growth?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Geotrichum nitrogen supply to lactic acid bacteria
+ - ecological_interactions#AI-2 regulation of Viili bacterial EPS production
+ - ecological_interactions#Three-species Viili EPS maximum
+ rationale: The abstract reports nutrient depletion/supplementation and AI-2 perturbation assays, but the inspected
+ source does not isolate the full nitrogen-to-signaling mediation chain. Full methods and growth-matched signaling
+ perturbations are needed to resolve this link. The measured nutrient, AI-2 and EPS responses remain supported.
+ evidence:
+ - reference: PMID:42372608
+ snippet: fungal metabolites may contribute to the activation of AI-2 signaling
+ posed_by: codex
+ posed_date: '2026-10-08'
metals_present: []
rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
@@ -312,20 +355,25 @@ curation_history:
curator: codex
action: CREATE_VIILI_EPS_SYNCOM
changes: Added the Viili fungus-bacterium EPS SynCom from PMID:42372608 with exact V9/V21/Y1 membership, fungus-to-lactic-acid-bacteria
- nitrogen and AI-2 quorum-sensing interactions, EPS outcome evidence, PubMed and DOI resources, and a methods-access knowledge
- gap.
+ nitrogen and AI-2 quorum-sensing interactions, EPS outcome evidence, PubMed and DOI resources, and a methods-access
+ knowledge gap.
llm_assisted: true
- timestamp: '2026-09-21T14:36:09Z'
curator: codex
action: ADDRESS_VIILI_EPS_REVIEW
- changes: >-
- Addressed adversarial review issues #1014 and #1015 by scoping the
- top-level EPS maximum to the tested microbial combinations and removing
- exopolysaccharide from the nitrogen-source metabolite list.
+ changes: 'Addressed adversarial review issues #1014 and #1015 by scoping the top-level EPS maximum to the tested
+ microbial combinations and removing exopolysaccharide from the nitrogen-source metabolite list.'
llm_assisted: true
- timestamp: '2026-10-01T04:54:40Z'
curator: codex
action: REMOVE_EMPTY_DOWNSTREAM
- changes: Removed the empty downstream list from the terminal Three-species Viili EPS maximum interaction after a corpus
- causal-graph audit found it was a non-informative stub.
+ changes: Removed the empty downstream list from the terminal Three-species Viili EPS maximum interaction after
+ a corpus causal-graph audit found it was a non-informative stub.
+ llm_assisted: true
+- timestamp: '2026-10-08T12:47:19Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain experimental nitrogen cross-feeding while bounding the signaling bridge.; Keep AI-2 perturbation
+ support without typing regulation as nutrient transfer.; Retain the three-member EPS maximum only among tested
+ combinations with explicit participants. Issue#1915; reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
llm_assisted: true
diff --git a/kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml b/kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml
index 0748005cc..0c6d33fd9 100644
--- a/kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml
+++ b/kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml
@@ -160,7 +160,9 @@ taxonomy:
explanation: Supports Petrimonas enrichment and its suspension-associated fermentative role.
ecological_interactions:
- name: Biofilm-Suspension Spatial Division of Labor
- description: Electrode biofilms perform reductive debromination while planktonic suspensions perform acidogenesis, partitioning contaminant degradation from carbon recovery.
+ description: 'Multi-omics supports a spatial division of labor in the waste-sludge reactor: electrode biofilms
+ are primarily associated with reductive debromination and planktonic suspensions with acidogenesis. The five
+ listed genera are representative enrichments, not an exhaustive membership or a defined five-strain consortium.'
interaction_type: NICHE_PARTITIONING
scope: COMMUNITY_LEVEL
biological_processes:
@@ -185,8 +187,10 @@ ecological_interactions:
snippet: planktonic suspensions mainly drove acidogenesis
explanation: Supports the suspension function within the spatially divided community.
- name: Biofilm Electroactivity and Dehalogenation
- description: Syntrophomonas and Geobacter are enriched as electroactive biofilm members, while Hydrogenophaga is enriched as a dehalogenator.
- interaction_type: NICHE_PARTITIONING
+ description: Biofilm enrichment associates Syntrophomonas and Geobacter with electroactivity and Hydrogenophaga
+ with dehalogenation. These are representative genus-level roles inferred from enrichment and multi-omics, not
+ separately measured electron or dehalogenation fluxes for every genus or evidence of niche partitioning within
+ this fraction.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biological process involved in interspecies interaction between organisms
@@ -199,9 +203,23 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: enriching electroactive bacteria (e.g., Syntrophomonas and Geobacter) and dehalogenators (e.g., Hydrogenophaga)
explanation: Supports the differentiated functions of the three named biofilm genera.
+ participating_taxa:
+ - preferred_term: Syntrophomonas
+ term:
+ id: NCBITaxon:862
+ label: Syntrophomonas
+ - preferred_term: Geobacter
+ term:
+ id: NCBITaxon:28231
+ label: Geobacter
+ - preferred_term: Hydrogenophaga
+ term:
+ id: NCBITaxon:47420
+ label: Hydrogenophaga
- name: Suspension Acidogenesis
- description: Sedimentibacter and Petrimonas are enriched in the planktonic suspension associated with hydrolysis, fatty-acid biosynthesis, and acidogenesis.
- interaction_type: NICHE_PARTITIONING
+ description: Suspension enrichment associates Sedimentibacter and Petrimonas with fermentation, hydrolysis, fatty-acid
+ biosynthesis and acidogenesis. These representative roles do not assign all activities to each genus or establish
+ niche partitioning between the two genera.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biological process involved in interspecies interaction between organisms
@@ -212,11 +230,23 @@ ecological_interactions:
- reference: PMID:41793807
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: enriching fermentative bacteria (e.g., Sedimentibacter and Petrimonas) and accelerating hydrolysis and fatty acid biosynthesis pathways
+ snippet: enriching fermentative bacteria (e.g., Sedimentibacter and Petrimonas) and accelerating hydrolysis
+ and fatty acid biosynthesis pathways
explanation: Supports the reported suspension-associated taxa and acidogenic mechanisms.
-- name: EET-Reinforced Biofilm-Suspension Syntrophy
- description: Extracellular electron transfer reinforces cooperation between the spatial fractions and contributes to dehalogenation and acidogenesis.
- interaction_type: SYNTROPHY
+ participating_taxa:
+ - preferred_term: Sedimentibacter
+ term:
+ id: NCBITaxon:190972
+ label: Sedimentibacter
+ - preferred_term: Petrimonas
+ term:
+ id: NCBITaxon:307628
+ label: Petrimonas
+- name: Modeled EET support for biofilm-suspension cooperation
+ description: 'PARTIAL: partial least squares path modeling identifies extracellular electron transfer as a factor
+ supporting cooperation between the biofilm and suspension and their dehalogenation and acidogenesis outputs.
+ The authors call this syntrophy, but the abstract does not resolve a product-removal thermodynamic dependency,
+ obligatory reciprocal growth or a direct EET interruption/rescue experiment.'
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biological process involved in interspecies interaction between organisms
@@ -225,19 +255,18 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Biofilm Electroactivity and Dehalogenation
- description: EET reinforces the electrode-biofilm side of the syntrophy,
- where electroactive Syntrophomonas and Geobacter and dehalogenating
- Hydrogenophaga are enriched.
+ description: 'PARTIAL: the path model links EET to biofilm-associated dehalogenation. Retain this inferred contribution,
+ not a directly perturbed EET-to-output mechanism or a flux assigned to each representative genus.'
- target: Suspension Acidogenesis
- description: EET also contributes to the suspension side of the syntrophy,
- where Sedimentibacter and Petrimonas are enriched with hydrolysis,
- fatty-acid biosynthesis, and acidogenesis.
+ description: 'PARTIAL: the path model links EET to suspension-associated acidogenesis. Retain this inferred
+ contribution, not a directly perturbed EET-to-output mechanism or a flux assigned to each representative genus.'
evidence:
- reference: PMID:41793807
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: extracellular electron transfer as the key factor reinforcing this biofilm-suspension syntrophy, significantly contributing to both dehalogenation and acidogenesis
- explanation: Supports EET as the mechanistic link between the two spatial fractions.
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: Partial least squares path modeling identified extracellular electron transfer as the key factor
+ explanation: Identifies the modeling basis of the proposed EET contribution; it is not an independent causal
+ perturbation.
environmental_factors:
- name: Waste activated sludge feedstock
value: waste activated sludge
@@ -302,3 +331,30 @@ external_resources:
explanation: Links the publication to the curated community system.
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare-earth processing role is reported for this electro-fermentation community.
+discussions:
+- discussion_id: sludge_causal_graph_scope_batch118
+ prompt: Which electron-transfer route causally links the biofilm and suspension outputs?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Biofilm-Suspension Spatial Division of Labor
+ - ecological_interactions#Biofilm Electroactivity and Dehalogenation
+ - ecological_interactions#Suspension Acidogenesis
+ - ecological_interactions#Modeled EET support for biofilm-suspension cooperation
+ rationale: The accessible abstract identifies a partial least squares path model, not the route-resolved inhibition/rescue
+ or partner-fitness controls needed to isolate EET mediation and thermodynamic dependence. Full methods and relevant
+ perturbation data are needed; compartment enrichment and reactor-level removal/carbon recovery remain supported.
+ evidence:
+ - reference: PMID:41793807
+ snippet: Partial least squares path modeling identified extracellular electron transfer as the key factor
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T12:47:20Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain observed spatial differentiation without exhaustive five-genus membership.; Limit biofilm roles
+ to its three representative genera and omit unsupported within-fraction partitioning.; Limit suspension roles
+ to its two representative genera without assigning each all pathways.; Qualify both EET arrows as computational
+ inference and leave unspecified dependency untyped. Issue#1916; reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
+ llm_assisted: true
diff --git a/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml b/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml
index da4ceb3ad..ac6e24573 100644
--- a/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml
+++ b/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml
@@ -64,97 +64,46 @@ taxonomy:
- *id001
ecological_interactions:
- name: Pseudomonas-Centered Metabolic Facilitation
- description: Seven simplified-SynCom partners with low substrate-use overlap
- promote Pseudomonas aeruginosa Q6 growth through spent-medium metabolites,
- including N-acetyl-L-serine among compounds enriched in mutually
- interacting strains.
- interaction_type: MUTUALISM
+ description: 'Seven selected helper strains promote P. aeruginosa Q6 growth in spent-medium assays; only three
+ of those pairs show bilateral positive effects. PARTIAL: differential substrate depletion and candidate secreted/consumed
+ compounds, including N-acetyl serine, support potential cross-feeding, not compound-specific rescue, resolved
+ stereochemistry or measured transfer in the rhizosphere. MUTUALISM cannot describe all seven helper pairs.'
+ interaction_type: CROSS_FEEDING
scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: N-acetyl-L-serine
- term:
- id: CHEBI:45441
- label: N-acetyl-L-serine
- biological_processes:
- - preferred_term: biofilm formation
- term:
- id: GO:0042710
- label: biofilm formation
- downstream:
- - target: Pseudomonas Biofilm Pathway Enrichment
- description: Metabolic facilitation by the seven helper strains supports the
- Pseudomonas-centered simplified community whose inoculation enriches
- Pseudomonas biofilm-formation functions in the rhizosphere.
evidence:
- - *id001
- reference: PMID:38840214
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: We identified compounds such as n-acetyl serine and lysine-hydroxyproline
- explanation: Names N-acetyl-L-serine as a spent-medium compound in strains with
- mutualistic effects on Pseudomonas aeruginosa Q6.
+ snippet: We identified that seven strains enhanced Pseudomonas aeruginosa Q6
+ explanation: Supports the positive spent-medium effect of the seven selected partners on Q6.
- reference: PMID:38840214
supports: SUPPORT
- evidence_source: COMPUTATIONAL
- snippet: increase in the relative abundance and biofilm-forming pathways of Pseudomonas
- post-SynCom inoculation
- explanation: Links the simplified SynCom phenotype to Pseudomonas biofilm-forming
- pathways in the inoculated rhizosphere.
-- name: Pseudomonas Biofilm Pathway Enrichment
- description: SynCom inoculation increases Pseudomonas abundance and enriches
- Pseudomonas biofilm-synthesis pathway genes in the watermelon rhizosphere.
- interaction_type: COLONIZATION_FACILITATION
- scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: biofilm formation
- term:
- id: GO:0042710
- label: biofilm formation
- downstream:
- - target: Watermelon Growth and Disease-Resistance Increase
- description: Pseudomonas biofilm-formation enrichment and rhizosphere
- colonization are linked to the SynCom's improved watermelon growth and
- Fusarium oxysporum resistance.
- evidence:
- - reference: PMID:38840214
- supports: SUPPORT
- evidence_source: COMPUTATIONAL
- snippet: SynCom inoculation was found to substantially increase the abundance of rhizosphere
- Pseudomonas
- explanation: Supports Pseudomonas enrichment after SynCom inoculation in the
- watermelon rhizosphere.
+ evidence_source: IN_VITRO
+ snippet: Among these, three strains engaged in mutualistic interactions
+ explanation: Restricts bilateral benefits to three pairs rather than all seven.
- reference: PMID:38840214
- supports: SUPPORT
- evidence_source: COMPUTATIONAL
- snippet: metagenomics analysis highlighted a significant enrichment of the Pseudomonas
- biofilm synthesis pathway in SynCom-treated groups
- explanation: Supports enrichment of Pseudomonas biofilm-formation functions
- in SynCom-inoculated rhizospheres.
-- name: Watermelon Growth and Disease-Resistance Increase
- description: The grafted-rhizosphere SynCom increases ungrafted-watermelon
- growth and reduces Fusarium oxysporum disease pressure in non-sterile
- greenhouse soil.
- interaction_type: COLONIZATION_FACILITATION
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: indicating metabolic cross-feeding potential among these species
+ explanation: The metabolomic candidates support potential exchange, not a causal single-metabolite assay.
