diff --git a/docs/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.html b/docs/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.html
index 775f57381..859e48de9 100644
--- a/docs/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.html
+++ b/docs/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.html
@@ -611,7 +611,7 @@ Ecological Interactions
Ecological interaction network for KB-1 Chlorinated Ethene Dechlorinating Consortium
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, syntrophy).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -619,13 +619,8 @@
Ecological Interactions
-
-
@@ -634,14 +629,21 @@ Ecological Interactions
-
Dehalococcoides-related organisms in KB-1 use chlorinated ethenes as electron acceptors under anaerobic conditions, driving sequential reductive dechlorination of PCE and TCE to ethene in laboratory microcosms and field groundwater.
+
KB-1 bioaugmentation produced ethene in laboratory microcosms and the Kelly Air Force Base field test. Field ethene accounted for chlorinated-ethene mass loss and KB-1-associated Dehalococcoides spread downgradient. These are consortium outcomes, not assignment of every PCE/TCE reaction to Dehalococcoides. Separate vitamin-free KB-1 enrichment experiments also sustained TCE-to-ethene conversion. The canonical taxa are a community subset, not a proven three-member inoculant or reciprocal syntrophy.
-
Source Taxon: Dehalococcoides spp. in KB-1
+
Participating Taxa:
+
+ Dehalococcoides spp. in KB-1,
+
+ Acetobacterium spp. in KB-1,
+
+ Sporomusa spp. in KB-1
+
+
@@ -696,6 +698,19 @@
Evidence
+
+
+
+ "Acetobacterium supports complete TCE dechlorination by Dehalococcoides"
+
+
+
Evidence
-
Acetobacterium and Sporomusa provide a supporting acetogenic guild in KB-1. Acetobacterium can synthesize the cobalamin lower ligand DMB, supporting Dehalococcoides dechlorination in vitamin-free medium and highlighting a cofactor-mediated syntrophic dependency.
+
Vitamin-free KB-1 transfers sustained TCE dechlorination with increased Acetobacterium abundance and cobalamin, supported by a DMB-biosynthesis operon. These positive community experiments support Acetobacterium-associated cofactor provision. PARTIAL - donor-resolved transfer, exclusive mediation and the return benefit remain unresolved. The canonical Acetobacterium woodii label is not verified as the source population Acetobacterium sp. KB-1; its grounding remains #1526. Acid inhibition is distinct from cofactor shortage: DMB did not rescue stalled low-pH dechlorination, whereas pH adjustment did.
+
-
Source Taxon: Acetobacterium spp. in KB-1
+
Participating Taxa:
+ Dehalococcoides spp. in KB-1,
-
Target Taxon: Dehalococcoides spp. in KB-1
+ Acetobacterium spp. in KB-1
+
+
@@ -744,7 +762,7 @@
Acetogen Cobamide Support
→ Reductive Dechlorination to Ethene
-
Acetogen-derived cobalamin support supplies the cofactor context required for complete Dehalococcoides reductive dechlorination in KB-1 without exogenous vitamins.
+
PARTIAL - Acetobacterium-associated cofactor availability can support Dehalococcoides dechlorination in the vitamin-free KB-1 laboratory cultures. Community transfers, cofactor measurements and biosynthetic genes support this route, but do not isolate its exclusive contribution or establish its mediation of the separate field bioaugmentation result.
Evidence
- SUPPORT (IN_VITRO)
- "the lower ligand of cobalamin, and Sporomusa are dominant acetogens"
+ "Acetobacterium supports complete TCE dechlorination by Dehalococcoides"
@@ -787,16 +805,17 @@ Evidence
-
Sporomusa is a dominant acetogen in vitamin-free KB-1 cultures. A Sporomusa sp. strain KB-1 isolate was also tested as a Dehalococcoides partner population; its phenolic cobamides did not by themselves satisfy Dehalococcoides corrinoid requirements, but DMB amendment guided cobalamin biosynthesis in Sporomusa sp. cocultures and supported Dehalococcoides reductive dechlorination activity and growth.
+
Controlled cocultures tested a Sporomusa sp. KB-1 isolate with Dehalococcoides strains BAV1, GT and FL2. DMB amendment changed donor cobamide chemistry and restored partner dechlorination and growth; without DMB, the phenolic cofactors did not support those requirements. FL2 still produced both VC and ethene. The explicit canonical participant is the KB-1-derived donor only: these external recipient strains are not established as the record's KB-1 Dehalococcoides population. This positive conditional partner-support result is not demonstrated mediation of the field endpoint.
+
-
Source Taxon: Sporomusa spp. in KB-1
+
Participating Taxa:
+ Sporomusa spp. in KB-1
-
Target Taxon: Dehalococcoides spp. in KB-1
+
@@ -823,26 +842,10 @@
Sporomusa DMB-Guided Cobalamin Support
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006766)
-
- cobalamin transport
- (GO:0015889 )
-
-
-
-
Downstream Effects:
-
-
-
→ Reductive Dechlorination to Ethene
-
DMB-guided cobalamin support can supply the corrinoid cofactor context required for Dehalococcoides reductive dechlorination.
-
-
-
-
Evidence
@@ -896,6 +899,25 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which same-system cofactor routes mediate KB-1 dechlorination?
+
+
Keep the positive field outcome, vitamin-free community support and controlled donor chemistry/partner phenotypes distinct. Remove the Sporomusa-to-KB-1-outcome arrow because external recipient strains were not identified as the KB-1 population. The Acetobacterium route remains PARTIAL for exact transfer and field mediation. Canonical taxonomy and non-graph blocks are preserved, not recertified; #1526 tracks Acetobacterium identity. Full 2013/2019 primary main texts read; 2019 selected tables/figures inspected, 2002 field abstract only. No separate supplements/raw-data audit or new graph structure.
+
+
Attaches to: ecological_interactions#Reductive Dechlorination to Ethene, ecological_interactions#Acetogen Cobamide Support, ecological_interactions#Sporomusa DMB-Guided Cobalamin Support
+
+
+
+
+
@@ -1155,7 +1177,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1168,7 +1190,7 @@
Evidence
var processes = [];
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1181,18 +1203,28 @@
Evidence
});
- var srcKey = "Dehalococcoides spp. in KB-1";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
+
+ "Dehalococcoides spp. in KB-1",
+
+ "Acetobacterium spp. in KB-1",
+
+ "Sporomusa spp. in KB-1"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1218,23 +1250,26 @@
Evidence
});
- var srcKey = "Acetobacterium spp. in KB-1";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Dehalococcoides spp. in KB-1";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Dehalococcoides spp. in KB-1",
+
+ "Acetobacterium spp. in KB-1"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:2";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1248,8 +1283,6 @@
Evidence
processes.push("vitamin metabolic process");
- processes.push("cobalamin transport");
-
var evidenceCount = 3;
@@ -1264,17 +1297,18 @@
Evidence
});
- var srcKey = "Sporomusa spp. in KB-1";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Dehalococcoides spp. in KB-1";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Sporomusa spp. in KB-1"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/docs/communities/KBase_Models_for_Zahmeeth_Original_PLOS.html b/docs/communities/KBase_Models_for_Zahmeeth_Original_PLOS.html
index 77ed36ac6..dfe68e90f 100644
--- a/docs/communities/KBase_Models_for_Zahmeeth_Original_PLOS.html
+++ b/docs/communities/KBase_Models_for_Zahmeeth_Original_PLOS.html
@@ -642,7 +642,7 @@
Ecological Interactions
Ecological interaction network for KBase Models for Zahmeeth Original PLOS
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, mutualism, niche partitioning).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -650,18 +650,8 @@
Ecological Interactions
-
-
-
-
Ecological Interactions
-
The Zahmeeth computational workflow adapted Run Flux Mutual Information Analysis to combine molecular communication, Shannon information theory, and metabolic flux analysis for quantifying information flow through modeled microbial community metabolism in bits.
-
-
-
-
-
-
-
-
-
-
Biological Processes:
-
-
-
- interspecies interaction between organisms
- (GO:0044419 )
-
-
-
-
-
-
-
-
Downstream Effects:
-
-
-
→ Idealized Two-Member Community Model Construction
-
The RFMIA framework was applied to idealized two-member microbial communities represented by genome-scale metabolic models.
-
-
-
-
-
-
-
-
Evidence
-
-
-
-
-
The RFMIA analysis was instantiated on idealized two-member communities, including Escherichia coli with Pseudomonas fluorescens and Bacteroides thetaiotaomicron with Klebsiella, allowing modeled community flux behavior to be compared with isolate behavior.