+- name: SSC8 watermelon growth promotion without added pathogen
+ description: The eight-member SSC8 improved ungrafted-watermelon growth in non-sterile greenhouse soil, with height,
+ root weight and dry weight comparable to the parent16-member SBC. This simplified-consortium experiment had
+ no added pathogen. The55.6% disease-index reduction and biofilm-pathway enrichment were measured for SBC and
+ must not be assigned to SSC8; neither plant protection nor biofilm mediation is established by this growth assay.
scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: defense response to fungus
- term:
- id: GO:0050832
- label: defense response to fungus
evidence:
- reference: PMID:38840214
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SynCom promoted ungrafted watermelon growth and alleviated disease
- explanation: Supports the SynCom plant-growth and Fusarium-wilt protection
- endpoint in non-sterile greenhouse soil.
+ snippet: none of the treatments in this potting experiment were supplemented with pathogen
+ explanation: Defines the no-added-pathogen scope of the simplified-consortium experiment.
- reference: PMID:38840214
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: significantly lower disease index (with a 55.6% reduction) and F. oxysporum
- abundance
- explanation: Quantifies the disease-resistance endpoint for SynCom-treated,
- Fusarium-challenged watermelon plants.
+ snippet: the growth parameters of the SSC8 group plants, including plant height, root weight, and dry weight,
+ were comparable to the initial SynCom (SBC) group
+ explanation: Preserves positive SSC8 growth results without transferring the parent disease-challenge outcome.
environmental_factors:
- name: defined synthetic community design
value: Initial 16 core bacterial strains from grafted watermelon rhizosphere were refined to eight synergistic
@@ -219,3 +168,29 @@ growth_media:
snippet: Each replicate was run in polypropylene pots filled with 600 g of dry, non-sterile soil
with no history of watermelon cultivation.
explanation: Describes the pot/soil cultivation vessel for the SynCom-inoculated watermelon plants.
+discussions:
+- discussion_id: watermelon_causal_graph_scope_batch118
+ prompt: Does SSC8 itself suppress Fusarium disease, and do its candidate metabolites or biofilms mediate that
+ effect?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Pseudomonas-Centered Metabolic Facilitation
+ - ecological_interactions#SSC8 watermelon growth promotion without added pathogen
+ rationale: The paper tests pathogen challenge and metagenomic biofilm-pathway enrichment for the parent16-member
+ SBC, whereas the simplified SSC8 experiment measures growth without added pathogen. Spent-medium benefit and
+ metabolomic candidates do not close that cross-experiment causal chain. An SSC8 pathogen challenge and mechanism-specific
+ controls would be required. The broad canonical membership placeholders also need separate supplement-grounded
+ curation under issue1919.
+ evidence:
+ - reference: PMID:38840214
+ snippet: none of the treatments in this potting experiment were supplemented with pathogen
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T12:47:20Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Preserve seven positive spent-medium responses and three bilateral pairs with only potential cross-feeding.;
+ Restrict the SSC8 outcome to measured growth without added pathogen. Issue#1917; reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
+ llm_assisted: true
diff --git a/kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml b/kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml
index 13a54d5b1..1ec43672d 100644
--- a/kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml
+++ b/kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml
@@ -114,10 +114,10 @@ taxonomy:
explanation: Supports bacterial carbon and sulfur metabolic guild activity in the modeled subnetwork.
ecological_interactions:
- name: Sulfate Suppression Of Methanogenesis
- description: Elevated sulfate reduced methane emissions, with hydrogenotrophic
- methanogenesis more strongly suppressed than acetoclastic methanogenesis,
- consistent with competition between sulfate-linked respiratory guilds and
- methanogenic carbon flow.
+ description: 'Sulfate addition reduced methane accumulation in the wetland microcosms. PARTIAL: metaproteomic
+ markers and fitted fluxes support stronger suppression of hydrogenotrophic than acetoclastic methanogenesis
+ and competition between sulfate-reducing bacterial and methanogenic guilds. This does not measure a universal
+ Bacteria-to-Archaea antagonism or establish direct acetate competition with acetoclastic methanogens.'
interaction_type: COMPETITION
scope: COMMUNITY_LEVEL
source_taxon:
@@ -148,12 +148,6 @@ ecological_interactions:
term:
id: GO:0015948
label: methanogenesis
- downstream:
- - target: Lactate-Sulfate Carbon And Sulfur Subnetwork
- description: >
- Sulfate addition both suppresses methane emissions and provides the
- electron acceptor routed through the lactate-to-acetate, hydrogen sulfide,
- and carbon dioxide subnetwork.
evidence:
- reference: PMID:38961111
supports: SUPPORT
@@ -161,15 +155,30 @@ ecological_interactions:
snippet: Elevated SO42- reduced CH4 emissions
explanation: Supports suppression of methane emissions under elevated sulfate.
- reference: PMID:38961111
- supports: SUPPORT
- evidence_source: IN_VITRO
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
snippet: hydrogenotrophic methanogenesis more suppressed than acetoclastic
- explanation: Supports pathway-specific methanogenesis suppression.
+ explanation: Pathway-specific suppression is inferred from metaproteomics and fitted metabolic fluxes, not independently
+ measured pathway-resolved methane flux.
+ - reference: PMID:38961111
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: SRB outcompeting hydrogenotrophic methanogens
+ explanation: Supports the authors guild-level competition interpretation, not all bacteria versus all archaea.
+ participating_taxa:
+ - preferred_term: wetland soil methanogenic archaea
+ term:
+ id: NCBITaxon:2157
+ label: Archaea
+ - preferred_term: wetland soil bacterial guilds
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
- name: Oxygen Shift From Methane To Carbon Dioxide
- description: Oxygen exposure shifted greenhouse gas emissions from CH4 toward
- CO2, reflecting redox-driven restructuring of carbon flow in the wetland
- soil community.
- interaction_type: NICHE_PARTITIONING
+ description: Oxygen-treated soil microcosms accumulated less methane and more carbon dioxide than the anoxic baseline.
+ The combined oxygen-plus-sulfate treatment showed a similar overall gas pattern to oxygen alone, not identity
+ of all microbial responses. This abiotic treatment effect is not an organism-to-organism niche-partitioning
+ interaction; residual methane in the measurements must not be equated with zero production.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: dioxygen
@@ -189,12 +198,6 @@ ecological_interactions:
term:
id: GO:0015948
label: methanogenesis
- downstream:
- - target: Lactate-Sulfate Carbon And Sulfur Subnetwork
- description: >
- Oxygen exposure redirects wetland carbon flow from methane toward carbon
- dioxide and, under elevated sulfate, participates in the oxic sulfate
- condition that revealed the lactate-centered sulfur subnetwork.
evidence:
- reference: PMID:38961111
supports: SUPPORT
@@ -206,11 +209,12 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: combined SO42- and O2 exposures on CH4 and CO2 emissions were similar to those of O2 exposure alone
explanation: Supports oxygen exposure as the dominant perturbation in the combined treatment.
-- name: Lactate-Sulfate Carbon And Sulfur Subnetwork
- description: Under elevated sulfate and oxic conditions, metaproteomics and
- stoichiometric modeling resolved a subnetwork that converts lactate and
- sulfate into acetate, hydrogen sulfide, and carbon dioxide.
- interaction_type: CROSS_FEEDING
+- name: Modeled lactate-sulfate carbon and sulfur subnetwork
+ description: 'PARTIAL: a nine-reaction stoichiometric model fitted to measured metabolite amounts supports sulfidogenic
+ lactate oxidation producing acetate, H2S and CO2 in the oxic sulfate treatment. Fitted fluxes and concordant
+ protein abundances are not directly measured interspecies transfer or unique donor-recipient cross-feeding.
+ Oxygen also suppressed sulfate-reduction activity relative to anoxic sulfate treatment, so this subnetwork is
+ not evidence of universally enhanced sulfate reduction under oxygen.'
scope: COMMUNITY_LEVEL
source_taxon:
preferred_term: wetland soil bacterial guilds
@@ -243,21 +247,34 @@ ecological_interactions:
term:
id: GO:0019420
label: dissimilatory sulfate reduction
- - preferred_term: organic substance catabolic process
+ - preferred_term: catabolic process
term:
id: GO:0009056
label: catabolic process
evidence:
- reference: PMID:38961111
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: Metaproteomics and stoichiometric modeling revealed a unique subnetwork involving carbon metabolism
- explanation: Supports the modeled community-level subnetwork.
+ explanation: Supports a model-resolved biochemical subnetwork, not unique directly measured interspecies metabolite
+ transfer.
- reference: PMID:38961111
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: converts lactate and SO42- to produce acetate, H2S, and CO2
- explanation: Supports the lactate-sulfate-to-acetate/H2S/CO2 transformation.
+ explanation: Supports a model-resolved biochemical subnetwork, not unique directly measured interspecies metabolite
+ transfer.
+ - reference: PMID:38961111
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: The fluxes of these reactions were fitted to the cumulative amounts of acetate, lactate, butyrate,
+ H2, CO2, CH4, and H2S produced or consumed over the 30 days of incubation.
+ explanation: Defines the measured inputs used for fitting; reaction fluxes remain inferred.
+ participating_taxa:
+ - preferred_term: wetland soil bacterial guilds
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
environmental_factors:
- name: Oxygen exposure
value: oxic microcosm treatment
@@ -518,3 +535,31 @@ rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare earth element processing role is curated for this
wetland oxygen-sulfate greenhouse gas microcosm community.
+discussions:
+- discussion_id: wetland_causal_graph_scope_batch118
+ prompt: Which guild-resolved transfers and causal dependencies are uniquely established beyond the fitted wetland
+ model?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Sulfate Suppression Of Methanogenesis
+ - ecological_interactions#Oxygen Shift From Methane To Carbon Dioxide
+ - ecological_interactions#Modeled lactate-sulfate carbon and sulfur subnetwork
+ rationale: Measured standing metabolites and endpoint metaproteomes constrain a nine-reaction model but do not
+ isolate donor-recipient fluxes or establish the two removed response-to-model arrows. Source results/discussion
+ also differ in statements about additivity and some oxygen-linked routes, so no stronger route-specific or universal-zero
+ conclusion is added. Model-code, raw-data and perturbation review would be needed to resolve those dependencies.
+ evidence:
+ - reference: PMID:38961111
+ snippet: The fluxes of these reactions were fitted to the cumulative amounts of acetate, lactate, butyrate,
+ H2, CO2, CH4, and H2S produced or consumed over the 30 days of incubation.
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T12:47:20Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain measured sulfate effect with guild-level, pathway-inferred competition.; Keep the measured oxygen
+ response untyped and do not convert residual methane to zero.; Qualify the fitted subnetwork without assigning
+ directly measured cross-feeding or universal oxygen stimulation. Issue#1918; reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index d8a035327..0cff7f593 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,42 @@ 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`.
+## Batch118: Treatment Identity And Modeled Mechanisms
+
+[Decisions](decisions/20261008-four-records-batch118.yaml),
+[provenance](cache-provenance-20261008-batch118.json),
+[validation](validation-20261008-batch118.json), and
+[self-adversarial review](adversarial-review-20261008-batch118.yaml) cover
+Viili, waste-sludge electrofermentation, watermelon SSC8, and wetland
+oxygen-sulfate microcosms. Twelve of 13 nodes and four of eight arrows
+remain, with four renames and no new topology.
+
+Viili retains experimental nitrogen provision and AI-2 regulation of EPS,
+while the nutrient-to-signaling mediation remains partial. Sludge roles
+are limited to the representative genera in each spatial fraction; its
+EET arrows remain explicitly model-based, not intervention-proven.
+
+Watermelon SSC8 retains positive growth results from its no-added-pathogen
+experiment. The parent 16-member SynCom's disease-challenge result and
+biofilm-pathway node are not assigned to SSC8. Seven helper strains promote
+Q6, but only three pairs show bilateral benefit. Metabolomic candidates
+remain potential exchange, not a validated compound-specific mechanism.
+The wetland graph retains measured gas responses and its fitted subnetwork
+without arrows that confuse shared exposure with causal succession.
+
+All four whole records were read. Watermelon and wetland primary main-body
+XML, methods, results, discussion, tables and captions were reviewed; original
+figure pixels, supplements, raw data and model code were not. Viili and
+sludge repairs are abstract-bounded. All 29 graph/discussion quotations
+match fresh primary sources and existing caches. No caches were changed.
+
+Four guarded writes and append-only histories preserve unrelated raw fields
+and 456 other records. Two participant-list users are added without changing
+the scope census, connectivity logic or thresholds. Repairs #1915-#1918
+await protected-main merge; metadata and composition follow-ups #1919/#1920
+remain open. No Edison extension or spend was required. Self-review is not
+independent approval, and the overall review remains incomplete.
+
## Batch117: Sequential Treatment And Evidence Boundaries
[Decisions](decisions/20261008-four-records-batch117.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch118.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch118.yaml
new file mode 100644
index 000000000..2e9d3fb8c
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch118.yaml
@@ -0,0 +1,417 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: fc5c4d103c134cee549a76e8c71addcf8c322e09
+scope:
+- kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml
+- kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml
+- kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml
+- kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch118.json
+findings:
+- issue: 1915
+ severity: P2
+ finding: Distinguish Viili nitrogen cross-feeding from AI-2 regulation
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1916
+ severity: P2
+ finding: Separate electro-fermentation fraction roles from modeled EET causality
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1917
+ severity: P2
+ finding: Separate SSC8 growth tests from parent SynCom disease and biofilm results
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1918
+ severity: P2
+ finding: Remove common-cause arrows from wetland oxygen-sulfate graph
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1919
+ severity: P2
+ finding: Resolve SSC8 composition and non-graph assay conflation in watermelon record
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1920
+ severity: P2
+ finding: Correct wetland bottle-volume and inferred medium-requirement metadata
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+adversarial_checks:
+- All13original nodes/eight arrows accounted for:12nodes/four arrows retained,one misassigned node/four arrows removed,four
+ renames,no new topology. Targets and discussion anchors resolve; no shortcut edge invented.
+- 'Viili positive evidence retained: nutrient depletion/supplementation and AI-2 perturbations support their respective
+ outcomes. The nitrogen-signaling bridge is partial,not growth-independent valine mediation. AI-2 regulation is
+ untyped rather than nutrient transfer. Prior1014/1015 fixes preserved.'
+- Sludge division of labor and reactor outcomes retained. Biofilm participants are three representative genera;
+ suspension participants are two. EET support is partial least squares inference,not an interruption/rescue experiment,genus-resolved
+ flux or obligatory thermodynamic syntrophy.
+- Watermelon SSC8 outcome is growth without added pathogen. Parent16-member SBC disease challenge and biofilm-pathway
+ enrichment are not transferred. Seven partners have positive spent-medium effects; only three pairs are bilateral.
+ Potential exchange is not compound-specific rescue or resolved stereochemistry. Exact SSC8 roster and non-graph
+ fields remain1919.
+- Wetland treatment responses remain experimental while pathway fluxes and competition are inferred. Shared exposure
+ does not establish response-to-model arrows. Model subnetwork is not direct donor-recipient transfer; residual
+ methane is not zero. Some source results/discussion statements differ and are not silently reconciled. Vessel
+ and ingredient issues remain1920.
+- Twenty-five graph and four discussion quotes match fresh primary texts and caches,not entailment certification.
+ Two complete main-body XML texts read including methods/tables/captions; no original pixels,supplements,raw data
+ or model-code audit. Viili/sludge are abstract-bounded; no claim of exhaustive full-text absence.
+- Four guarded writes and append-only histories preserve456otherrecords,923caches,unrelated raw blocks and previous
+ histories/decisions. Shared evidence aliases detached. Canonical taxon IDs/labels/ranks unchanged. No cache import.
+- Twelve focused tests plus ten control/mutation/restored-control probes pass. Mutations reject erasing nutrient
+ benefit,misclassifying signaling,overstating EET,wrong fraction credit,seven mutualisms,compound certainty,parent-to-SSC8
+ assay transfer,common-cause arrows and direct model cross-feeding. No canonical files changed during probes.
+- All four records pass schema,strict,terms,full-record references,snippets,rank and history.1101selected tests
+ including palette pass; not full Linux CI certification. Network has57unchanged warnings and zero structural defects.456pages/1364nodes/523arrows
+ exactly match descriptions with deterministic rendering,not screenshot QA.
+- Participant-list users rise296to298; scope census remains414community-level,136mixed,278community-only,1568taxa,1280solelycredited.
+ This census is not actual participant coverage. Connectivity logic and all thresholds unchanged.
+- Issues1915-1918 are addressed pending protected-main merge;1919/1920 remain open. No Edison extension or credits.
+ Prior Ruegeria1883 still needs configured authentication. Self-adversarial review is not independent approval;
+ root1836 and real exact-head protected checks remain required.
+- Corpus380reviewed,26pending,54needs_research across460records. Overall goal,protected merge and branch deletion
+ remain incomplete. Postcommit docs-current and exact-head publication are separate gates,not preasserted here.
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Erase validated nitrogen cross-feeding
+ test: test_viili_retains_validated_nitrogen_and_tested_eps_maximum
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 21
+ assertion: assert nitrogen["interaction_type"] == "CROSS_FEEDING"
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/interaction_type
+ before: CROSS_FEEDING
+ after: COMPETITION
+ - mutation: Type AI2 regulation as nutrient delivery
+ test: test_viili_ai2_regulation_is_not_fungal_nutrient_transfer
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 35
+ assertion: assert "interaction_type" not in signal
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/1/interaction_type
+ before: null
+ after: CROSS_FEEDING
+ - mutation: Promote nitrogen bridge to isolated signaling mechanism
+ test: test_viili_signaling_bridge_is_partial_but_eps_regulation_is_supported
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 46
+ assertion: assert nitrogen["downstream"][0]["description"].startswith("PARTIAL:")
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/downstream/0/description
+ before: 'PARTIAL: fungal nitrogen provision supports bacterial growth and is accompanied by stronger quorum-sensing
+ activity. It may contribute to activation of the AI-2 regulatory node, but the abstract does not isolate
+ valine-specific mediation from growth effects.'
+ after: Valine alone directly activates AI2.
+ - mutation: Credit suspension genera to biofilm
+ test: test_sludge_fraction_participants_are_not_all_five_genera
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 58
+ assertion: assert [t["preferred_term"] for t in biofilm["participating_taxa"]] == [
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/1/participating_taxa
+ before:
+ - preferred_term: Syntrophomonas
+ term:
+ id: NCBITaxon:862
+ label: Syntrophomonas
+ - preferred_term: Geobacter
+ term:
+ id: NCBITaxon:28231
+ label: Geobacter
+ - preferred_term: Hydrogenophaga
+ term:
+ id: NCBITaxon:47420
+ label: Hydrogenophaga
+ after:
+ - preferred_term: Syntrophomonas
+ term:
+ id: NCBITaxon:862
+ label: Syntrophomonas
+ - preferred_term: Geobacter
+ term:
+ id: NCBITaxon:28231
+ label: Geobacter
+ - preferred_term: Hydrogenophaga
+ term:
+ id: NCBITaxon:47420
+ label: Hydrogenophaga
+ - preferred_term: Petrimonas
+ term:
+ id: NCBITaxon:307628
+ label: Petrimonas
+ gtdb_grounding_status: GROUNDED
+ gtdb_classification:
+ gtdb_id: GTDB:g__Petrimonas
+ gtdb_taxon: Petrimonas
+ gtdb_lineage: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Petrimonas
+ ncbi_source_id: NCBITaxon:307628
+ majority_fraction: 1.0
+ support_genomes: 8
+ total_genomes: 8
+ is_reclassified: false
+ mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__
+ rank; 1 GTDB taxa under the NCBI taxon]
+ notes: Enriched fermentative genus in the planktonic suspension; no species or strain is identified in
+ the abstract.
+ - mutation: Recast PLS support as experimental intervention
+ test: test_sludge_eet_model_is_not_a_route_resolved_intervention
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 76
+ assertion: assert model["evidence"][0]["evidence_source"] == "COMPUTATIONAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/3/evidence/0/evidence_source
+ before: COMPUTATIONAL
+ after: IN_VITRO
+ - path: records/1/ecological_interactions/3/evidence/0/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Declare all helper pairs mutualistic
+ test: test_watermelon_seven_positive_partners_are_not_seven_mutualisms
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 86
+ assertion: assert facilitation["interaction_type"] == "CROSS_FEEDING"
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/0/interaction_type
+ before: CROSS_FEEDING
+ after: MUTUALISM
+ - mutation: Promote candidate exchange to proven compound mediation
+ test: test_watermelon_candidates_do_not_establish_specific_metabolite_transfer
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 100
+ assertion: assert facilitation["evidence"][2]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/0/evidence/2/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Assign parent pathogen challenge to SSC8
+ test: test_ssc8_growth_does_not_inherit_parent_pathogen_challenge
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 108
+ assertion: assert "must not be assigned to SSC8" in outcome["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/1/description
+ before: The eight-member SSC8 improved ungrafted-watermelon growth in non-sterile greenhouse soil, with
+ height, root weight and dry weight comparable to the parent16-member SBC. This simplified-consortium experiment
+ had no added pathogen. The55.6% disease-index reduction and biofilm-pathway enrichment were measured for
+ SBC and must not be assigned to SSC8; neither plant protection nor biofilm mediation is established by
+ this growth assay.
+ after: SSC8 proved Fusarium resistance with55.6%less disease.
+ - mutation: Restore common-cause wetland arrow
+ test: test_wetland_treatment_responses_are_not_causes_of_fitted_subnetwork
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 126
+ assertion: assert not sulfate.get("downstream") and not oxygen.get("downstream")
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/0/downstream
+ before: null
+ after:
+ - target: Modeled lactate-sulfate carbon and sulfur subnetwork
+ description: Methane suppression causes this model.
+ - mutation: Type fitted subnetwork as direct cross-feeding
+ test: test_wetland_model_is_not_directly_measured_cross_feeding
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 140
+ assertion: assert "interaction_type" not in model
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/2/interaction_type
+ before: null
+ after: CROSS_FEEDING
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml: b39ce1ba60102209db112c70cc7f1a64b16e8b1f889cecdaff6d3e2d3f149c02
+ kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml: 96790620c4f70dd5ca498af0636db53fc9fb7d6779a96851bb31385b71c6f329
+ kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml: 4eda48481991d8d22dad2d32ec24284d8580ba33e540377b8f5509bced74c31b
+ kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml: 0703409d520c9c561d99c075761f37adff7ca856e14b3d438df2080e975e1e1a
+ tests/test_causal_review_batch118.py: aa5608897c5eaecc64b78ee158357124603e07b2e46d98e9f03c5f4bb9ff6297
+ probe_script_sha256: f9b246f22ec24202639616027aa392c5e08fa7a5f0f9d81bba4683a4cb8b1c77
+ scope: In-memory control/mutation/restored-control; no canonical writes and not additional pytest tests.
+ artifact: /private/tmp/communitymech-batch118/adversarial-regression-proof.json
+ sha256: cd1b6c338c91efc8b8f6b5a99273b896bd6c68e11bb4f31560ba77db63af796f
+verification:
+ combined_regressions: 1101 passed in 379.68s (0:06:19)
+ new_regression_tests: 12
+ total_recorded_gate_outputs: 41
+ primary_graph_snippet_proof:
+ graph_quotations: 25
+ discussion_quotations: 4
+ fresh_primary_literal_matches: 29
+ all_cached_literal_matches: 29
+ retained_nodes: 12
+ removed_nodes: 1
+ renamed_nodes: 4
+ retained_arrows: 4
+ removed_arrows: 4
+ 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/Viili_Fungus_Bacterium_EPS_SynCom.yaml:
+ MATCH: 17
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml:
+ MATCH: 19
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml:
+ MATCH: 15
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml:
+ MATCH: 33
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9035
+ categories:
+ MATCH: 8890
+ RENDERING: 28
+ 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-batch118.yaml: 7e901fb9fa8882cead15b1bb895f7108e285b7b80dbbe3bf6ce089d4f2ea88f6
+ tests/test_causal_review_batch118.py: aa5608897c5eaecc64b78ee158357124603e07b2e46d98e9f03c5f4bb9ff6297
+ tests/test_participating_taxa.py: 6cb1226981cf15eb2f1fd74e15bbf1365fb2b162ea28fbfc94504dbfa33f6b11
+ tests/test_community_level_connectivity_credit.py: 996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a
+ tests/test_causal_review_batch109.py: 921f9541c07a8251b4f813fb9b6fd29945f78cc74dc10e61b68dc1978b90daa1
+ tests/test_datamodel.py: f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25
+ reports/causal_graph_review/cache-provenance-20261008-batch118.json: 36984968b7b432e92261a2e616e14628311118015432dc64056ee1489bcaf553
+ kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml: b39ce1ba60102209db112c70cc7f1a64b16e8b1f889cecdaff6d3e2d3f149c02
+ kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml: 96790620c4f70dd5ca498af0636db53fc9fb7d6779a96851bb31385b71c6f329
+ kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml: 4eda48481991d8d22dad2d32ec24284d8580ba33e540377b8f5509bced74c31b
+ kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml: 0703409d520c9c561d99c075761f37adff7ca856e14b3d438df2080e975e1e1a
+ history_sha256:
+ history/records/Viili_Fungus_Bacterium_EPS_SynCom/2026-10-08T124721Z-codex-2774fb.yaml: db9f0fb2b0bb5407b8cbbc79d72c5ae25e8d78a094caba43dca903111f65e6ac
+ history/records/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community/2026-10-08T124721Z-codex-ba3224.yaml: 78a6145ad7c5c83621080df476d69910eb2ecca06f3a8c5c13a23920eab81bdc
+ history/records/Watermelon_Rhizosphere_Fusarium_SynCom8/2026-10-08T124721Z-codex-4fbc8e.yaml: 9c2511d3ab47cde0e4e040f0824d244d1e7ba6575f1501bca78ffa204f7dfbe7
+ history/records/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community/2026-10-08T124721Z-codex-37eb64.yaml: 41a9b042fdef7dac87465e7273cf5d18179832a2e12d3d6dffcce0e71fd403fd
+ unchanged_records: 456
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 879
+ cache_changes: []
+ 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: 1280
+ delta_from_batch117:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ explanation: Two explicit participant-list users added for sludge and wetland guild roles;298total. The existing
+ scope census is unchanged because all records retain community-level scope. Sole-credit does not certify actual
+ participant coverage. Connectivity logic and thresholds are unchanged.
+corpus:
+ records: 460
+ nodes: 1378
+ edges: 531
+ review_status_counts:
+ needs_research: 54
+ pending: 26
+ reviewed: 380
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary established Python3.13 lint environment; project dependencies unchanged.
+limitations:
+- Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects.
+ Whole four records and all13existing nodes/eight arrows reviewed; retain12nodes/four arrows,remove one misassigned
+ node/four unsupported arrows,rename four nodes,no new topology.
+- Fresh EuropePMC abstracts and Crossref identities checked for all four. Watermelon and wetland complete main-body
+ XML text including methods/results/discussion,table text and captions read. No original figure pixels,separate
+ supplementary files,raw data or wetland model code audited. Snippet matching does not establish entailment.
+- Viili and sludge repairs are abstract-bounded. DOI/publisher search yielded accessible abstracts; no open full
+ text was inspected. No exhaustive absence claim,access bypass,publication-body import or cache change.