-
-
-
+
Mixed-bag models generally had higher mutual-information scores than compartmentalized models. The authors attribute this to pooling reactions without intermember transport constraints; this is a model-architecture interpretation, not observed niche partitioning or a selectively validated biological transport mechanism. Methods/Results identify E. coli iML1515 and B. theta iAH991; the abstract names different pairs. The two canonical participants delimit the modeled comparison, not a four-member consortium; the source/metadata discrepancy remains #1527.
+
Participating Taxa:
+ Escherichia coli,
-
Biological Processes:
-
+ Bacteroides thetaiotaomicron
-
- interspecies interaction between organisms
- (GO:0044419 )
-
+
-
-
-
Downstream Effects:
-
-
→ Mixed-Bag and Compartmentalized GEM Comparison
-
The idealized two-member models supplied the test cases for comparing mixed-bag and compartmentalized community genome-scale model structures.
-
-
-
-
→ In Silico Community-Formation Dependencies
-
The paired idealized communities were also used to identify model dependencies that justified community formation relative to isolate simulations.
-
-
-
-
@@ -787,20 +694,7 @@
Evidence
- SUPPORT (COMPUTATIONAL)
"RFMIA (Run Flux Mutual Information Analysis), was applied to idealized two-member microbial communities"
-
-
-
-
-
-
- "one of E. coli and Pseudomonas fluorescens and another of Bacteroides thetaiotaomicron (B. theta) and Klebsiella"
+ "mixed-bag framework conducts greater information flow than the compartmentalized framework"
@@ -810,75 +704,20 @@ Evidence
-
The workflow compared mixed-bag and compartmentalized genome-scale metabolic modeling frameworks for the same idealized two-member communities, separating model-architecture effects from isolated-community information-flow contrasts.
-
-
-
-
-
-
-
-
-
-
Biological Processes:
-
-
-
- interspecies interaction between organisms
- (GO:0044419 )
-
-
-
-
-
-
-
-
Downstream Effects:
-
-
-
→ Greater Community Information Flow
-
Comparing the alternative GEM frameworks produced the specific result that mixed-bag community models conducted more information flow than compartmentalized ones.
-
-
-
+
Model-Conditional Growth Contrasts
+
Community models grew on dextrin where the E. coli isolate model did not. Aerobic isolated B. theta growth and information flow were manually set to zero, with that constraint lifted in community models; the contrast is not independently predicted partner rescue. Model growth does not establish actual strain growth, resolved cross-feeding, stable community formation or reciprocal benefit. Methods/Results identify E. coli iML1515 and B. theta iAH991; the abstract names different pairs. The two canonical participants delimit the modeled comparison, not a four-member consortium; the source/metadata discrepancy remains #1527.
-
Evidence
-
-
-
-
-
Simulated pairwise communities exposed community-only dependencies, including aerobic B. thetaiotaomicron growth when coupled with E. coli and community dextrin growth in cases where E. coli could not grow as an isolate.
-
+
Participating Taxa:
+ Escherichia coli,
+ Bacteroides thetaiotaomicron
+
@@ -892,29 +731,7 @@
In Silico Community-Formation Dependencies
-
Biological Processes:
-
-
-
- interspecies interaction between organisms
- (GO:0044419 )
-
-
-
-
-
-
-
-
Downstream Effects:
-
-
→ Greater Community Information Flow
-
The modeled dependency examples accompanied the broader finding that two-member community models carried more metabolic information flow than isolate models.
-
-
-
-
@@ -930,20 +747,7 @@
Evidence
- SUPPORT (COMPUTATIONAL)
"Our work reveals dependencies among organisms that justify community formation"
-
-
-
-
-
-
- "including that B. theta only grows in aerobic environments when coupled with E. coli and that community models grew on dextrin despite that E. coli failed to grow as an isolate"
+ "despite that E. coli failed to grow as an isolate"
@@ -954,28 +758,23 @@ Evidence
-
The RFMIA simulations reported higher information flow through the idealized two-member community models than through isolated organism models, tying the KBase model workflows to a quantitative community-level information-flow output.
-
+
RFMIA generally returned higher mutual-information scores for the community models than for isolated models under the tested nutrient combinations. These are computed information-theoretic outputs in bits, not measured molecular communication, a universal growth advantage or mutualism. Methods/Results identify E. coli iML1515 and B. theta iAH991; the abstract names different pairs. The two canonical participants delimit the modeled comparison, not a four-member consortium; the source/metadata discrepancy remains #1527.
+
Participating Taxa:
+ Escherichia coli,
+ Bacteroides thetaiotaomicron
+
+
-
Biological Processes:
-
-
- interspecies interaction between organisms
- (GO:0044419 )
-
-
@@ -1041,6 +840,25 @@
Associated Datasets
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which model-dependent findings persist with verified partners and experimentally tested constraints?
+
+
Remove adaptation/construction nodes and all five procedural or co-occurrence arrows. Keep three existing modeled observations without imposing a new causal chain. Primary full v1 PDF text/captions read and selected Methods, equations, table, architecture and charts visually inspected; no independent mathematical derivation, supplement/code/raw simulation audit or model rerun. Manually imposed aerobic constraints cannot validate partner rescue. #1527 tracks non-graph model/partner metadata and #1528 the mismatching cached abstract. Canonical identifiers and raw non-graph blocks are preserved; no new graph structure.
+
+
Attaches to: ecological_interactions#Model-Architecture-Dependent Information Flow, ecological_interactions#Model-Conditional Growth Contrasts, ecological_interactions#Greater Community Information Flow
+
+
+
+
+
@@ -1204,20 +1022,16 @@ External Resources
(function() {
var intId = "interaction:0";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("interspecies interaction between organisms");
-
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "RFMIA Community Information-Flow Adaptation",
+ label: "Model-Architecture-Dependent Information Flow",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1228,52 +1042,37 @@ External Resources
- })();
-
- (function() {
- var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("interspecies interaction between organisms");
+ var participantKeys = [
+ "Escherichia coli",
- var evidenceCount = 2;
+ "Bacteroides thetaiotaomicron"
- nodes.push({
- id: intId,
- label: "Idealized Two-Member Community Model Construction",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
});
-
-
-
})();
(function() {
- var intId = "interaction:2";
- var intType = "NICHE_PARTITIONING";
+ var intId = "interaction:1";
+ var intType = "UNKNOWN";
var metabolites = [];
- var processes = [];
+ metabolites.push("dextrin");
- processes.push("interspecies interaction between organisms");
+ var processes = [];
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Mixed-Bag and Compartmentalized GEM Comparison",
+ label: "Model-Conditional Growth Contrasts",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1284,51 +1083,28 @@ External Resources
- })();
-
- (function() {
- var intId = "interaction:3";
- var intType = "CROSS_FEEDING";
- var metabolites = [];
-
-
- metabolites.push("dextrin");
-
-
- var processes = [];
-
+ var participantKeys = [
- processes.push("interspecies interaction between organisms");
+ "Escherichia coli",
+ "Bacteroides thetaiotaomicron"
- var evidenceCount = 2;
-
- nodes.push({
- id: intId,
- label: "In Silico Community-Formation Dependencies",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
});
-
-
-
})();
(function() {
- var intId = "interaction:4";
- var intType = "MUTUALISM";
+ var intId = "interaction:2";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("interspecies interaction between organisms");
-
-
var evidenceCount = 1;
nodes.push({
@@ -1344,6 +1120,19 @@ External Resources
+ var participantKeys = [
+
+ "Escherichia coli",
+
+ "Bacteroides thetaiotaomicron"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
@@ -1365,7 +1154,7 @@ External Resources
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 = 9;
+ var nodeCount = 7;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/KBase_ORT_Workflow_Community_Model.html b/docs/communities/KBase_ORT_Workflow_Community_Model.html
index ce19c8bd9..3cdc48f84 100644
--- a/docs/communities/KBase_ORT_Workflow_Community_Model.html
+++ b/docs/communities/KBase_ORT_Workflow_Community_Model.html
@@ -642,7 +642,7 @@ Ecological Interactions
Ecological interaction network for KBase ORT Workflow Community Model
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (syntrophy).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -650,8 +650,8 @@
Ecological Interactions
@@ -659,14 +659,21 @@ Ecological Interactions
-
Ammonia-oxidizing archaea (Nitrososphaeraceae) and nitrite-oxidizing bacteria (Nitrospiraceae) form a coupled nitrification network in Columbia River sediments. The archaeon oxidizes ammonium to nitrite, which is then consumed by Nitrospiraceae to produce nitrate. This syntrophic coupling is fundamental to nitrogen cycling in the sediment microbiome and demonstrates metabolic interdependence between archaeal and bacterial partners. The partnership enables complete nitrification from ammonium to nitrate, feeding nitrate to downstream denitrifiers.