+- Viili retains experimental nutrient provision and AI-2 perturbation support; nitrogen-to-signaling mediation remains
+ PARTIAL and regulation is not nutrient transfer. Prior tested-combination EPS and no-EPS-as-nitrogen fixes1014/1015
+ preserved.
+- Sludge compartment roles remain representative enrichments. EET arrows retain partial least squares model support
+ without route-specific intervention or thermodynamic-dependency claims. Scientific observations are not discarded
+ because causal mediation is inferred.
+- Watermelon retains seven positive spent-medium effects and three mutually beneficial pairs,not seven mutualisms.
+ SSC8 growth assay used no added pathogen. Parent16-member disease/biofilm results are not SSC8 outcomes; candidate
+ metabolites are not specific causal mediators or stereochemically resolved exchange. Missing SSC8 roster/non-graph
+ fields remain issue1919.
+- Wetland measured gas effects remain; marker proteins/fitted fluxes are not pathway-resolved direct flux measurements.
+ Removed arrows confused shared exposure with succession. Results/discussion contain differences about additivity
+ and oxygen-linked routes; no silent resolution or universal-zero methane claim. Non-graph vessel/ingredient evidence
+ issues remain1920.
+- Fresh all-state1154issue titles/bodies searched initially; pre-creation receipt records fresh count. Matching1452/1014/1015/644
+ bodies read and distinct. Hidden/ignored-inclusive local search found135paths excluding.git,docs,site,references_cache,.env;
+ not a historical PR-comment audit.
+- Four guarded writes preserve unrelated raw YAML blocks,456otherrecords,923caches,all prior histories/decisions.
+ Four append-only record histories and four curation events. Canonical taxon identities unchanged. Existing shared
+ evidence aliases detached before graph editing.
+- 'Existing-graph repair with no new nodes/directions: no Edison run,provider submission or credit spend. Prior
+ authorized Ruegeria1883 authentication blocker not retried without state change; no credential inspected. Self-adversarial
+ review is not independent approval. Overall review,protected merge and branch deletion remain incomplete.'
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch118.json b/reports/causal_graph_review/cache-provenance-20261008-batch118.json
new file mode 100644
index 000000000..eb565cb3d
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch118.json
@@ -0,0 +1,445 @@
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+ "primary_text_sha256": "519833278eff9c75c153b8487c379494faac74c871f28116d9df61dd809ce721",
+ "license": [
+ "Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated 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 will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data."
+ ],
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+ "primary_text_sha256": "684fb73348e88b42163d37afd485ee5254a5bfbff2d2a6762658422f57e3faf4",
+ "license": [
+ "Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. 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 or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/."
+ ],
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+ "actual_read_scope": [
+ "Fresh EuropePMC abstracts and Crossref identities checked for all four. Watermelon and wetland complete main-body XML text including methods/results/discussion,table text and captions read. No original figure pixels,separate supplementary files,raw data or wetland model code audited. Snippet matching does not establish entailment.",
+ "Viili and sludge repairs are abstract-bounded. DOI/publisher search yielded accessible abstracts; no open full text was inspected. No exhaustive absence claim,access bypass,publication-body import or cache change.",
+ "Viili retains experimental nutrient provision and AI-2 perturbation support; nitrogen-to-signaling mediation remains PARTIAL and regulation is not nutrient transfer. Prior tested-combination EPS and no-EPS-as-nitrogen fixes1014/1015 preserved.",
+ "Sludge compartment roles remain representative enrichments. EET arrows retain partial least squares model support without route-specific intervention or thermodynamic-dependency claims. Scientific observations are not discarded because causal mediation is inferred.",
+ "Watermelon retains seven positive spent-medium effects and three mutually beneficial pairs,not seven mutualisms. SSC8 growth assay used no added pathogen. Parent16-member disease/biofilm results are not SSC8 outcomes; candidate metabolites are not specific causal mediators or stereochemically resolved exchange. Missing SSC8 roster/non-graph fields remain issue1919.",
+ "Wetland measured gas effects remain; marker proteins/fitted fluxes are not pathway-resolved direct flux measurements. Removed arrows confused shared exposure with succession. Results/discussion contain differences about additivity and oxygen-linked routes; no silent resolution or universal-zero methane claim. Non-graph vessel/ingredient evidence issues remain1920."
+ ]
+ },
+ "limitations": [
+ "Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects. Whole four records and all13existing nodes/eight arrows reviewed; retain12nodes/four arrows,remove one misassigned node/four unsupported arrows,rename four nodes,no new topology.",
+ "Fresh EuropePMC abstracts and Crossref identities checked for all four. Watermelon and wetland complete main-body XML text including methods/results/discussion,table text and captions read. No original figure pixels,separate supplementary files,raw data or wetland model code audited. Snippet matching does not establish entailment.",
+ "Viili and sludge repairs are abstract-bounded. DOI/publisher search yielded accessible abstracts; no open full text was inspected. No exhaustive absence claim,access bypass,publication-body import or cache change.",
+ "Viili retains experimental nutrient provision and AI-2 perturbation support; nitrogen-to-signaling mediation remains PARTIAL and regulation is not nutrient transfer. Prior tested-combination EPS and no-EPS-as-nitrogen fixes1014/1015 preserved.",
+ "Sludge compartment roles remain representative enrichments. EET arrows retain partial least squares model support without route-specific intervention or thermodynamic-dependency claims. Scientific observations are not discarded because causal mediation is inferred.",
+ "Watermelon retains seven positive spent-medium effects and three mutually beneficial pairs,not seven mutualisms. SSC8 growth assay used no added pathogen. Parent16-member disease/biofilm results are not SSC8 outcomes; candidate metabolites are not specific causal mediators or stereochemically resolved exchange. Missing SSC8 roster/non-graph fields remain issue1919.",
+ "Wetland measured gas effects remain; marker proteins/fitted fluxes are not pathway-resolved direct flux measurements. Removed arrows confused shared exposure with succession. Results/discussion contain differences about additivity and oxygen-linked routes; no silent resolution or universal-zero methane claim. Non-graph vessel/ingredient evidence issues remain1920.",
+ "Fresh all-state1154issue titles/bodies searched initially; pre-creation receipt records fresh count. Matching1452/1014/1015/644 bodies read and distinct. Hidden/ignored-inclusive local search found135paths excluding.git,docs,site,references_cache,.env; not a historical PR-comment audit.",
+ "Four guarded writes preserve unrelated raw YAML blocks,456otherrecords,923caches,all prior histories/decisions. Four append-only record histories and four curation events. Canonical taxon identities unchanged. Existing shared evidence aliases detached before graph editing.",
+ "Existing-graph repair with no new nodes/directions: no Edison run,provider submission or credit spend. Prior authorized Ruegeria1883 authentication blocker not retried without state change; no credential inspected. Self-adversarial review is not independent approval. Overall review,protected merge and branch deletion remain incomplete."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
new file mode 100644
index 000000000..991d3ed91
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
@@ -0,0 +1,901 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: fc5c4d103c134cee549a76e8c71addcf8c322e09
+baseline_commit: fc5c4d103c134cee549a76e8c71addcf8c322e09
+base_tree: 497842ab64399d377c2737def4e0d93516085f99
+pre_source_baseline_sha256: 9620412b06bcabd8fcfed3e1cb24dbbf534c133cd06b01d5d637b579f7536abc
+issues:
+- 1915
+- 1916
+- 1917
+- 1918
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1919
+- 1920
+source_access:
+ retrieval_manifest:
+ viili:
+ pmid: '42372608'
+ doi: 10.1016/j.ijfoodmicro.2026.111922
+ pmcid: null
+ title: Synthetic microbial communities reveal the mechanisms of fungus-bacterium metabolic interactions regulating
+ exopolysaccharide production in Viili.
+ metadata: /private/tmp/communitymech-batch118/viili-metadata.json
+ metadata_sha256: acdb72012f55b553c20984e007d5e71e8aaf6e73da7ac525ed70fdff2508b4d6
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42372608+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ abstract: /private/tmp/communitymech-batch118/viili-abstract.txt
+ abstract_sha256: b8462e1f1f1831441fa864bb7fc804b90168550918dd52d0e160f8e272d3edd1
+ crossref: /private/tmp/communitymech-batch118/viili-crossref.json
+ crossref_sha256: a8eff9c7cc801281753dd153623f2bcf68b9719257224a739fe2321d9be9167c
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+ doi: 10.1016/j.watres.2026.125665
+ pmcid: null
+ title: Biofilm-suspension syntrophy drives synergistic electro-fermentation through engineered spatial division
+ of labor for concurrent carbon recovery and pollutant degradation.
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+ metadata_sha256: 83332357b1ecd87b0306b675a368528b3904527816a22ab9dcab92730cf8be83
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+ status: retrieved
+ abstract: /private/tmp/communitymech-batch118/sludge-abstract.txt
+ abstract_sha256: 6a16c574c85afaf974c421b4cb2d8705931f7877e5083a59a960f04bcb292f8a
+ crossref: /private/tmp/communitymech-batch118/sludge-crossref.json
+ crossref_sha256: e17ff78a6c4acf67bc8a9647a4ea70781b3fd6d9f5d1647c32d0b71502b17cc9
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+ watermelon:
+ pmid: '38840214'
+ doi: 10.1186/s40168-024-01814-z
+ pmcid: PMC11151650
+ title: Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon
+ against Fusarium oxysporum via microbial synergistic effects.
+ metadata: /private/tmp/communitymech-batch118/watermelon-metadata.json
+ metadata_sha256: 829cfe50b9b3ac7e7ca453efdac4f63b283d82deeef018efa4b63f270ad54444
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A38840214+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11151650/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch118/watermelon-abstract.txt
+ abstract_sha256: 96026e62476a4d0ffd0fe8e78601d5026122a54e40c1c9153dea5c958cbda9cc
+ xml: /private/tmp/communitymech-batch118/watermelon-primary.xml
+ xml_sha256: 0235927bbc7f4943fc5b585dd0afd1ba162f8e51c3af53e62d69d1adf6afd83d
+ primary_text: /private/tmp/communitymech-batch118/watermelon-primary.txt
+ primary_text_sha256: 519833278eff9c75c153b8487c379494faac74c871f28116d9df61dd809ce721
+ license:
+ - Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
+ permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you
+ give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons
+ licence, and indicate if changes were made. The images or other third party material in this article are
+ included in the article's Creative Commons licence, unless indicated 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 will need to obtain permission directly from the
+ copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The
+ Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies
+ to the data made available in this article, unless otherwise stated in a credit line to the data.
+ crossref: /private/tmp/communitymech-batch118/watermelon-crossref.json
+ crossref_sha256: 0581a1fdf05c19e5f4a3bc037e397116d4e92c4d5cde814433c4d5ca3ae3c148
+ crossref_license:
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+ URL: https://creativecommons.org/licenses/by/4.0
+ wetland:
+ pmid: '38961111'
+ doi: 10.1038/s41522-024-00525-5
+ pmcid: PMC11222425
+ title: Metaproteomics-informed stoichiometric modeling reveals the responses of wetland microbial communities
+ to oxygen and sulfate exposure.
+ metadata: /private/tmp/communitymech-batch118/wetland-metadata.json
+ metadata_sha256: 3a3c821cc7256ebf6a8b3e1c9299e321289a733407155e86a1fec35e66059d19
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A38961111+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11222425/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch118/wetland-abstract.txt
+ abstract_sha256: df38817b6a2a96587633c61b2844a878beea2e6587aca131b4e8f20b34680efd
+ xml: /private/tmp/communitymech-batch118/wetland-primary.xml
+ xml_sha256: 08b3674b2a30714f73df5df3d8d280cbf67730d8985b66ac9bcee1fb7347fa5b
+ primary_text: /private/tmp/communitymech-batch118/wetland-primary.txt
+ primary_text_sha256: 684fb73348e88b42163d37afd485ee5254a5bfbff2d2a6762658422f57e3faf4
+ license:
+ - "Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which\
+ \ permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you\
+ \ give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons\
+ \ licence, and indicate if changes were made. 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 or exceeds the permitted use, you will need to obtain permission\
+ \ directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/."
+ crossref: /private/tmp/communitymech-batch118/wetland-crossref.json
+ crossref_sha256: 18ccd7589ee46358bf3acc4439a7347f13162545d83bd1a3956eb1dc2f293185
+ crossref_license:
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+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0
+ actual_read_scope:
+ - Fresh EuropePMC abstracts and Crossref identities checked for all four. Watermelon and wetland complete main-body
+ XML text including methods/results/discussion,table text and captions read. No original figure pixels,separate
+ supplementary files,raw data or wetland model code audited. Snippet matching does not establish entailment.
+ - Viili and sludge repairs are abstract-bounded. DOI/publisher search yielded accessible abstracts; no open full
+ text was inspected. No exhaustive absence claim,access bypass,publication-body import or cache change.
+ - Viili retains experimental nutrient provision and AI-2 perturbation support; nitrogen-to-signaling mediation
+ remains PARTIAL and regulation is not nutrient transfer. Prior tested-combination EPS and no-EPS-as-nitrogen
+ fixes1014/1015 preserved.
+ - Sludge compartment roles remain representative enrichments. EET arrows retain partial least squares model support
+ without route-specific intervention or thermodynamic-dependency claims. Scientific observations are not discarded
+ because causal mediation is inferred.
+ - Watermelon retains seven positive spent-medium effects and three mutually beneficial pairs,not seven mutualisms.
+ SSC8 growth assay used no added pathogen. Parent16-member disease/biofilm results are not SSC8 outcomes; candidate
+ metabolites are not specific causal mediators or stereochemically resolved exchange. Missing SSC8 roster/non-graph
+ fields remain issue1919.
+ - Wetland measured gas effects remain; marker proteins/fitted fluxes are not pathway-resolved direct flux measurements.
+ Removed arrows confused shared exposure with succession. Results/discussion contain differences about additivity
+ and oxygen-linked routes; no silent resolution or universal-zero methane claim. Non-graph vessel/ingredient
+ evidence issues remain1920.
+primary_artifacts:
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+ /private/tmp/communitymech-batch118/wetland-abstract.txt: df38817b6a2a96587633c61b2844a878beea2e6587aca131b4e8f20b34680efd
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+ /private/tmp/communitymech-batch118/wetland-primary.txt: 684fb73348e88b42163d37afd485ee5254a5bfbff2d2a6762658422f57e3faf4
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+reviewed_counts:
+ original_nodes: 13
+ retained_nodes: 12
+ removed_nodes: 1
+ original_arrows: 8
+ retained_arrows: 4
+ removed_arrows: 4
+ renamed_nodes: 4
+ graph_quotations: 25
+ discussion_quotations: 4
+ new_discussions: 4
+primary_graph_snippet_count: 25
+snippet_checks:
+- record: Viili_Fungus_Bacterium_EPS_SynCom
+ node: Geotrichum nitrogen supply to lactic acid bacteria
+ evidence_index: 0
+ reference: PMID:42372608
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/viili-abstract.txt
+ cache_artifact: references_cache/PMID_42372608.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Viili_Fungus_Bacterium_EPS_SynCom
+ node: Geotrichum nitrogen supply to lactic acid bacteria
+ evidence_index: 1
+ reference: PMID:42372608
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/viili-abstract.txt
+ cache_artifact: references_cache/PMID_42372608.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Viili_Fungus_Bacterium_EPS_SynCom
+ node: AI-2 regulation of Viili bacterial EPS production
+ evidence_index: 0
+ reference: PMID:42372608
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/viili-abstract.txt
+ cache_artifact: references_cache/PMID_42372608.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Viili_Fungus_Bacterium_EPS_SynCom
+ node: AI-2 regulation of Viili bacterial EPS production
+ evidence_index: 1
+ reference: PMID:42372608
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/viili-abstract.txt
+ cache_artifact: references_cache/PMID_42372608.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Viili_Fungus_Bacterium_EPS_SynCom
+ node: AI-2 regulation of Viili bacterial EPS production
+ evidence_index: 2
+ reference: PMID:42372608
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/viili-abstract.txt
+ cache_artifact: references_cache/PMID_42372608.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Viili_Fungus_Bacterium_EPS_SynCom
+ node: Three-species Viili EPS maximum
+ evidence_index: 0
+ reference: PMID:42372608
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/viili-abstract.txt
+ cache_artifact: references_cache/PMID_42372608.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community
+ node: Biofilm-Suspension Spatial Division of Labor
+ evidence_index: 0
+ reference: PMID:41793807
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/sludge-abstract.txt
+ cache_artifact: references_cache/PMID_41793807.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community
+ node: Biofilm-Suspension Spatial Division of Labor
+ evidence_index: 1
+ reference: PMID:41793807
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/sludge-abstract.txt
+ cache_artifact: references_cache/PMID_41793807.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community
+ node: Biofilm-Suspension Spatial Division of Labor
+ evidence_index: 2
+ reference: PMID:41793807
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/sludge-abstract.txt
+ cache_artifact: references_cache/PMID_41793807.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community
+ node: Biofilm Electroactivity and Dehalogenation
+ evidence_index: 0
+ reference: PMID:41793807
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/sludge-abstract.txt
+ cache_artifact: references_cache/PMID_41793807.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community
+ node: Suspension Acidogenesis
+ evidence_index: 0
+ reference: PMID:41793807
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/sludge-abstract.txt
+ cache_artifact: references_cache/PMID_41793807.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community
+ node: Modeled EET support for biofilm-suspension cooperation
+ evidence_index: 0
+ reference: PMID:41793807
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/sludge-abstract.txt
+ cache_artifact: references_cache/PMID_41793807.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Watermelon_Rhizosphere_Fusarium_SynCom8
+ node: Pseudomonas-Centered Metabolic Facilitation
+ evidence_index: 0
+ reference: PMID:38840214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/watermelon-primary.txt
+ cache_artifact: references_cache/PMID_38840214.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Watermelon_Rhizosphere_Fusarium_SynCom8
+ node: Pseudomonas-Centered Metabolic Facilitation
+ evidence_index: 1
+ reference: PMID:38840214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/watermelon-primary.txt
+ cache_artifact: references_cache/PMID_38840214.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Watermelon_Rhizosphere_Fusarium_SynCom8
+ node: Pseudomonas-Centered Metabolic Facilitation
+ evidence_index: 2
+ reference: PMID:38840214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/watermelon-primary.txt
+ cache_artifact: references_cache/PMID_38840214.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Watermelon_Rhizosphere_Fusarium_SynCom8
+ node: SSC8 watermelon growth promotion without added pathogen
+ evidence_index: 0
+ reference: PMID:38840214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/watermelon-primary.txt
+ cache_artifact: references_cache/PMID_38840214.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Watermelon_Rhizosphere_Fusarium_SynCom8
+ node: SSC8 watermelon growth promotion without added pathogen
+ evidence_index: 1
+ reference: PMID:38840214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/watermelon-primary.txt
+ cache_artifact: references_cache/PMID_38840214.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+ node: Sulfate Suppression Of Methanogenesis
+ evidence_index: 0
+ reference: PMID:38961111
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/wetland-primary.txt
+ cache_artifact: references_cache/PMID_38961111.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+ node: Sulfate Suppression Of Methanogenesis
+ evidence_index: 1
+ reference: PMID:38961111
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/wetland-primary.txt
+ cache_artifact: references_cache/PMID_38961111.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+ node: Sulfate Suppression Of Methanogenesis
+ evidence_index: 2
+ reference: PMID:38961111
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/wetland-primary.txt
+ cache_artifact: references_cache/PMID_38961111.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+ node: Oxygen Shift From Methane To Carbon Dioxide
+ evidence_index: 0
+ reference: PMID:38961111
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/wetland-primary.txt
+ cache_artifact: references_cache/PMID_38961111.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+ node: Oxygen Shift From Methane To Carbon Dioxide
+ evidence_index: 1
+ reference: PMID:38961111
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/wetland-primary.txt
+ cache_artifact: references_cache/PMID_38961111.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+ node: Modeled lactate-sulfate carbon and sulfur subnetwork
+ evidence_index: 0
+ reference: PMID:38961111
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/wetland-primary.txt
+ cache_artifact: references_cache/PMID_38961111.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+ node: Modeled lactate-sulfate carbon and sulfur subnetwork
+ evidence_index: 1
+ reference: PMID:38961111
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/wetland-primary.txt
+ cache_artifact: references_cache/PMID_38961111.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+ node: Modeled lactate-sulfate carbon and sulfur subnetwork
+ evidence_index: 2
+ reference: PMID:38961111
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/wetland-primary.txt
+ cache_artifact: references_cache/PMID_38961111.md
+ scope: Normalized contiguous literal match, not entailment proof.
+discussion_snippet_checks:
+- record: Viili_Fungus_Bacterium_EPS_SynCom
+ node: viili_causal_graph_scope_batch118
+ evidence_index: 0
+ reference: PMID:42372608
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/viili-abstract.txt
+ cache_artifact: references_cache/PMID_42372608.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community
+ node: sludge_causal_graph_scope_batch118
+ evidence_index: 0
+ reference: PMID:41793807
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/sludge-abstract.txt
+ cache_artifact: references_cache/PMID_41793807.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Watermelon_Rhizosphere_Fusarium_SynCom8
+ node: watermelon_causal_graph_scope_batch118
+ evidence_index: 0
+ reference: PMID:38840214
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/watermelon-primary.txt
+ cache_artifact: references_cache/PMID_38840214.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wetland_Oxygen_Sulfate_GHG_Microcosm_Community
+ node: wetland_causal_graph_scope_batch118
+ evidence_index: 0
+ reference: PMID:38961111
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch118/wetland-primary.txt
+ cache_artifact: references_cache/PMID_38961111.md
+ scope: Normalized contiguous literal match, not entailment proof.
+cache_changes: []
+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 baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects.
+ Whole four records and all13existing nodes/eight arrows reviewed; retain12nodes/four arrows,remove one misassigned
+ node/four unsupported arrows,rename four nodes,no new topology.
+- Fresh EuropePMC abstracts and Crossref identities checked for all four. Watermelon and wetland complete main-body
+ XML text including methods/results/discussion,table text and captions read. No original figure pixels,separate
+ supplementary files,raw data or wetland model code audited. Snippet matching does not establish entailment.
+- Viili and sludge repairs are abstract-bounded. DOI/publisher search yielded accessible abstracts; no open full
+ text was inspected. No exhaustive absence claim,access bypass,publication-body import or cache change.
+- Viili retains experimental nutrient provision and AI-2 perturbation support; nitrogen-to-signaling mediation remains
+ PARTIAL and regulation is not nutrient transfer. Prior tested-combination EPS and no-EPS-as-nitrogen fixes1014/1015
+ preserved.
+- Sludge compartment roles remain representative enrichments. EET arrows retain partial least squares model support
+ without route-specific intervention or thermodynamic-dependency claims. Scientific observations are not discarded
+ because causal mediation is inferred.
+- Watermelon retains seven positive spent-medium effects and three mutually beneficial pairs,not seven mutualisms.
+ SSC8 growth assay used no added pathogen. Parent16-member disease/biofilm results are not SSC8 outcomes; candidate
+ metabolites are not specific causal mediators or stereochemically resolved exchange. Missing SSC8 roster/non-graph
+ fields remain issue1919.
+- Wetland measured gas effects remain; marker proteins/fitted fluxes are not pathway-resolved direct flux measurements.
+ Removed arrows confused shared exposure with succession. Results/discussion contain differences about additivity
+ and oxygen-linked routes; no silent resolution or universal-zero methane claim. Non-graph vessel/ingredient evidence
+ issues remain1920.
+- Fresh all-state1154issue titles/bodies searched initially; pre-creation receipt records fresh count. Matching1452/1014/1015/644
+ bodies read and distinct. Hidden/ignored-inclusive local search found135paths excluding.git,docs,site,references_cache,.env;
+ not a historical PR-comment audit.
+- Four guarded writes preserve unrelated raw YAML blocks,456otherrecords,923caches,all prior histories/decisions.
+ Four append-only record histories and four curation events. Canonical taxon identities unchanged. Existing shared
+ evidence aliases detached before graph editing.
+- 'Existing-graph repair with no new nodes/directions: no Edison run,provider submission or credit spend. Prior
+ authorized Ruegeria1883 authentication blocker not retried without state change; no credential inspected. Self-adversarial
+ review is not independent approval. Overall review,protected merge and branch deletion remain incomplete.'
+records:
+- path: kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml
+ id: CommunityMech:000408
+ original_sha256: 492b05ae487137b8fc4d8dda20f2722fd637857a0236a29b43a79f505b9cb62e
+ record_sha256: b39ce1ba60102209db112c70cc7f1a64b16e8b1f889cecdaff6d3e2d3f149c02
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain experimental nitrogen cross-feeding while bounding the signaling bridge.; Keep AI-2 perturbation
+ support without typing regulation as nutrient transfer.; Retain the three-member EPS maximum only among tested
+ combinations with explicit participants.
+ node_decisions:
+ - node: Geotrichum nitrogen supply to lactic acid bacteria
+ rationale: Retain experimental nitrogen cross-feeding while bounding the signaling bridge.
+ - node: AI-2 regulation of Viili bacterial EPS production
+ rationale: Keep AI-2 perturbation support without typing regulation as nutrient transfer.
+ - node: Three-species Viili EPS maximum
+ rationale: Retain the three-member EPS maximum only among tested combinations with explicit participants.
+ removed_node_decisions: []
+ renamed_nodes:
+ G. candidum activation of AI-2-linked EPS production: AI-2 regulation of Viili bacterial EPS production
+ edges_before:
+ - &id001
+ source: Geotrichum nitrogen supply to lactic acid bacteria
+ target: G. candidum activation of AI-2-linked EPS production
+ description: The fungus-associated nitrogen supply was coupled with stronger lactic-acid-bacterial growth, quorum-sensing
+ activity, and EPS production.
+ - &id003
+ source: G. candidum activation of AI-2-linked EPS production
+ target: Three-species Viili EPS maximum
+ description: AI-2-mediated quorum sensing positively regulated EPS synthesis in the three-member Viili consortium.
+ edges_after:
+ - &id002
+ source: Geotrichum nitrogen supply to lactic acid bacteria
+ target: AI-2 regulation of Viili bacterial EPS production
+ description: 'PARTIAL: fungal nitrogen provision supports bacterial growth and is accompanied by stronger quorum-sensing
+ activity. It may contribute to activation of the AI-2 regulatory node, but the abstract does not isolate valine-specific
+ mediation from growth effects.'
+ - &id004
+ source: AI-2 regulation of Viili bacterial EPS production
+ target: Three-species Viili EPS maximum
+ description: AI-2 activation and inhibition support positive regulation of bacterial EPS synthesis and thus
+ a contribution to the three-member output. They do not establish AI-2 as the sole explanation of the tested
+ consortium maximum.
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: 'PARTIAL: fungal nitrogen provision supports bacterial growth and is accompanied by stronger quorum-sensing
+ activity. It may contribute to activation of the AI-2 regulatory node, but the abstract does not isolate valine-specific
+ mediation from growth effects.'
+ - before: *id003
+ after: *id004
+ rationale: AI-2 activation and inhibition support positive regulation of bacterial EPS synthesis and thus a
+ contribution to the three-member output. They do not establish AI-2 as the sole explanation of the tested
+ consortium maximum.