+
The ORT proof-of-concept uses Nitrososphaeraceae and Nitrospiraceae MAG-derived models for ammonium-to-nitrite and nitrite-to-nitrate transformations. Sequential substrate coupling is represented computationally, not experimentally measured partner transfer, obligatory syntrophy or an assembled two-strain culture.
+
Participating Taxa:
+
+ Nitrososphaeraceae archaeon,
+
+ Nitrospiraceae bacterium
+
+
+
Metabolites:
@@ -691,7 +698,7 @@
Coupled Nitrification in Columbia River Sediments
- nitrification
+ ammonia oxidation
(GO:0019329 )
@@ -704,9 +711,8 @@ Coupled Nitrification in Columbia River Sediments
Downstream Effects:
-
→ Nitrate-to-Nitrogen Gas Denitrification
-
Coupled archaeal and bacterial nitrification produces nitrate that feeds the downstream Steroidobacteraceae denitrifiers.
-
+
→ Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+
PARTIAL - sequential modeled nitrification supplies nitrate for modeled denitrification. This is a substrate route in the proof-of-concept simulation, not proof of an exclusive environmental nitrate source, obligatory partner dependence or genome-supported completion to nitrogen gas.
Evidence
- SUPPORT (COMPUTATIONAL)
- "predict nitrogen cycling patterns with site-specific insight into the chemical and biological drivers of nitrification and denitrification processes"
+ "nitrification and denitrification"
@@ -735,14 +741,21 @@ Evidence
-
Two Steroidobacteraceae denitrifiers consume nitrate produced by nitrifying organisms and reduce it through denitrification to nitrogen gas. This terminal step in the nitrogen cycle completes the transformation of fixed nitrogen back to atmospheric N2. The denitrifiers depend on upstream nitrification to provide nitrate substrate, demonstrating sequential metabolic coupling across the community. Genome-scale models also connected the denitrifier reactions to metabolome-derived carbon sources, enabling precise identification of biogeochemical limiting factors.
+
Two Steroidobacteraceae MAG-derived models represent nitrate reduction to dissolved nitrogen. Neither MAG encoded nitrogen-gas production; the N2O-to-N2 reaction was added by gapfilling. The positive simulation output is therefore conditional on model assumptions, not demonstrated complete metabolism of either organism or measured field nitrogen loss. The two canonical denitrifier names remain distinct despite sharing a family identifier.
+
Participating Taxa:
+
+ Steroidobacteraceae denitrifier 1,
+
+ Steroidobacteraceae denitrifier 2
+
+
+
Metabolites:
@@ -753,19 +766,7 @@
Nitrate-to-Nitrogen Gas Denitrification
nitrogen
(
CHEBI:17997 ),
-
- betaine
- (
CHEBI:17750 ),
-
- leucine
- (
CHEBI:15603 ),
-
- choline
- (
CHEBI:15354 )
+ class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17997)
@@ -798,20 +799,7 @@
Evidence
- SUPPORT (COMPUTATIONAL)
"GSMs identified additional carbon sources utilized, enabling more precise identification of the biogeochemical limiting factors in the system"
-
-
-
-
-
-
- "predict nitrogen cycling patterns with site-specific insight into the chemical and biological drivers of nitrification and denitrification processes"
+ "nitrification and denitrification"
@@ -821,13 +809,24 @@ Evidence
-
The ORT site model incorporated additional organic carbon compounds detected in the bulk Columbia River sediment metabolome. This allowed Steroidobacteraceae denitrifier models to use 15-23 unique carbon sources, including glycine betaine, leucine, and choline, instead of restricting denitrification to acetate as in the generalized literature-based model.
+
Site models used 15-23 additional carbon substrates, with betaine, leucine and choline among the examples. Bulk metabolomics informed model media, with some unmeasured necessities assumed nonlimiting. These modeled exchanges add chemical detail; they are not traced member flux or experimentally identified field limitations, and the reported substrate count is not assigned to every denitrifier.
+
+
Participating Taxa:
+
+ Nitrososphaeraceae archaeon,
+
+ Nitrospiraceae bacterium,
+
+ Steroidobacteraceae denitrifier 1,
+
+ Steroidobacteraceae denitrifier 2
+
+
@@ -866,8 +865,8 @@
Metabolome-Informed Carbon Source Utilization
Downstream Effects:
-
→ Nitrate-to-Nitrogen Gas Denitrification
-
Metabolome-derived organic carbon sources constrain the denitrifier reactions that reduce nitrate through the modeled nitrogen cycle.
+
→ Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+
PARTIAL - modeled carbon uptake contributes substrate and stoichiometric context to the denitrification representation. The exchange calculations support this model-level coupling, not selective demonstration that these example compounds control field denitrification or are consumed by both denitrifiers.
Associated Datasets
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which modeled nitrogen and carbon routes are supported by measured organism activity?
+
+
Retain both existing model-level substrate arrows, explicitly PARTIAL for biological validation. Nitrogen-gas completion is gapfilled, and neither denitrifier MAG encoded it. The single-chemistry-input demonstration compares model stoichiometries using common rate assumptions; no high-resolution empirical time series validates its predicted trajectories. Iterative KBase/PFLOTRAN coupling is a proposed capability, not a demonstrated feedback experiment. Full publisher main text/Methods/Table1/captions read; no figure pixels, supplements, code, raw data or narrative execution inspected. #1527 tracks non-graph metadata and #1528 cache provenance; all canonical IDs/labels remain unchanged. No new graph structure.
+
+
Attaches to: ecological_interactions#Modeled Coupled Nitrification, ecological_interactions#Modeled Nitrate Reduction with Gapfilled Nitrogen Production, ecological_interactions#Modeled Metabolome-Informed Carbon Utilization
+
+
+
+
+
@@ -1108,7 +1126,7 @@ External Resources
(function() {
var intId = "interaction:0";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1122,14 +1140,14 @@ External Resources
var processes = [];
- processes.push("nitrification");
+ processes.push("ammonia oxidation");
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Coupled Nitrification in Columbia River Sediments",
+ label: "Modeled Coupled Nitrification",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1140,11 +1158,24 @@ External Resources
+ var participantKeys = [
+
+ "Nitrososphaeraceae archaeon",
+
+ "Nitrospiraceae bacterium"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:1";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1152,12 +1183,6 @@ External Resources
metabolites.push("nitrogen");
- metabolites.push("betaine");
-
- metabolites.push("leucine");
-
- metabolites.push("choline");
-
var processes = [];
@@ -1165,11 +1190,11 @@ External Resources
processes.push("denitrification");
- var evidenceCount = 2;
+ var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Nitrate-to-Nitrogen Gas Denitrification",
+ label: "Modeled Nitrate Reduction with Gapfilled Nitrogen Production",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1180,11 +1205,24 @@ External Resources
+ var participantKeys = [
+
+ "Steroidobacteraceae denitrifier 1",
+
+ "Steroidobacteraceae denitrifier 2"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:2";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1205,7 +1243,7 @@ External Resources
nodes.push({
id: intId,
- label: "Metabolome-Informed Carbon Source Utilization",
+ label: "Modeled Metabolome-Informed Carbon Utilization",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1216,6 +1254,23 @@ External Resources
+ var participantKeys = [
+
+ "Nitrososphaeraceae archaeon",
+
+ "Nitrospiraceae bacterium",
+
+ "Steroidobacteraceae denitrifier 1",
+
+ "Steroidobacteraceae denitrifier 2"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/history/records/KB1_Chlorinated_Ethene_Dechlorinating_Consortium/2026-10-06T182704Z-codex-64a338.yaml b/history/records/KB1_Chlorinated_Ethene_Dechlorinating_Consortium/2026-10-06T182704Z-codex-64a338.yaml
new file mode 100644
index 000000000..0b6bdc16a
--- /dev/null
+++ b/history/records/KB1_Chlorinated_Ethene_Dechlorinating_Consortium/2026-10-06T182704Z-codex-64a338.yaml
@@ -0,0 +1,24 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml
+ slug: KB1_Chlorinated_Ethene_Dechlorinating_Consortium
+session:
+ id: 2026-10-06T182704Z-codex-64a338
+ timestamp: '2026-10-06T18:27:04Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1523
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Separate KB-1 community and field endpoints from external-recipient cofactor experiments.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml
diff --git a/history/records/KBase_Models_for_Zahmeeth_Original_PLOS/2026-10-06T182704Z-codex-1ab001.yaml b/history/records/KBase_Models_for_Zahmeeth_Original_PLOS/2026-10-06T182704Z-codex-1ab001.yaml
new file mode 100644
index 000000000..4d3c99f2b
--- /dev/null
+++ b/history/records/KBase_Models_for_Zahmeeth_Original_PLOS/2026-10-06T182704Z-codex-1ab001.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml
+ slug: KBase_Models_for_Zahmeeth_Original_PLOS
+session:
+ id: 2026-10-06T182704Z-codex-1ab001
+ timestamp: '2026-10-06T18:27:04Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1524
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain model-dependent outputs without workflow causality or imposed-constraint
+ rescue claims.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml
diff --git a/history/records/KBase_ORT_Workflow_Community_Model/2026-10-06T182705Z-codex-10ac84.yaml b/history/records/KBase_ORT_Workflow_Community_Model/2026-10-06T182705Z-codex-10ac84.yaml
new file mode 100644
index 000000000..8da70acb0
--- /dev/null
+++ b/history/records/KBase_ORT_Workflow_Community_Model/2026-10-06T182705Z-codex-10ac84.yaml
@@ -0,0 +1,24 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/KBase_ORT_Workflow_Community_Model.yaml
+ slug: KBase_ORT_Workflow_Community_Model
+session:
+ id: 2026-10-06T182705Z-codex-10ac84
+ timestamp: '2026-10-06T18:27:05Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1525
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Expose ORT gapfilled nitrogen completion and bound modeled substrate routes.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml
diff --git a/kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml b/kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml
index 2204506e6..fbb6732fc 100644
--- a/kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml
+++ b/kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml
@@ -114,16 +114,12 @@ taxonomy:
explanation: Supports Sporomusa as an acetogenic KB-1 member.