+ removed_edge_decisions: []
+ references:
+ - PMID:42372608
+ issues:
+ - 1915
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Viili_Fungus_Bacterium_EPS_SynCom/2026-10-08T124721Z-codex-2774fb.yaml
+- path: kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml
+ id: CommunityMech:000328
+ original_sha256: 6b4be381bfb2f468d20d030319f47e1a25a61e81e8cb09a25d482de3cbdd669d
+ record_sha256: 96790620c4f70dd5ca498af0636db53fc9fb7d6779a96851bb31385b71c6f329
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain observed spatial differentiation without exhaustive five-genus membership.; Limit biofilm roles
+ to its three representative genera and omit unsupported within-fraction partitioning.; Limit suspension roles
+ to its two representative genera without assigning each all pathways.; Qualify both EET arrows as computational
+ inference and leave unspecified dependency untyped.
+ node_decisions:
+ - node: Biofilm-Suspension Spatial Division of Labor
+ rationale: Retain observed spatial differentiation without exhaustive five-genus membership.
+ - node: Biofilm Electroactivity and Dehalogenation
+ rationale: Limit biofilm roles to its three representative genera and omit unsupported within-fraction partitioning.
+ - node: Suspension Acidogenesis
+ rationale: Limit suspension roles to its two representative genera without assigning each all pathways.
+ - node: Modeled EET support for biofilm-suspension cooperation
+ rationale: Qualify both EET arrows as computational inference and leave unspecified dependency untyped.
+ removed_node_decisions: []
+ renamed_nodes:
+ EET-Reinforced Biofilm-Suspension Syntrophy: Modeled EET support for biofilm-suspension cooperation
+ edges_before:
+ - &id005
+ source: EET-Reinforced Biofilm-Suspension Syntrophy
+ target: Biofilm Electroactivity and Dehalogenation
+ description: EET reinforces the electrode-biofilm side of the syntrophy, where electroactive Syntrophomonas
+ and Geobacter and dehalogenating Hydrogenophaga are enriched.
+ - &id007
+ source: EET-Reinforced Biofilm-Suspension Syntrophy
+ target: Suspension Acidogenesis
+ description: EET also contributes to the suspension side of the syntrophy, where Sedimentibacter and Petrimonas
+ are enriched with hydrolysis, fatty-acid biosynthesis, and acidogenesis.
+ edges_after:
+ - &id006
+ source: Modeled EET support for biofilm-suspension cooperation
+ target: Biofilm Electroactivity and Dehalogenation
+ description: 'PARTIAL: the path model links EET to biofilm-associated dehalogenation. Retain this inferred contribution,
+ not a directly perturbed EET-to-output mechanism or a flux assigned to each representative genus.'
+ - &id008
+ source: Modeled EET support for biofilm-suspension cooperation
+ target: Suspension Acidogenesis
+ description: 'PARTIAL: the path model links EET to suspension-associated acidogenesis. Retain this inferred
+ contribution, not a directly perturbed EET-to-output mechanism or a flux assigned to each representative genus.'
+ retained_edge_decisions:
+ - before: *id005
+ after: *id006
+ rationale: 'PARTIAL: the path model links EET to biofilm-associated dehalogenation. Retain this inferred contribution,
+ not a directly perturbed EET-to-output mechanism or a flux assigned to each representative genus.'
+ - before: *id007
+ after: *id008
+ rationale: 'PARTIAL: the path model links EET to suspension-associated acidogenesis. Retain this inferred contribution,
+ not a directly perturbed EET-to-output mechanism or a flux assigned to each representative genus.'
+ removed_edge_decisions: []
+ references:
+ - PMID:41793807
+ issues:
+ - 1916
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community/2026-10-08T124721Z-codex-ba3224.yaml
+- path: kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml
+ id: CommunityMech:000098
+ original_sha256: 856114bb31684927cb8e8f615e21f6b138aecd1555bdc127819e500060986f20
+ record_sha256: 4eda48481991d8d22dad2d32ec24284d8580ba33e540377b8f5509bced74c31b
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Preserve seven positive spent-medium responses and three bilateral pairs with only potential cross-feeding.;
+ Restrict the SSC8 outcome to measured growth without added pathogen.
+ node_decisions:
+ - node: Pseudomonas-Centered Metabolic Facilitation
+ rationale: Preserve seven positive spent-medium responses and three bilateral pairs with only potential cross-feeding.
+ - node: SSC8 watermelon growth promotion without added pathogen
+ rationale: Restrict the SSC8 outcome to measured growth without added pathogen.
+ removed_node_decisions:
+ - node: Pseudomonas Biofilm Pathway Enrichment
+ rationale: Biofilm-pathway enrichment was measured for the parent16-member SBC, not SSC8; retain this distinction
+ in the discussion instead of a misassigned SSC8 node.
+ renamed_nodes:
+ Watermelon Growth and Disease-Resistance Increase: SSC8 watermelon growth promotion without added pathogen
+ edges_before:
+ - &id009
+ source: Pseudomonas-Centered Metabolic Facilitation
+ target: Pseudomonas Biofilm Pathway Enrichment
+ description: Metabolic facilitation by the seven helper strains supports the Pseudomonas-centered simplified
+ community whose inoculation enriches Pseudomonas biofilm-formation functions in the rhizosphere.
+ - &id010
+ source: Pseudomonas Biofilm Pathway Enrichment
+ target: Watermelon Growth and Disease-Resistance Increase
+ description: Pseudomonas biofilm-formation enrichment and rhizosphere colonization are linked to the SynCom's
+ improved watermelon growth and Fusarium oxysporum resistance.
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - edge: *id009
+ rationale: 'The endpoints belong to different experiments: SSC8 spent-medium/growth assays versus the parent16-member
+ SBC metagenome/pathogen trial; no same-system causal chain is demonstrated.'
+ - edge: *id010
+ rationale: 'The endpoints belong to different experiments: SSC8 spent-medium/growth assays versus the parent16-member
+ SBC metagenome/pathogen trial; no same-system causal chain is demonstrated.'
+ references:
+ - PMID:38840214
+ issues:
+ - 1917
+ - 1919
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Watermelon_Rhizosphere_Fusarium_SynCom8/2026-10-08T124721Z-codex-4fbc8e.yaml
+- path: kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml
+ id: CommunityMech:000255
+ original_sha256: 09e38c8531e35cefc0fb86d7b04b90e85f2f6621c285032c8efaf8c956570403
+ record_sha256: 0703409d520c9c561d99c075761f37adff7ca856e14b3d438df2080e975e1e1a
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain measured sulfate effect with guild-level, pathway-inferred competition.; Keep the measured oxygen
+ response untyped and do not convert residual methane to zero.; Qualify the fitted subnetwork without assigning
+ directly measured cross-feeding or universal oxygen stimulation.
+ node_decisions:
+ - node: Sulfate Suppression Of Methanogenesis
+ rationale: Retain measured sulfate effect with guild-level, pathway-inferred competition.
+ - node: Oxygen Shift From Methane To Carbon Dioxide
+ rationale: Keep the measured oxygen response untyped and do not convert residual methane to zero.
+ - node: Modeled lactate-sulfate carbon and sulfur subnetwork
+ rationale: Qualify the fitted subnetwork without assigning directly measured cross-feeding or universal oxygen
+ stimulation.
+ removed_node_decisions: []
+ renamed_nodes:
+ Lactate-Sulfate Carbon And Sulfur Subnetwork: Modeled lactate-sulfate carbon and sulfur subnetwork
+ edges_before:
+ - &id011
+ source: Sulfate Suppression Of Methanogenesis
+ target: Lactate-Sulfate Carbon And Sulfur Subnetwork
+ description: 'Sulfate addition both suppresses methane emissions and provides the electron acceptor routed through
+ the lactate-to-acetate, hydrogen sulfide, and carbon dioxide subnetwork.
+
+ '
+ - &id012
+ source: Oxygen Shift From Methane To Carbon Dioxide
+ target: Lactate-Sulfate Carbon And Sulfur Subnetwork
+ description: 'Oxygen exposure redirects wetland carbon flow from methane toward carbon dioxide and, under elevated
+ sulfate, participates in the oxic sulfate condition that revealed the lactate-centered sulfur subnetwork.
+
+ '
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - edge: *id011
+ rationale: Methane suppression and the oxygen gas shift are treatment responses, not causes of the separately
+ fitted lactate-sulfate subnetwork; the original arrow confounds common exposure with causal succession.
+ - edge: *id012
+ rationale: Methane suppression and the oxygen gas shift are treatment responses, not causes of the separately
+ fitted lactate-sulfate subnetwork; the original arrow confounds common exposure with causal succession.
+ references:
+ - PMID:38961111
+ issues:
+ - 1918
+ - 1920
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community/2026-10-08T124721Z-codex-37eb64.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 2a55d5db9..3bb2c1893 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -439,10 +439,10 @@ kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml CommunityMech:00
kb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml CommunityMech:000337 0c48b3d9ff279efcfef5d313adc37d6cd7cb7d76a70281a67e551b5128e6ccfe 4 2 95.0 reports/causal_graph_review/decisions/20261008-four-records-batch117.yaml reviewed
kb/communities/Urine_Nitrification_SynCom.yaml CommunityMech:000117 2a5490ff757ecc26e5f16250860f0d9463b6ec4c4463c6df0359156f86671cd2 3 2 93.3 reports/causal_graph_review/decisions/20261008-four-records-batch117.yaml reviewed
kb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml CommunityMech:000213 6423810bc3c64954b2ea8471c4821aabbdef9fd8298b3cbbdbad8defe798d662 3 2 100.0 reports/causal_graph_review/decisions/20261008-four-records-batch117.yaml reviewed
-kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml CommunityMech:000408 492b05ae487137b8fc4d8dda20f2722fd637857a0236a29b43a79f505b9cb62e 3 2 96.7 pending
-kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml CommunityMech:000328 6b4be381bfb2f468d20d030319f47e1a25a61e81e8cb09a25d482de3cbdd669d 4 2 100.0 pending
-kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml CommunityMech:000098 856114bb31684927cb8e8f615e21f6b138aecd1555bdc127819e500060986f20 3 2 100.0 pending
-kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml CommunityMech:000255 09e38c8531e35cefc0fb86d7b04b90e85f2f6621c285032c8efaf8c956570403 3 2 100.0 pending
+kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml CommunityMech:000408 b39ce1ba60102209db112c70cc7f1a64b16e8b1f889cecdaff6d3e2d3f149c02 3 2 93.3 reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml reviewed
+kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml CommunityMech:000328 96790620c4f70dd5ca498af0636db53fc9fb7d6779a96851bb31385b71c6f329 4 2 92.5 reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml reviewed
+kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml CommunityMech:000098 4eda48481991d8d22dad2d32ec24284d8580ba33e540377b8f5509bced74c31b 2 0 60.0 reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml reviewed
+kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml CommunityMech:000255 0703409d520c9c561d99c075761f37adff7ca856e14b3d438df2080e975e1e1a 3 0 68.3 reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml reviewed
kb/communities/Wheat_Consortium_C1.yaml CommunityMech:000076 85d31a840c65d17f94c0682554165bfb33ac23168ca21cbcc45e8eb986e22dbe 3 0 75.0 pending
kb/communities/Wheat_Consortium_C6.yaml CommunityMech:000077 8a0747e8c630c65a8f0f56009905770543266386bb0c8f08e9a32e1426dcbfaa 6 0 75.0 pending
kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml CommunityMech:000414 2836c0fbd27593a8f35cbd3a676164300df8ae316681cd7c813f5708008977d6 2 0 70.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index e5b1fcc4d..e2f60da21 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -2,14 +2,14 @@
"scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
"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.",
"records": 460,
- "nodes": 1379,
- "edges": 535,
+ "nodes": 1378,
+ "edges": 531,
"records_without_nodes": 10,
- "records_without_edges": 187,
+ "records_without_edges": 189,
"review_status_counts": {
"needs_research": 54,
- "pending": 30,
- "reviewed": 376
+ "pending": 26,
+ "reviewed": 380
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch118.json b/reports/causal_graph_review/validation-20261008-batch118.json
new file mode 100644
index 000000000..c4a1c26eb
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch118.json
@@ -0,0 +1,1086 @@
+{
+ "base_commit": "fc5c4d103c134cee549a76e8c71addcf8c322e09",
+ "scope": [
+ "kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml",
+ "kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml",
+ "kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml",
+ "kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch118.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/focused.log",
+ "log_sha256": "679bcd3315d09198ad3a7a5b4f9a195c73ce67f11bea4bf2c1c849e8b0e0cc0b",
+ "output_tail": "............ [100%]\n12 passed in 2.66s\n"
+ },
+ {
+ "check": "Viili_Fungus_Bacterium_EPS_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Viili_Fungus_Bacterium_EPS_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Viili_Fungus_Bacterium_EPS_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch118/Viili_Fungus_Bacterium_EPS_SynCom-strict.tsv",
+ "kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Viili_Fungus_Bacterium_EPS_SynCom-strict.log",
+ "log_sha256": "c0ce5e378285eae54f8af7f1418a5ef07df3e2cccbe0619f9dfc6da0f9ad22ee",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch118/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-batch118/Viili_Fungus_Bacterium_EPS_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Viili_Fungus_Bacterium_EPS_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Viili_Fungus_Bacterium_EPS_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Viili_Fungus_Bacterium_EPS_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Viili_Fungus_Bacterium_EPS_SynCom-references.log",
+ "log_sha256": "c04247bd9d710965257a22b34cfa9da677d88ec30c3e285439ee9c59222d5966",
+ "output_tail": "Validating kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.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/Viili_Fungus_Bacterium_EPS_SynCom.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": "Viili_Fungus_Bacterium_EPS_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Viili_Fungus_Bacterium_EPS_SynCom-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": "Viili_Fungus_Bacterium_EPS_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Viili_Fungus_Bacterium_EPS_SynCom-rank.log",
+ "log_sha256": "b074a65d94cad78b339668f4d6f0a85ab4ff1d238788fe81260e0eb06fd73b1a",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000408\",\n \"name\": \"Viili Fungus-Bacterium EPS SynCom\",\n \"score\": 93.3,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\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 \"interaction_type\"\n ],\n \"path\": \"kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Viili_Fungus_Bacterium_EPS_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Viili_Fungus_Bacterium_EPS_SynCom/2026-10-08T124721Z-codex-2774fb.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Viili_Fungus_Bacterium_EPS_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch118/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-strict.tsv",