ecological_interactions:
- name: Reductive Dechlorination to Ethene
- description: Dehalococcoides-related organisms in KB-1 use chlorinated ethenes as electron acceptors under
- anaerobic conditions, driving sequential reductive dechlorination of PCE and TCE to ethene in laboratory
- microcosms and field groundwater.
- interaction_type: SYNTROPHY
+ description: KB-1 bioaugmentation produced ethene in laboratory microcosms and the Kelly Air Force Base field
+ test. Field ethene accounted for chlorinated-ethene mass loss and KB-1-associated Dehalococcoides spread downgradient.
+ These are consortium outcomes, not assignment of every PCE/TCE reaction to Dehalococcoides. Separate vitamin-free
+ KB-1 enrichment experiments also sustained TCE-to-ethene conversion. The canonical taxa are a community subset,
+ not a proven three-member inoculant or reciprocal syntrophy.
scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: Dehalococcoides spp. in KB-1
- term:
- id: NCBITaxon:61434
- label: Dehalococcoides
metabolites:
- preferred_term: trichloroethene
term:
@@ -149,22 +145,33 @@ ecological_interactions:
evidence_source: IN_VIVO
snippet: ethene production accounted for the observed mass loss
explanation: Supports ethene as the dechlorination end product.
-- name: Acetogen Cobamide Support
- description: Acetobacterium and Sporomusa provide a supporting acetogenic guild in KB-1. Acetobacterium
- can synthesize the cobalamin lower ligand DMB, supporting Dehalococcoides dechlorination in vitamin-free
- medium and highlighting a cofactor-mediated syntrophic dependency.
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Acetobacterium spp. in KB-1
+ - reference: PMID:31441646
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Acetobacterium supports complete TCE dechlorination by Dehalococcoides
+ explanation: Supports the separate KB-1 laboratory endpoint, not proof that this mechanism caused the earlier
+ field response.
+ participating_taxa:
+ - preferred_term: Dehalococcoides spp. in KB-1
+ term:
+ id: NCBITaxon:61434
+ label: Dehalococcoides
+ - preferred_term: Acetobacterium spp. in KB-1
term:
id: NCBITaxon:33952
label: Acetobacterium woodii
- target_taxon:
- preferred_term: Dehalococcoides spp. in KB-1
+ - preferred_term: Sporomusa spp. in KB-1
term:
- id: NCBITaxon:61434
- label: Dehalococcoides
+ id: NCBITaxon:2375
+ label: Sporomusa
+- name: Acetogen Cobamide Support
+ description: 'Vitamin-free KB-1 transfers sustained TCE dechlorination with increased Acetobacterium abundance
+ and cobalamin, supported by a DMB-biosynthesis operon. These positive community experiments support Acetobacterium-associated
+ cofactor provision. PARTIAL - donor-resolved transfer, exclusive mediation and the return benefit remain unresolved.
+ The canonical Acetobacterium woodii label is not verified as the source population Acetobacterium sp. KB-1;
+ its grounding remains #1526. Acid inhibition is distinct from cofactor shortage: DMB did not rescue stalled
+ low-pH dechlorination, whereas pH adjustment did.'
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: cobalamin
term:
@@ -175,40 +182,42 @@ ecological_interactions:
term:
id: GO:0006766
label: vitamin metabolic process
- downstream:
- - target: Reductive Dechlorination to Ethene
- description: Acetogen-derived cobalamin support supplies the cofactor context required for
- complete Dehalococcoides reductive dechlorination in KB-1 without exogenous vitamins.
evidence:
- reference: PMID:31441646
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: the lower ligand of cobalamin, and Sporomusa are dominant acetogens
- explanation: Supports acetogens as cobamide-related supporting partners in KB-1.
+ snippet: Acetobacterium supports complete TCE dechlorination by Dehalococcoides
+ explanation: Supports community cofactor support; full primary transfers, gene analysis and Table 1 strengthen
+ the interpretation without establishing a traced exclusive transfer or A. woodii identity.
- reference: PMID:31441646
supports: SUPPORT
evidence_source: IN_VITRO
snippet: substantial increase in cobalamin
- explanation: Supports cobalamin availability as part of the Acetobacterium-Dehalococcoides interaction.
-- name: Sporomusa DMB-Guided Cobalamin Support
- description: Sporomusa is a dominant acetogen in vitamin-free KB-1 cultures. A
- Sporomusa sp. strain KB-1 isolate was also tested as a Dehalococcoides partner
- population; its phenolic cobamides did not by themselves satisfy Dehalococcoides
- corrinoid requirements, but DMB amendment guided cobalamin biosynthesis in
- Sporomusa sp. cocultures and supported Dehalococcoides reductive dechlorination
- activity and growth.
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Sporomusa spp. in KB-1
- term:
- id: NCBITaxon:2375
- label: Sporomusa
- target_taxon:
- preferred_term: Dehalococcoides spp. in KB-1
+ explanation: Supports the positive cofactor measurement, not an independently isolated mediator of the field
+ outcome.
+ participating_taxa:
+ - preferred_term: Dehalococcoides spp. in KB-1
term:
id: NCBITaxon:61434
label: Dehalococcoides
+ - preferred_term: Acetobacterium spp. in KB-1
+ term:
+ id: NCBITaxon:33952
+ label: Acetobacterium woodii
+ downstream:
+ - target: Reductive Dechlorination to Ethene
+ description: PARTIAL - Acetobacterium-associated cofactor availability can support Dehalococcoides dechlorination
+ in the vitamin-free KB-1 laboratory cultures. Community transfers, cofactor measurements and biosynthetic
+ genes support this route, but do not isolate its exclusive contribution or establish its mediation of the
+ separate field bioaugmentation result.
+- name: Sporomusa DMB-Guided Cobalamin Support
+ description: 'Controlled cocultures tested a Sporomusa sp. KB-1 isolate with Dehalococcoides strains BAV1, GT
+ and FL2. DMB amendment changed donor cobamide chemistry and restored partner dechlorination and growth; without
+ DMB, the phenolic cofactors did not support those requirements. FL2 still produced both VC and ethene. The explicit
+ canonical participant is the KB-1-derived donor only: these external recipient strains are not established as
+ the record''s KB-1 Dehalococcoides population. This positive conditional partner-support result is not demonstrated
+ mediation of the field endpoint.'
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: cobalamin
term:
@@ -223,35 +232,31 @@ ecological_interactions:
term:
id: GO:0006766
label: vitamin metabolic process
- - preferred_term: cobalamin transport
- term:
- id: GO:0015889
- label: cobalamin transport
- downstream:
- - target: Reductive Dechlorination to Ethene
- description: DMB-guided cobalamin support can supply the corrinoid cofactor
- context required for Dehalococcoides reductive dechlorination.
evidence:
- reference: PMID:31441646
supports: SUPPORT
evidence_source: IN_VITRO
snippet: the lower ligand of cobalamin, and Sporomusa are dominant acetogens
- explanation: Establishes Sporomusa as a dominant acetogenic member of the KB-1
- cultures grown without exogenous vitamins.
+ explanation: Supports Sporomusa presence in KB-1, not identity of the external Dehalococcoides recipients in
+ the separate coculture experiment.
- reference: PMID:23479750
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Sporomusa ovata and Sporomusa sp. strain KB-1, as Dehalococcoides
- partner populations
- explanation: Identifies Sporomusa sp. strain KB-1 as a tested Dehalococcoides
- coculture partner.