+ "kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-strict.log",
+ "log_sha256": "48489e6b40e38974f6e5c9f60b68a3a955f29056591c0b0a925239d720c5fb5a",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch118/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-batch118/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-strict.tsv\n"
+ },
+ {
+ "check": "Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-references.log",
+ "log_sha256": "3b627ee93b110912af87405c87da8f969456bbe0d90aaf7f5e2291444f436a13",
+ "output_tail": "Validating kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.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/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.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": "Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-snippets.log",
+ "log_sha256": "8084678f5cf248d78dd90bd74538a6320ef0dcc9940ae3e5b5f759e13588ade6",
+ "output_tail": "# 19 evidence snippets scanned across 1 files\n MATCH 19\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": "Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-rank.log",
+ "log_sha256": "cdd31bf6b4d1f4e241cb8ccbeb7fa6fcc3cac95e36b825e3fa679f0a29c97aa5",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000328\",\n \"name\": \"Waste-Sludge Electro-Fermentation Biofilm-Suspension Community\",\n \"score\": 92.5,\n \"taxonomy\": 5,\n \"connected_taxa\": 5,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community/2026-10-08T124721Z-codex-ba3224.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Watermelon_Rhizosphere_Fusarium_SynCom8-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Watermelon_Rhizosphere_Fusarium_SynCom8-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Watermelon_Rhizosphere_Fusarium_SynCom8-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch118/Watermelon_Rhizosphere_Fusarium_SynCom8-strict.tsv",
+ "kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Watermelon_Rhizosphere_Fusarium_SynCom8-strict.log",
+ "log_sha256": "e7af10569b9416c3749b74bb4a0b1a3d4a4a40c70836a505442e8b2ad6cf5a90",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch118/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-batch118/Watermelon_Rhizosphere_Fusarium_SynCom8-strict.tsv\n"
+ },
+ {
+ "check": "Watermelon_Rhizosphere_Fusarium_SynCom8-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Watermelon_Rhizosphere_Fusarium_SynCom8-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Watermelon_Rhizosphere_Fusarium_SynCom8-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Watermelon_Rhizosphere_Fusarium_SynCom8-references.log",
+ "log_sha256": "2d84107f0d499f442abc2e64029ec067215ee538e547307e7fbcb16c019ccfb2",
+ "output_tail": "Validating kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.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/Watermelon_Rhizosphere_Fusarium_SynCom8.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": "Watermelon_Rhizosphere_Fusarium_SynCom8-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Watermelon_Rhizosphere_Fusarium_SynCom8-snippets.log",
+ "log_sha256": "826e9c1ef5038bfe5995c8f56b27f9f6d8418cb9a40f124b1547f2d75876c305",
+ "output_tail": "# 15 evidence snippets scanned across 1 files\n MATCH 15\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": "Watermelon_Rhizosphere_Fusarium_SynCom8-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Watermelon_Rhizosphere_Fusarium_SynCom8-rank.log",
+ "log_sha256": "81bdfa4ffd4afe421229bea3274eaecdfce3396cbd5a08db06231c7a40742b1f",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000098\",\n \"name\": \"Watermelon Rhizosphere Fusarium-Protective SynCom8\",\n \"score\": 60.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 5,\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/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Watermelon_Rhizosphere_Fusarium_SynCom8-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Watermelon_Rhizosphere_Fusarium_SynCom8/2026-10-08T124721Z-codex-4fbc8e.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Watermelon_Rhizosphere_Fusarium_SynCom8-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch118/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-strict.tsv",
+ "kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-strict.log",
+ "log_sha256": "82258ac02a8afafacc280cea55156c0ad98bfbe7ebca88e177fc0e74ec15fe44",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch118/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-batch118/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-strict.tsv\n"
+ },
+ {
+ "check": "Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-references.log",
+ "log_sha256": "e5cd58434da9a72a068386947978efc52e7949de7c2794f33e5c3f5a7dedfff8",
+ "output_tail": "Validating kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.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/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.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": "Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-snippets.log",
+ "log_sha256": "6f2de9fb4d8c177ffbcd0ad88a37a36fb65a242f256bee6a97070647234944fe",
+ "output_tail": "# 33 evidence snippets scanned across 1 files\n MATCH 33\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": "Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-rank.log",
+ "log_sha256": "14523fa43f9fd0a51dceb373f16aec8d358acae27e5292b19789d0dc9ff46b99",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000255\",\n \"name\": \"Wetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\",\n \"score\": 68.3,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community/2026-10-08T124721Z-codex-37eb64.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community-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-batch118/verification/inventory.log",
+ "log_sha256": "daf14522f0e6fb077f1ff754068c6ef21165ae75c87c0b97c22157883a375589",
+ "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\": 1378,\n \"edges\": 531,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 189,\n \"review_status_counts\": {\n \"needs_research\": 54,\n \"pending\": 26,\n \"reviewed\": 380\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-batch118/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-batch118/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-batch118/verification/rank-all.log",
+ "log_sha256": "8e25bb1f6265c3922fddfcb336ed79d5508c26466483274a6a80403ed26aae67",
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Mutualism\t2\t2\t0\t3\t2\t3\t\t0\t0\n427\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\n428\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\n429\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\n430\t100.0\tkb/communities/DVM_Triculture.yaml\tCommunityMech:000021\tDVM Tri-culture\t3\t3\t0\t4\t2\t7\t\t0\t0\n431\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\n432\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\n433\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\n434\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\n435\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\n436\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\n437\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\n438\t100.0\tkb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml\tCommunityMech:000156\tNeocallimastix-Methanobrevibacter Xylanolytic Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n439\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\n440\t100.0\tkb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\tCommunityMech:000052\tPelotomaculum-Methanothermobacter Syntrophic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n441\t100.0\tkb/communities/Phenol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n442\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\n443\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\n444\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\n445\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\n446\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\n447\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n448\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n449\t100.0\tkb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\tCommunityMech:000100\tTeosinte-Derived Maize Biofertilizer SynCom7\t4\t4\t0\t6\t2\t12\t\t0\t0\n450\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\n451\t100.0\tkb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\tCommunityMech:000282\tThermophilic Lignocellulose-degrading Composting SynCom\t5\t5\t0\t3\t2\t3\t\t0\t0\n452\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n453\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n454\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\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\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\n457\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\n458\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\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\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-batch118/verification/render.log",
+ "log_sha256": "5bb66b7921fc5e4555bd35a26467ad1027ccaacf1e8aec5a5d4a7b2575385490",
+ "output_tail": "unitymech-causal-batch118/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch118/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch118/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch118/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-batch118/verification/render-repeat.log",
+ "log_sha256": "5bb66b7921fc5e4555bd35a26467ad1027ccaacf1e8aec5a5d4a7b2575385490",
+ "output_tail": "unitymech-causal-batch118/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 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Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch118/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch118/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch118/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch118/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-batch118/verification/connectivity-survey.log",
+ "log_sha256": "a59f8529f4058a2e35945f1f0e355a54efe97b952ed333bf6d5b925f3ab050cb",
+ "output_tail": "{\"records\": 460, \"with_community_level\": 414, \"mixed\": 136, \"community_level_only\": 278, \"taxa\": 1568, \"credited_solely_by_the_rule\": 1280}\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_batch12.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-batch118/verification/regressions.log",
+ "log_sha256": "d4b35c09ff9df10720b478330918ab9583b212fc1e33f91c277481686eb95979",
+ "output_tail": "........................................................................ [ 6%]\n........................................................................ [ 13%]\n........................................................................ [ 19%]\n........................................................................ [ 26%]\n........................................................................ [ 32%]\n........................................................................ [ 39%]\n........................................................................ [ 45%]\n........................................................................ [ 52%]\n........................................................................ [ 58%]\n........................................................................ [ 65%]\n........................................................................ [ 71%]\n........................................................................ [ 78%]\n........................................................................ [ 85%]\n........................................................................ [ 91%]\n........................................................................ [ 98%]\n..................... [100%]\n1101 passed in 379.68s (0:06:19)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch118/verification/just-lint.log",
+ "log_sha256": "0e47922f9ae779fb98cd0c1b939de8923e9bd55bcaf3d2f9ea9c983facf01820",
+ "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\n371 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-batch118/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-batch118/verification/audit-snippets-all.log",
+ "log_sha256": "c03c191dfb368c34c9f3aff15d286edb9b633e915a05a1484540d8f855c9695f",
+ "output_tail": "# 9035 evidence snippets scanned across 460 files\n MATCH 8890\n RENDERING 28\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-batch118/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects. Whole four records and all13existing nodes/eight arrows reviewed; retain12nodes/four arrows,remove one misassigned node/four unsupported arrows,rename four nodes,no new topology.",
+ "Fresh EuropePMC abstracts and Crossref identities checked for all four. Watermelon and wetland complete main-body XML text including methods/results/discussion,table text and captions read. No original figure pixels,separate supplementary files,raw data or wetland model code audited. Snippet matching does not establish entailment.",
+ "Viili and sludge repairs are abstract-bounded. DOI/publisher search yielded accessible abstracts; no open full text was inspected. No exhaustive absence claim,access bypass,publication-body import or cache change.",
+ "Viili retains experimental nutrient provision and AI-2 perturbation support; nitrogen-to-signaling mediation remains PARTIAL and regulation is not nutrient transfer. Prior tested-combination EPS and no-EPS-as-nitrogen fixes1014/1015 preserved.",
+ "Sludge compartment roles remain representative enrichments. EET arrows retain partial least squares model support without route-specific intervention or thermodynamic-dependency claims. Scientific observations are not discarded because causal mediation is inferred.",
+ "Watermelon retains seven positive spent-medium effects and three mutually beneficial pairs,not seven mutualisms. SSC8 growth assay used no added pathogen. Parent16-member disease/biofilm results are not SSC8 outcomes; candidate metabolites are not specific causal mediators or stereochemically resolved exchange. Missing SSC8 roster/non-graph fields remain issue1919.",
+ "Wetland measured gas effects remain; marker proteins/fitted fluxes are not pathway-resolved direct flux measurements. Removed arrows confused shared exposure with succession. Results/discussion contain differences about additivity and oxygen-linked routes; no silent resolution or universal-zero methane claim. Non-graph vessel/ingredient evidence issues remain1920.",
+ "Fresh all-state1154issue titles/bodies searched initially; pre-creation receipt records fresh count. Matching1452/1014/1015/644 bodies read and distinct. Hidden/ignored-inclusive local search found135paths excluding.git,docs,site,references_cache,.env; not a historical PR-comment audit.",
+ "Four guarded writes preserve unrelated raw YAML blocks,456otherrecords,923caches,all prior histories/decisions. Four append-only record histories and four curation events. Canonical taxon identities unchanged. Existing shared evidence aliases detached before graph editing.",