+ snippet: Sporomusa ovata and Sporomusa sp. strain KB-1, as Dehalococcoides partner populations
+ explanation: Identifies the KB-1-derived donor isolate in the controlled partner experiment, not an intact KB-1
+ consortium assay.
- reference: PMID:23479750
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Dehalococcoides dechlorination activity and growth occurred in M. barkeri
- and Sporomusa sp. co-cultures amended with 10 µM 5',6'-dimethylbenzimidazole
- explanation: Supports DMB-guided cobalamin biosynthesis by Sporomusa sp. as a
- mechanism that can restore Dehalococcoides dechlorination activity and growth.
+ snippet: Dehalococcoides dechlorination activity and growth occurred in M. barkeri and Sporomusa sp. co-cultures
+ amended with 10 µM 5',6'-dimethylbenzimidazole
+ explanation: Preserves positive DMB-conditional dechlorination and growth. The full primary text distinguishes
+ BAV1, GT and FL2 and their different final products; it does not establish a field-site mechanism.
+ participating_taxa:
+ - preferred_term: Sporomusa spp. in KB-1
+ term:
+ id: NCBITaxon:2375
+ label: Sporomusa
environmental_factors:
- name: Anaerobic contaminated groundwater
value: Reducing conditions after methanol and acetate amendment
@@ -291,3 +296,27 @@ growth_media:
evidence_source: IN_VITRO
snippet: TCE-amended mineral medium devoid of vitamins
explanation: Supports the growth medium and vitamin-omission perturbation.
+discussions:
+- discussion_id: kb1_partner_identity_and_field_mediation
+ prompt: Which same-system cofactor routes mediate KB-1 dechlorination?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Reductive Dechlorination to Ethene
+ - ecological_interactions#Acetogen Cobamide Support
+ - ecological_interactions#Sporomusa DMB-Guided Cobalamin Support
+ rationale: 'Keep the positive field outcome, vitamin-free community support and controlled donor chemistry/partner
+ phenotypes distinct. Remove the Sporomusa-to-KB-1-outcome arrow because external recipient strains were not
+ identified as the KB-1 population. The Acetobacterium route remains PARTIAL for exact transfer and field mediation.
+ Canonical taxonomy and non-graph blocks are preserved, not recertified; #1526 tracks Acetobacterium identity.
+ Full 2013/2019 primary main texts read; 2019 selected tables/figures inspected, 2002 field abstract only. No
+ separate supplements/raw-data audit or new graph structure.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T18:27:03Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Separate KB-1 community and field endpoints from external-recipient cofactor experiments. Issue #1523;
+ reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml'
+ llm_assisted: true
diff --git a/kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml b/kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml
index 3693cd9e6..f718df951 100644
--- a/kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml
+++ b/kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml
@@ -148,162 +148,83 @@ taxonomy:
snippet: another of Bacteroides thetaiotaomicron (B. theta) and Klebsiella
explanation: Establishes Klebsiella as a member of the computational community models.
ecological_interactions:
-- name: RFMIA Community Information-Flow Adaptation
- description: >
- The Zahmeeth computational workflow adapted Run Flux Mutual Information
- Analysis to combine molecular communication, Shannon information theory, and
- metabolic flux analysis for quantifying information flow through modeled
- microbial community metabolism in bits.
+- name: Model-Architecture-Dependent Information Flow
+ description: 'Mixed-bag models generally had higher mutual-information scores than compartmentalized models. The
+ authors attribute this to pooling reactions without intermember transport constraints; this is a model-architecture
+ interpretation, not observed niche partitioning or a selectively validated biological transport mechanism. Methods/Results
+ identify E. coli iML1515 and B. theta iAH991; the abstract names different pairs. The two canonical participants
+ delimit the modeled comparison, not a four-member consortium; the source/metadata discrepancy remains #1527.'
scope: COMMUNITY_LEVEL
- interaction_type: CROSS_FEEDING
- biological_processes:
- - preferred_term: interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Idealized Two-Member Community Model Construction
- description: >
- The RFMIA framework was applied to idealized two-member microbial
- communities represented by genome-scale metabolic models.
evidence:
- reference: doi:10.1101/2023.08.23.554558
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: adapted a model that blends molecular communication and Shannon Information theory
- to be able to quantify the information flow through metabolism in bits
- explanation: >
- Supports the computational RFMIA adaptation used to quantify metabolic
- information flow in bits.
-- name: Idealized Two-Member Community Model Construction
- description: >
- The RFMIA analysis was instantiated on idealized two-member communities,
- including Escherichia coli with Pseudomonas fluorescens and Bacteroides
- thetaiotaomicron with Klebsiella, allowing modeled community flux behavior
- to be compared with isolate behavior.
- scope: COMMUNITY_LEVEL
- interaction_type: CROSS_FEEDING
- biological_processes:
- - preferred_term: interspecies interaction between organisms
+ snippet: mixed-bag framework conducts greater information flow than the compartmentalized framework
+ explanation: Primary-checked abstract fragment supports the model comparison; transport explanation remains
+ an interpretation rather than demonstrated ecological causation.
+ participating_taxa:
+ - preferred_term: Escherichia coli
term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Mixed-Bag and Compartmentalized GEM Comparison
- description: >
- The idealized two-member models supplied the test cases for comparing
- mixed-bag and compartmentalized community genome-scale model structures.
- - target: In Silico Community-Formation Dependencies
- description: >
- The paired idealized communities were also used to identify model
- dependencies that justified community formation relative to isolate
- simulations.
- evidence:
- - reference: doi:10.1101/2023.08.23.554558
- supports: SUPPORT
- evidence_source: COMPUTATIONAL
- snippet: RFMIA (Run Flux Mutual Information Analysis), was applied to idealized two-member
- microbial communities
- explanation: >
- Establishes that the computational information-flow method was applied to
- idealized two-member microbial community models.
- - reference: doi:10.1101/2023.08.23.554558
- supports: SUPPORT
- evidence_source: COMPUTATIONAL
- snippet: one of E. coli and Pseudomonas fluorescens and another of Bacteroides thetaiotaomicron
- (B. theta) and Klebsiella
- explanation: >
- Names the two idealized two-member model communities used in the RFMIA
- comparison.
-- name: Mixed-Bag and Compartmentalized GEM Comparison
- description: >
- The workflow compared mixed-bag and compartmentalized genome-scale metabolic
- modeling frameworks for the same idealized two-member communities, separating
- model-architecture effects from isolated-community information-flow
- contrasts.
- scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- biological_processes:
- - preferred_term: interspecies interaction between organisms
+ id: NCBITaxon:562
+ label: Escherichia coli
+ - preferred_term: Bacteroides thetaiotaomicron
term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Greater Community Information Flow
- description: >
- Comparing the alternative GEM frameworks produced the specific result that
- mixed-bag community models conducted more information flow than
- compartmentalized ones.
- evidence:
- - reference: doi:10.1101/2023.08.23.554558
- supports: SUPPORT
- evidence_source: COMPUTATIONAL
- snippet: mixed-bag framework conducts greater information flow than the compartmentalized
- framework for community genome-scale metabolic models
- explanation: >
- Supports the community GEM architecture comparison and its
- information-flow result.
-- name: In Silico Community-Formation Dependencies
- description: >
- Simulated pairwise communities exposed community-only dependencies, including
- aerobic B. thetaiotaomicron growth when coupled with E. coli and community
- dextrin growth in cases where E. coli could not grow as an isolate.
+ id: NCBITaxon:818
+ label: Bacteroides thetaiotaomicron
+- name: Model-Conditional Growth Contrasts
+ description: 'Community models grew on dextrin where the E. coli isolate model did not. Aerobic isolated B. theta
+ growth and information flow were manually set to zero, with that constraint lifted in community models; the
+ contrast is not independently predicted partner rescue. Model growth does not establish actual strain growth,
+ resolved cross-feeding, stable community formation or reciprocal benefit. Methods/Results identify E. coli iML1515
+ and B. theta iAH991; the abstract names different pairs. The two canonical participants delimit the modeled
+ comparison, not a four-member consortium; the source/metadata discrepancy remains #1527.'
scope: COMMUNITY_LEVEL
- interaction_type: CROSS_FEEDING
metabolites:
- preferred_term: dextrin
term:
id: CHEBI:28675
label: dextrin
- concentration: Model carbon source supporting community growth but not E. coli isolate growth
- biological_processes:
- - preferred_term: interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Greater Community Information Flow
- description: >
- The modeled dependency examples accompanied the broader finding that
- two-member community models carried more metabolic information flow than
- isolate models.
+ notes: Model carbon substrate in the dextrin growth comparison, not a measured concentration or traced interstrain
+ flux.
evidence:
- reference: doi:10.1101/2023.08.23.554558
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: Our work reveals dependencies among organisms that justify community formation
- explanation: >
- Supports the in silico identification of dependencies that motivate the
- modeled community state.
- - reference: doi:10.1101/2023.08.23.554558
- supports: SUPPORT
- evidence_source: COMPUTATIONAL
- snippet: including that B. theta only grows in aerobic environments when coupled with E. coli
- and that community models grew on dextrin despite that E. coli failed to grow
- as an isolate
- explanation: >
- Gives the two abstract-level examples of predicted community dependencies.
+ snippet: despite that E. coli failed to grow as an isolate
+ explanation: Primary-checked Results fragment supports the dextrin contrast. The read Methods explicitly impose
+ the aerobic isolated B. theta zero-growth/MI rule; the comparison cannot independently validate rescue.
+ participating_taxa:
+ - preferred_term: Escherichia coli
+ term:
+ id: NCBITaxon:562
+ label: Escherichia coli
+ - preferred_term: Bacteroides thetaiotaomicron
+ term:
+ id: NCBITaxon:818
+ label: Bacteroides thetaiotaomicron
- name: Greater Community Information Flow
- description: >
- The RFMIA simulations reported higher information flow through the idealized
- two-member community models than through isolated organism models, tying the
- KBase model workflows to a quantitative community-level information-flow
- output.
+ description: 'RFMIA generally returned higher mutual-information scores for the community models than for isolated
+ models under the tested nutrient combinations. These are computed information-theoretic outputs in bits, not
+ measured molecular communication, a universal growth advantage or mutualism. Methods/Results identify E. coli
+ iML1515 and B. theta iAH991; the abstract names different pairs. The two canonical participants delimit the
+ modeled comparison, not a four-member consortium; the source/metadata discrepancy remains #1527.'
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
- biological_processes:
- - preferred_term: interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
evidence:
- reference: doi:10.1101/2023.08.23.554558
supports: SUPPORT
evidence_source: COMPUTATIONAL
snippet: information flow is greater through communities than isolated models
- explanation: >
- Supports the downstream quantitative result that community models carried
- more metabolic information flow than isolate models.
+ explanation: Primary-checked abstract fragment supports the reported computational trend, bounded by Methods/Results
+ and selected chart inspection; not every environmental condition or biological system.
+ participating_taxa:
+ - preferred_term: Escherichia coli
+ term:
+ id: NCBITaxon:562
+ label: Escherichia coli
+ - preferred_term: Bacteroides thetaiotaomicron
+ term:
+ id: NCBITaxon:818
+ label: Bacteroides thetaiotaomicron
external_resources:
- name: KBase narrative
repository: KBASE
@@ -316,3 +237,27 @@ external_resources:
evidence_source: COMPUTATIONAL
snippet: 'KBase: The United States Department of Energy Systems Biology Knowledgebase.'
explanation: Supports the KBase platform provenance for this public narrative resource.
+discussions:
+- discussion_id: rfmia_model_assumptions_and_partners
+ prompt: Which model-dependent findings persist with verified partners and experimentally tested constraints?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Model-Architecture-Dependent Information Flow
+ - ecological_interactions#Model-Conditional Growth Contrasts
+ - ecological_interactions#Greater Community Information Flow
+ rationale: 'Remove adaptation/construction nodes and all five procedural or co-occurrence arrows. Keep three existing
+ modeled observations without imposing a new causal chain. Primary full v1 PDF text/captions read and selected
+ Methods, equations, table, architecture and charts visually inspected; no independent mathematical derivation,
+ supplement/code/raw simulation audit or model rerun. Manually imposed aerobic constraints cannot validate partner
+ rescue. #1527 tracks non-graph model/partner metadata and #1528 the mismatching cached abstract. Canonical identifiers
+ and raw non-graph blocks are preserved; no new graph structure.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T18:27:04Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain model-dependent outputs without workflow causality or imposed-constraint rescue claims. Issue
+ #1524; reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml'
+ llm_assisted: true
diff --git a/kb/communities/KBase_ORT_Workflow_Community_Model.yaml b/kb/communities/KBase_ORT_Workflow_Community_Model.yaml
index 2336de05f..d95754012 100644
--- a/kb/communities/KBase_ORT_Workflow_Community_Model.yaml
+++ b/kb/communities/KBase_ORT_Workflow_Community_Model.yaml
@@ -137,83 +137,77 @@ taxonomy:
snippet: environmental metagenomic data from a river system
explanation: Establishes the second denitrifier as a member of the nitrogen-cycling community.
ecological_interactions:
-- name: Coupled Nitrification in Columbia River Sediments
- description: Ammonia-oxidizing archaea (Nitrososphaeraceae) and nitrite-oxidizing bacteria (Nitrospiraceae)
- form a coupled nitrification network in Columbia River sediments. The archaeon oxidizes ammonium to
- nitrite, which is then consumed by Nitrospiraceae to produce nitrate. This syntrophic coupling is
- fundamental to nitrogen cycling in the sediment microbiome and demonstrates metabolic interdependence
- between archaeal and bacterial partners. The partnership enables complete nitrification from ammonium
- to nitrate, feeding nitrate to downstream denitrifiers.
- interaction_type: SYNTROPHY
+- name: Modeled Coupled Nitrification
+ description: The ORT proof-of-concept uses Nitrososphaeraceae and Nitrospiraceae MAG-derived models for ammonium-to-nitrite
+ and nitrite-to-nitrate transformations. Sequential substrate coupling is represented computationally, not experimentally
+ measured partner transfer, obligatory syntrophy or an assembled two-strain culture.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: ammonium
term:
id: CHEBI:28938
label: ammonium
- concentration: Oxidized by archaeon
+ notes: Contextual modeled substrate/product, not a measured member-specific concentration or flux; nitrogen
+ production includes an explicitly gapfilled reaction.
- preferred_term: nitrite
term:
id: CHEBI:16301
label: nitrite
- concentration: Produced by archaeon, consumed by bacterium
+ notes: Contextual modeled substrate/product, not a measured member-specific concentration or flux; nitrogen
+ production includes an explicitly gapfilled reaction.
- preferred_term: nitrate
term:
id: CHEBI:17632
label: nitrate
- concentration: Produced by bacterium
+ notes: Contextual modeled substrate/product, not a measured member-specific concentration or flux; nitrogen
+ production includes an explicitly gapfilled reaction.
biological_processes:
- - preferred_term: nitrification
+ - preferred_term: ammonia oxidation
term:
id: GO:0019329
label: ammonia oxidation
- downstream:
- - target: Nitrate-to-Nitrogen Gas Denitrification
- description: >
- Coupled archaeal and bacterial nitrification produces nitrate that feeds
- the downstream Steroidobacteraceae denitrifiers.
+ notes: Applies to the modeled archaeal first step, not the entire two-step nitrification pathway.
evidence:
- reference: PMID:34726691
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: predict nitrogen cycling patterns with site-specific insight into the chemical and biological
- drivers of nitrification and denitrification processes
- explanation: Demonstrates coupled nitrification as a key process in the Columbia River sediment community.
-- name: Nitrate-to-Nitrogen Gas Denitrification
- description: Two Steroidobacteraceae denitrifiers consume nitrate produced by nitrifying organisms and
- reduce it through denitrification to nitrogen gas. This terminal step in the nitrogen cycle completes
- the transformation of fixed nitrogen back to atmospheric N2. The denitrifiers depend on upstream nitrification
- to provide nitrate substrate, demonstrating sequential metabolic coupling across the community. Genome-scale
- models also connected the denitrifier reactions to metabolome-derived carbon sources, enabling precise
- identification of biogeochemical limiting factors.
- interaction_type: SYNTROPHY
+ snippet: nitrification and denitrification
+ explanation: This primary-checked process phrase identifies the modeled processes. The inspected Methods specify
+ MAG selection and gapfilling; Results report simulated trajectories, not empirical field flux.
+ participating_taxa:
+ - preferred_term: Nitrososphaeraceae archaeon
+ term:
+ id: NCBITaxon:1033997
+ label: Nitrososphaeraceae
+ - preferred_term: Nitrospiraceae bacterium
+ term:
+ id: NCBITaxon:189779
+ label: Nitrospiraceae
+ downstream:
+ - target: Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ description: PARTIAL - sequential modeled nitrification supplies nitrate for modeled denitrification. This is
+ a substrate route in the proof-of-concept simulation, not proof of an exclusive environmental nitrate source,
+ obligatory partner dependence or genome-supported completion to nitrogen gas.
+- name: Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ description: Two Steroidobacteraceae MAG-derived models represent nitrate reduction to dissolved nitrogen. Neither
+ MAG encoded nitrogen-gas production; the N2O-to-N2 reaction was added by gapfilling. The positive simulation
+ output is therefore conditional on model assumptions, not demonstrated complete metabolism of either organism
+ or measured field nitrogen loss. The two canonical denitrifier names remain distinct despite sharing a family
+ identifier.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: nitrate
term:
id: CHEBI:17632
label: nitrate
- concentration: Consumed by denitrifiers
+ notes: Contextual modeled substrate/product, not a measured member-specific concentration or flux; nitrogen
+ production includes an explicitly gapfilled reaction.
- preferred_term: nitrogen
term:
id: CHEBI:17997
label: dinitrogen
- concentration: Produced as N2 gas
- - preferred_term: betaine
- term:
- id: CHEBI:17750
- label: glycine betaine
- concentration: Carbon source for denitrifiers
- - preferred_term: leucine
- term:
- id: CHEBI:15603
- label: L-leucine
- concentration: Carbon source for denitrifiers
- - preferred_term: choline
- term:
- id: CHEBI:15354
- label: choline
- concentration: Carbon source for denitrifiers
+ notes: Contextual modeled substrate/product, not a measured member-specific concentration or flux; nitrogen
+ production includes an explicitly gapfilled reaction.
biological_processes:
- preferred_term: denitrification
term:
@@ -223,53 +217,75 @@ ecological_interactions:
- reference: PMID:34726691
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: GSMs identified additional carbon sources utilized, enabling more precise identification
- of the biogeochemical limiting factors in the system
- explanation: Demonstrates that denitrifiers utilize diverse carbon sources beyond traditional models.
- - reference: PMID:34726691
- supports: SUPPORT
- evidence_source: COMPUTATIONAL
- snippet: predict nitrogen cycling patterns with site-specific insight into the chemical and biological
- drivers of nitrification and denitrification processes
- explanation: Establishes denitrification as a key process coupled to nitrification in the community.
-- name: Metabolome-Informed Carbon Source Utilization
- description: The ORT site model incorporated additional organic carbon compounds
- detected in the bulk Columbia River sediment metabolome. This allowed
- Steroidobacteraceae denitrifier models to use 15-23 unique carbon sources,
- including glycine betaine, leucine, and choline, instead of restricting
- denitrification to acetate as in the generalized literature-based model.
- interaction_type: SYNTROPHY
+ snippet: nitrification and denitrification
+ explanation: This primary-checked process phrase identifies the modeled processes. The inspected Methods specify
+ MAG selection and gapfilling; Results report simulated trajectories, not empirical field flux.
+ participating_taxa:
+ - preferred_term: Steroidobacteraceae denitrifier 1
+ term:
+ id: NCBITaxon:2689614
+ label: Steroidobacteraceae
+ - preferred_term: Steroidobacteraceae denitrifier 2
+ term:
+ id: NCBITaxon:2689614
+ label: Steroidobacteraceae
+- name: Modeled Metabolome-Informed Carbon Utilization
+ description: Site models used 15-23 additional carbon substrates, with betaine, leucine and choline among the
+ examples. Bulk metabolomics informed model media, with some unmeasured necessities assumed nonlimiting. These
+ modeled exchanges add chemical detail; they are not traced member flux or experimentally identified field limitations,
+ and the reported substrate count is not assigned to every denitrifier.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: glycine betaine
term:
id: CHEBI:17750
label: glycine betaine
+ notes: Reported model substrate example; not assigned as an observed uptake flux of every canonical participant.
- preferred_term: leucine
term:
id: CHEBI:15603
label: L-leucine
+ notes: Reported model substrate example; not assigned as an observed uptake flux of every canonical participant.
- preferred_term: choline
term:
id: CHEBI:15354
label: choline
+ notes: Reported model substrate example; not assigned as an observed uptake flux of every canonical participant.
biological_processes:
- preferred_term: organic substance catabolic process
term:
id: GO:0009056
label: catabolic process
- downstream:
- - target: Nitrate-to-Nitrogen Gas Denitrification
- description: Metabolome-derived organic carbon sources constrain the
- denitrifier reactions that reduce nitrate through the modeled nitrogen cycle.
+ notes: Model catabolic context, not measured carbon turnover by every MAG.
evidence:
- reference: PMID:34726691
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: site models used 15–23 unique additional carbon sources, such as betaine,
- leucine and choline
- explanation: Supports the metabolome-informed carbon substrates used by the
- genome-scale models.
+ snippet: site models used 15–23 unique additional carbon sources, such as betaine, leucine and choline
+ explanation: Primary-checked body excerpt supports the reported site-model substrate range; not a measured concentration
+ or the same substrate list in every denitrifier.
+ participating_taxa:
+ - preferred_term: Nitrososphaeraceae archaeon
+ term:
+ id: NCBITaxon:1033997
+ label: Nitrososphaeraceae
+ - preferred_term: Nitrospiraceae bacterium
+ term:
+ id: NCBITaxon:189779
+ label: Nitrospiraceae
+ - preferred_term: Steroidobacteraceae denitrifier 1
+ term:
+ id: NCBITaxon:2689614
+ label: Steroidobacteraceae
+ - preferred_term: Steroidobacteraceae denitrifier 2
+ term:
+ id: NCBITaxon:2689614
+ label: Steroidobacteraceae
+ downstream:
+ - target: Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ description: PARTIAL - modeled carbon uptake contributes substrate and stoichiometric context to the denitrification
+ representation. The exchange calculations support this model-level coupling, not selective demonstration that
+ these example compounds control field denitrification or are consumed by both denitrifiers.
external_resources:
- name: KBase narrative
repository: KBASE
@@ -288,3 +304,27 @@ external_resources:
evidence_source: COMPUTATIONAL
snippet: 'KBase: The United States Department of Energy Systems Biology Knowledgebase.'
explanation: Supports the KBase platform provenance for this workflow narrative.
+discussions:
+- discussion_id: ort_gapfilling_and_environmental_validation
+ prompt: Which modeled nitrogen and carbon routes are supported by measured organism activity?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Modeled Coupled Nitrification
+ - ecological_interactions#Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ - ecological_interactions#Modeled Metabolome-Informed Carbon Utilization
+ rationale: 'Retain both existing model-level substrate arrows, explicitly PARTIAL for biological validation. Nitrogen-gas
+ completion is gapfilled, and neither denitrifier MAG encoded it. The single-chemistry-input demonstration compares
+ model stoichiometries using common rate assumptions; no high-resolution empirical time series validates its
+ predicted trajectories. Iterative KBase/PFLOTRAN coupling is a proposed capability, not a demonstrated feedback
+ experiment. Full publisher main text/Methods/Table1/captions read; no figure pixels, supplements, code, raw
+ data or narrative execution inspected. #1527 tracks non-graph metadata and #1528 cache provenance; all canonical
+ IDs/labels remain unchanged. No new graph structure.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T18:27:04Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Expose ORT gapfilled nitrogen completion and bound modeled substrate routes. Issue #1525; reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml'
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index c9c32b361..ed1885bb6 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -225,3 +225,15 @@ the baseline exactly; its exit code of zero does not mean an all-match result.
Textual matching also does not establish scientific support or independent source
provenance. In particular, selected `.txt` excerpts have a separate trust limitation
tracked in [issue 1362](https://github.com/CultureBotAI/CommunityMech/issues/1362).
+
+## Batch56: KB1 And KBase Models
+
+[Decisions](decisions/20261006-three-records-batch56.yaml),
+[validation](validation-20261006-batch56.json) and
+[self-adversarial review](adversarial-review-20261006-batch56.yaml) distinguish
+KB-1 community/field outcomes from external-recipient coculture rescue, preserve
+RFMIA outputs without workflow causality or imposed-constraint rescue claims,
+and expose ORT's gapfilled nitrogen-gas reaction. Nine existing nodes and three
+qualified arrows remain; no new graph structure or provider spend.
+Non-graph identity/model metadata and cached-abstract provenance remain open
+under #1526-#1528. Exact cache matching is not independent provenance approval.
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch56.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch56.yaml
new file mode 100644
index 000000000..a5f640965
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch56.yaml
@@ -0,0 +1,259 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: e9893c06c181d1705eb2917ef865f0579ba19761
+scope:
+- kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml
+- kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml
+- kb/communities/KBase_ORT_Workflow_Community_Model.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch56.json
+findings:
+- issue: 1523
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate KB-1 community and field endpoints from external-recipient cofactor experiments.
+ disposition: Close only after protected-main merge.
+- issue: 1524
+ severity: P2
+ status: addressed_in_this_change
+ finding: Retain model-dependent outputs without workflow causality or imposed-constraint rescue claims.
+ disposition: Close only after protected-main merge.
+- issue: 1525
+ severity: P2
+ status: addressed_in_this_change
+ finding: Expose ORT gapfilled nitrogen completion and bound modeled substrate routes.
+ disposition: Close only after protected-main merge.
+- issue: 1526
+ severity: P2
+ status: unresolved_non_graph
+ finding: KB1 Acetobacterium species grounding and non-graph study scope.
+ disposition: Keep open after graph repair merge.
+- issue: 1527
+ severity: P2
+ status: unresolved_non_graph
+ finding: Model pair/narrative/design metadata, including two exposed RFMIA membership warnings.
+ disposition: Keep open after graph repair merge.
+- issue: 1528
+ severity: P2
+ status: unresolved_non_graph
+ finding: ORT/RFMIA cached-abstract provenance and dependent non-graph excerpts.
+ disposition: Keep open after graph repair merge.
+adversarial_checks:
+- Whole three records and every11 original nodes/9 arrows read. Full2013/2019 KB1 primary main texts;2019
+ Tables1-2/Figures2-5 visually inspected,2002 field abstract only. No2013 original images or separate
+ supplements/raw data inspected.
+- Preserve positive field bioaugmentation, vitamin-free KB1 community support and controlled DMB-guided
+ Sporomusa donor chemistry/partner growth. Neither missing exclusive-transfer perturbation nor missing
+ field mediation negates these positive observations.
+- Sporomusa KB1 donor cocultures used BAV1/GT/FL2 recipients, not established as the canonical KB1 recipient
+ population. FL2 retained VC plus ethene. Remove only the unsupported cross-system downstream arrow,
+ retain the conditional donor-support node and its positive evidence.
+- Acetobacterium-associated cofactor support-to-dechlorination remains PARTIAL for donor-resolved/exclusive
+ transfer and field generalization. Species grounding A.woodii is not established by comparison of biosynthetic
+ genes. DMB and pH rescue are distinct perturbations. Non-graph taxonomy/conditions remain1526.
+- Full RFMIA v1 PDF main text/captions read; selected equations, Methods, Table1, architecture and Figures7-9
+ visually inspected. No independent mathematical derivation, external supplement/code/raw-simulation
+ audit, or KBase/model execution.
+- RFMIA Methods/Results use E.coli/B.theta; abstract names different pairs. All three retained nodes explicitly
+ use the Methods pair, not a four-member culture. Two alternative canonical taxa are left visibly DISCONNECTED
+ pending1527, not silently added as graph participants.
+- Aerobic isolated B.theta MI/growth were manually zeroed. Preserve modeled dextrin growth and generally
+ higher community/architecture-dependent MI, but do not call imposed contrasts independent partner rescue,
+ measured molecular communication, reciprocal fitness or universal growth benefit. Two procedure nodes
+ and all five workflow/co-occurrence arrows removed.
+- ORT full publisher main text/Methods/Table1/captions read; no original images, external supplements,
+ raw data/code or narrative execution. Neither denitrifier MAG encoded N2 production; terminal conversion
+ was gapfilled. Distinct denitrifier names retained despite shared family CURIE.
+- Retain two PARTIAL modeled nitrate/carbon substrate routes, not exclusive environmental nitrate supply,
+ demonstrated syntrophy, per-denitrifier15-23 substrates or empirically identified field limits. Model
+ rates were shared across stoichiometry comparisons; no high-resolution time series validation. Iterative
+ coupling is proposed capability, not demonstrated feedback.
+- All920 cache files byte-identical. Retained RFMIA/ORT graph fragments additionally verified against
+ independently retrieved primary artifacts. Full mismatching cache abstracts and nongraph snippets are
+ not certified;1528 remains unresolved. Source-text formatting and cache MATCH cannot prove provenance.
+ Platform source scope corrected to title/header/opening paragraphs, not nonexistent indexed abstract.
+- Actual schema/strict/term/reference/snippet/history/rank gates completed.457 other records and raw nongraph
+ blocks preserved. Nine retained nodes use canonical explicit subsets;3 PARTIAL arrows remain. All34
+ baseline network warnings preserved plus2 exposed RFMIA membership warnings, zero structural defects.
+ No matching-rule or census-bound changes.
+- All record diffs, regression assertions and every-node/arrow partitions inspected. Generated descriptions
+ match source text across456 pages and repeat rendering is deterministic; no browser screenshot claim.
+ Final ledger tests rerun after the metadata-only source-scope correction.
+- 827 all-state issue titles/bodies and38 ignored/hidden local matches with declared exclusions inspected,
+ not every historical comment/PR.1523-1525 addressed but open until protected-main merge;1526-1528 unresolved.
+ No Edison dryrun, provider spend/report or new structure. Self-review is not independent approval.
+verification:
+ combined_regressions: 526 passed in 185.75s (0:03:05)
+ new_regression_tests: 7
+ schema_strict_terms_history: Passed with actual output digests
+ references: CLI Total checks counts reported issues, not executed checks. Exit0 and MATCH do not certify
+ source provenance or scientific support. Retained graph fragments were checked against primary sources;
+ mismatching cached abstracts/nongraph excerpts remain1528. Coverage476, Linux DOI lookup1091 and selected.txt
+ trust1362 remain limitations.
+ snippet_counts_by_record:
+ kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml:
+ MATCH: 16
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml:
+ MATCH: 10
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/KBase_ORT_Workflow_Community_Model.yaml:
+ MATCH: 11
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ network:
+ existing_findings_preserved: 34
+ added_findings:
+ KBase_Models_for_Zahmeeth_Original_PLOS:
+ - type: DISCONNECTED
+ taxon: Klebsiella
+ taxon_id: NCBITaxon:570
+ taxon_data:
+ taxon_term:
+ preferred_term: Klebsiella
+ term:
+ id: NCBITaxon:570
+ label: Klebsiella
+ gtdb_grounding_status: GROUNDED
+ gtdb_classification:
+ gtdb_id: GTDB:g__Klebsiella
+ gtdb_taxon: Klebsiella
+ gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella
+ ncbi_source_id: NCBITaxon:570
+ majority_fraction: 1.0
+ support_genomes: 44527
+ total_genomes: 44529
+ is_reclassified: false
+ mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded
+ at g__ rank; 2 GTDB taxa under the NCBI taxon]
+ functional_role:
+ - CROSS_FEEDER
+ evidence:
+ - reference: doi:10.1101/2023.08.23.554558
+ supports: SUPPORT
+ evidence_source: COMPUTATIONAL
+ snippet: another of Bacteroides thetaiotaomicron (B. theta) and Klebsiella
+ explanation: Establishes Klebsiella as a member of the computational community models.
+ message: Taxon 'Klebsiella' has no interactions
+ - type: DISCONNECTED
+ taxon: Pseudomonas fluorescens
+ taxon_id: NCBITaxon:294
+ taxon_data:
+ taxon_term:
+ preferred_term: Pseudomonas fluorescens
+ term:
+ id: NCBITaxon:294
+ label: Pseudomonas fluorescens
+ gtdb_grounding_status: AMBIGUOUS
+ gtdb_candidates:
+ - GTDB:s__Pseudomonas_E_alvandae
+ - GTDB:s__Pseudomonas_E_asgharzadehiana
+ - GTDB:s__Pseudomonas_E_azotoformans_A
+ - GTDB:s__Pseudomonas_E_brassicacearum
+ - GTDB:s__Pseudomonas_E_crudilactis
+ - GTDB:s__Pseudomonas_E_edaphica
+ - GTDB:s__Pseudomonas_E_fluorescens
+ - GTDB:s__Pseudomonas_E_fluorescens_AP
+ - GTDB:s__Pseudomonas_E_fluorescens_AQ
+ - GTDB:s__Pseudomonas_E_fluorescens_B
+ - GTDB:s__Pseudomonas_E_fluorescens_H
+ - GTDB:s__Pseudomonas_E_fluorescens_S
+ - GTDB:s__Pseudomonas_E_kilonensis
+ - GTDB:s__Pseudomonas_E_lactis
+ - GTDB:s__Pseudomonas_E_lactucae
+ - GTDB:s__Pseudomonas_E_paracarnis
+ - GTDB:s__Pseudomonas_E_petroselini
+ - GTDB:s__Pseudomonas_E_poae
+ - GTDB:s__Pseudomonas_E_protegens
+ - GTDB:s__Pseudomonas_E_reactans
+ - GTDB:s__Pseudomonas_E_salomonii
+ - GTDB:s__Pseudomonas_E_simiae
+ - GTDB:s__Pseudomonas_E_sp002874965
+ functional_role:
+ - CROSS_FEEDER
+ evidence:
+ - reference: doi:10.1101/2023.08.23.554558
+ supports: SUPPORT
+ evidence_source: COMPUTATIONAL
+ snippet: idealized two-member microbial communities, one of E. coli and Pseudomonas fluorescens
+ explanation: Establishes P. fluorescens as a member of the computational community models.