+ "Existing-graph repair with no new nodes/directions: no Edison run,provider submission or credit spend. Prior authorized Ruegeria1883 authentication blocker not retried without state change; no credential inspected. Self-adversarial review is not independent approval. Overall review,protected merge and branch deletion remain incomplete."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml": {
+ "MATCH": 17,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml": {
+ "MATCH": 19,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml": {
+ "MATCH": 15,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml": {
+ "MATCH": 33,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 61,
+ "cache_changes": [],
+ "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": {
+ "/private/tmp/communitymech-batch118/baseline.json": "9620412b06bcabd8fcfed3e1cb24dbbf534c133cd06b01d5d637b579f7536abc",
+ "/private/tmp/communitymech-batch118/issue-dedup-current.json": "cb64ae4e68d3b6a2f830d0f30decabc51b96c8bff83445011742aca48acd0edd",
+ "/private/tmp/communitymech-batch118/local-matches.txt": "6588099442855b7c4098c1272366a687a8ef929fcac9a6b2521b22fe1a5ad031",
+ "/private/tmp/communitymech-batch118/primary-manifest.json": "3b7a17c777014bcb9150e2084a0ddb8d996a68fe0df8da036ae43d3f385ef829",
+ "/private/tmp/communitymech-batch118/sludge-abstract.txt": "6a16c574c85afaf974c421b4cb2d8705931f7877e5083a59a960f04bcb292f8a",
+ "/private/tmp/communitymech-batch118/sludge-crossref.json": "e17ff78a6c4acf67bc8a9647a4ea70781b3fd6d9f5d1647c32d0b71502b17cc9",
+ "/private/tmp/communitymech-batch118/sludge-metadata.json": "83332357b1ecd87b0306b675a368528b3904527816a22ab9dcab92730cf8be83",
+ "/private/tmp/communitymech-batch118/target-baseline.json": "426cf11cd4065e267e571253dd5803ddf339fb9d68012cad00771b383799a44b",
+ "/private/tmp/communitymech-batch118/viili-abstract.txt": "b8462e1f1f1831441fa864bb7fc804b90168550918dd52d0e160f8e272d3edd1",
+ "/private/tmp/communitymech-batch118/viili-crossref.json": "a8eff9c7cc801281753dd153623f2bcf68b9719257224a739fe2321d9be9167c",
+ "/private/tmp/communitymech-batch118/viili-metadata.json": "acdb72012f55b553c20984e007d5e71e8aaf6e73da7ac525ed70fdff2508b4d6",
+ "/private/tmp/communitymech-batch118/watermelon-abstract.txt": "96026e62476a4d0ffd0fe8e78601d5026122a54e40c1c9153dea5c958cbda9cc",
+ "/private/tmp/communitymech-batch118/watermelon-crossref.json": "0581a1fdf05c19e5f4a3bc037e397116d4e92c4d5cde814433c4d5ca3ae3c148",
+ "/private/tmp/communitymech-batch118/watermelon-metadata.json": "829cfe50b9b3ac7e7ca453efdac4f63b283d82deeef018efa4b63f270ad54444",
+ "/private/tmp/communitymech-batch118/watermelon-primary.txt": "519833278eff9c75c153b8487c379494faac74c871f28116d9df61dd809ce721",
+ "/private/tmp/communitymech-batch118/watermelon-primary.xml": "0235927bbc7f4943fc5b585dd0afd1ba162f8e51c3af53e62d69d1adf6afd83d",
+ "/private/tmp/communitymech-batch118/wetland-abstract.txt": "df38817b6a2a96587633c61b2844a878beea2e6587aca131b4e8f20b34680efd",
+ "/private/tmp/communitymech-batch118/wetland-crossref.json": "18ccd7589ee46358bf3acc4439a7347f13162545d83bd1a3956eb1dc2f293185",
+ "/private/tmp/communitymech-batch118/wetland-metadata.json": "3a3c821cc7256ebf6a8b3e1c9299e321289a733407155e86a1fec35e66059d19",
+ "/private/tmp/communitymech-batch118/wetland-primary.txt": "684fb73348e88b42163d37afd485ee5254a5bfbff2d2a6762658422f57e3faf4",
+ "/private/tmp/communitymech-batch118/wetland-primary.xml": "08b3674b2a30714f73df5df3d8d280cbf67730d8985b66ac9bcee1fb7347fa5b",
+ "references_cache/PMID_38840214.txt": "a9bbb013a7e798817ce3f0a64abda0e8d65f0ffc1b5fb911105fb4ec45e8520c",
+ "references_cache/PMID_38961111.md": "4352a8ca392e792add0ecbc56ed741fa218649586a50ddba0edd5f1825ed817d",
+ "references_cache/PMID_41793807.txt": "a8444983607f3ced9a27234967d54bad090cc85dfa55e41348c362db0df7b1d7",
+ "references_cache/PMID_42372608.txt": "a7cfafffb15cd457db550238df6882108acee90e1be2d754a129c774fb584d8f"
+ },
+ "immutable_prior_history_and_decision_files": 879,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 25,
+ "discussion_quotations": 4,
+ "fresh_primary_literal_matches": 29,
+ "all_cached_literal_matches": 29,
+ "retained_nodes": 12,
+ "removed_nodes": 1,
+ "renamed_nodes": 4,
+ "retained_arrows": 4,
+ "removed_arrows": 4,
+ "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": 1364,
+ "arrows": 523
+ },
+ "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": 1280
+ },
+ "delta_from_batch117": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "explanation": "Two explicit participant-list users added for sludge and wetland guild roles;298total. The existing scope census is unchanged because all records retain community-level scope. Sole-credit does not certify 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": 9035,
+ "categories": {
+ "MATCH": 8890,
+ "RENDERING": 28,
+ "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": 1378,
+ "edges": 531,
+ "records_without_nodes": 10,
+ "records_without_edges": 189,
+ "review_status_counts": {
+ "needs_research": 54,
+ "pending": 26,
+ "reviewed": 380
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml": "7e901fb9fa8882cead15b1bb895f7108e285b7b80dbbe3bf6ce089d4f2ea88f6",
+ "tests/test_causal_review_batch118.py": "aa5608897c5eaecc64b78ee158357124603e07b2e46d98e9f03c5f4bb9ff6297",
+ "tests/test_participating_taxa.py": "6cb1226981cf15eb2f1fd74e15bbf1365fb2b162ea28fbfc94504dbfa33f6b11",
+ "tests/test_community_level_connectivity_credit.py": "996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a",
+ "tests/test_causal_review_batch109.py": "921f9541c07a8251b4f813fb9b6fd29945f78cc74dc10e61b68dc1978b90daa1",
+ "tests/test_datamodel.py": "f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25",
+ "reports/causal_graph_review/cache-provenance-20261008-batch118.json": "36984968b7b432e92261a2e616e14628311118015432dc64056ee1489bcaf553",
+ "kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml": "b39ce1ba60102209db112c70cc7f1a64b16e8b1f889cecdaff6d3e2d3f149c02",
+ "kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml": "96790620c4f70dd5ca498af0636db53fc9fb7d6779a96851bb31385b71c6f329",
+ "kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml": "4eda48481991d8d22dad2d32ec24284d8580ba33e540377b8f5509bced74c31b",
+ "kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml": "0703409d520c9c561d99c075761f37adff7ca856e14b3d438df2080e975e1e1a"
+ },
+ "pre_research_baseline": {
+ "base_commit": "fc5c4d103c134cee549a76e8c71addcf8c322e09",
+ "base_tree": "497842ab64399d377c2737def4e0d93516085f99",
+ "research_worktree": "/private/tmp/communitymech-causal-batch118",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch118/baseline-rank.log",
+ "sha256": "6bc3a3ae2c6d03230c41a53406b367dcd1df071a76ff03d14324c529173b276b"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch118/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-batch118/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-batch118/baseline-downstream.log",
+ "sha256": "dc16964394ed9a9040380142410fdf0a13a3950288670413d7f959803526618d"
+ }
+ ],
+ "baseline_sha256": "9620412b06bcabd8fcfed3e1cb24dbbf534c133cd06b01d5d637b579f7536abc"
+ },
+ "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_batch118.py b/tests/test_causal_review_batch118.py
new file mode 100644
index 000000000..d1e92c4dc
--- /dev/null
+++ b/tests/test_causal_review_batch118.py
@@ -0,0 +1,170 @@
+"""Keep treatment identity and inferential limits in four reviewed causal 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-batch118.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / row["path"]).read_text()) for row in rows]
+
+
+def test_viili_retains_validated_nitrogen_and_tested_eps_maximum():
+ _, _, docs = records()
+ nitrogen, _, outcome = docs[0]["ecological_interactions"]
+ assert nitrogen["interaction_type"] == "CROSS_FEEDING"
+ assert "depletion/supplementation" in nitrogen["description"]
+ assert "independent of growth" in nitrogen["description"]
+ assert {m["term"]["id"] for m in nitrogen["metabolites"]} == {
+ "CHEBI:27266",
+ "CHEBI:33709",
+ }
+ assert "among all tested microbial combinations" in outcome["evidence"][0]["snippet"]
+ assert len(outcome["participating_taxa"]) == 3
+
+
+def test_viili_ai2_regulation_is_not_fungal_nutrient_transfer():
+ _, _, docs = records()
+ signal = docs[0]["ecological_interactions"][1]
+ assert "interaction_type" not in signal
+ assert "not evidence that G. candidum supplies AI-2" in signal["description"]
+ assert signal["evidence"][1]["supports"] == "SUPPORT"
+ assert "activation and inhibition" in signal["evidence"][1]["snippet"]
+ assert signal["evidence"][2]["supports"] == "PARTIAL"
+
+
+def test_viili_signaling_bridge_is_partial_but_eps_regulation_is_supported():
+ _, _, docs = records()
+ nitrogen, signal, outcome = docs[0]["ecological_interactions"]
+ assert nitrogen["downstream"][0]["target"] == signal["name"]
+ assert nitrogen["downstream"][0]["description"].startswith("PARTIAL:")
+ assert "growth effects" in nitrogen["downstream"][0]["description"]
+ assert signal["downstream"][0]["target"] == outcome["name"]
+ assert "positive regulation" in signal["downstream"][0]["description"]
+ assert "sole explanation" in signal["downstream"][0]["description"]
+
+
+def test_sludge_fraction_participants_are_not_all_five_genera():
+ _, _, docs = records()
+ division, biofilm, suspension, _ = docs[1]["ecological_interactions"]
+ assert division["interaction_type"] == "NICHE_PARTITIONING"
+ assert "not an exhaustive membership" in division["description"]
+ assert [t["preferred_term"] for t in biofilm["participating_taxa"]] == [
+ "Syntrophomonas",
+ "Geobacter",
+ "Hydrogenophaga",
+ ]
+ assert [t["preferred_term"] for t in suspension["participating_taxa"]] == [
+ "Sedimentibacter",
+ "Petrimonas",
+ ]
+ assert "interaction_type" not in biofilm and "interaction_type" not in suspension
+
+
+def test_sludge_eet_model_is_not_a_route_resolved_intervention():
+ _, _, docs = records()
+ model = docs[1]["ecological_interactions"][3]
+ assert "interaction_type" not in model
+ assert model["description"].startswith("PARTIAL:")
+ assert "interruption/rescue" in model["description"]
+ assert model["evidence"][0]["evidence_source"] == "COMPUTATIONAL"
+ assert model["evidence"][0]["supports"] == "PARTIAL"
+ assert "Partial least squares path modeling" in model["evidence"][0]["snippet"]
+ assert len(model["downstream"]) == 2
+ assert all(e["description"].startswith("PARTIAL:") for e in model["downstream"])
+
+
+def test_watermelon_seven_positive_partners_are_not_seven_mutualisms():
+ _, _, docs = records()
+ facilitation = docs[2]["ecological_interactions"][0]
+ assert facilitation["interaction_type"] == "CROSS_FEEDING"
+ assert "only three" in facilitation["description"]
+ assert "seven strains enhanced" in facilitation["evidence"][0]["snippet"]
+ assert "three strains engaged in mutualistic interactions" in (
+ facilitation["evidence"][1]["snippet"]
+ )
+
+
+def test_watermelon_candidates_do_not_establish_specific_metabolite_transfer():
+ _, _, docs = records()
+ facilitation = docs[2]["ecological_interactions"][0]
+ assert "metabolites" not in facilitation and "biological_processes" not in facilitation
+ assert "not compound-specific rescue" in facilitation["description"]
+ assert "resolved stereochemistry" in facilitation["description"]
+ assert facilitation["evidence"][2]["supports"] == "PARTIAL"
+
+
+def test_ssc8_growth_does_not_inherit_parent_pathogen_challenge():
+ _, _, docs = records()
+ outcome = docs[2]["ecological_interactions"][1]
+ assert outcome["name"] == "SSC8 watermelon growth promotion without added pathogen"
+ assert "interaction_type" not in outcome and "biological_processes" not in outcome
+ assert "must not be assigned to SSC8" in outcome["description"]
+ assert "no added pathogen" in outcome["description"]
+ assert "none of the treatments" in outcome["evidence"][0]["snippet"]
+ assert "comparable to the initial SynCom" in outcome["evidence"][1]["snippet"]
+
+
+def test_ssc8_has_no_parent_biofilm_node_or_cross_experiment_arrows():
+ _, rows, docs = records()
+ nodes = docs[2]["ecological_interactions"]
+ assert len(nodes) == 2 and not any(n.get("downstream") for n in nodes)
+ assert len(rows[2]["removed_node_decisions"]) == 1
+ assert len(rows[2]["removed_edge_decisions"]) == 2
+ assert "Pseudomonas Biofilm Pathway Enrichment" not in [n["name"] for n in nodes]
+
+
+def test_wetland_treatment_responses_are_not_causes_of_fitted_subnetwork():
+ _, rows, docs = records()
+ sulfate, oxygen, _ = docs[3]["ecological_interactions"]
+ assert not sulfate.get("downstream") and not oxygen.get("downstream")
+ assert len(rows[3]["removed_edge_decisions"]) == 2
+ assert sulfate["interaction_type"] == "COMPETITION"
+ assert sulfate["evidence"][0]["supports"] == "SUPPORT"
+ assert sulfate["evidence"][1]["evidence_source"] == "COMPUTATIONAL"
+ assert sulfate["evidence"][1]["supports"] == "PARTIAL"
+ assert "direct acetate competition" in sulfate["description"]
+ assert "interaction_type" not in oxygen
+ assert "residual methane" in oxygen["description"]
+
+
+def test_wetland_model_is_not_directly_measured_cross_feeding():
+ _, _, docs = records()
+ model = docs[3]["ecological_interactions"][2]
+ assert "interaction_type" not in model
+ assert "nine-reaction" in model["description"]
+ assert "not directly measured interspecies transfer" in model["description"]
+ assert "not evidence of universally enhanced sulfate reduction" in model["description"]
+ assert all(e["supports"] == "PARTIAL" for e in model["evidence"])
+ assert [t["preferred_term"] for t in model["participating_taxa"]] == [
+ "wetland soil bacterial guilds"
+ ]
+
+
+def test_review_accounts_for_every_node_arrow_and_unchanged_cache():
+ ledger, rows, docs = records()
+ counts = ledger["reviewed_counts"]
+ assert counts["original_nodes"] == 13 and counts["retained_nodes"] == 12
+ assert counts["removed_nodes"] == 1 and counts["renamed_nodes"] == 4
+ assert counts["original_arrows"] == 8 and counts["retained_arrows"] == 4
+ assert counts["removed_arrows"] == 4
+ assert counts["graph_quotations"] == 25 and counts["discussion_quotations"] == 4
+ assert ledger["cache_changes"] == [] and not ledger["independent_approval"]
+ assert ledger["edison"]["new_nodes_or_directions"] == 0
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == (
+ row["record_sha256"]
+ )
+ names = [n["name"] for n in doc["ecological_interactions"]]
+ assert [r["node"] for r in row["node_decisions"]] == names
+ assert len(row["history_files"]) == 1
+ assert doc["curation_history"][-1]["llm_assisted"]
+ for node in doc["ecological_interactions"]:
+ assert "downstream" not in node or node["downstream"]
+ assert all(e["target"] in names for e in node.get("downstream", []))
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index cdd267428..50bb905ed 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -452,6 +452,8 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml",
"Urine_Nitrification_SynCom.yaml",
"Viili_Fungus_Bacterium_EPS_SynCom.yaml",
+ "Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml",
+ "Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml",
"Wheat_Consortium_C1.yaml",
"Wheat_Consortium_C6.yaml",
"Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml",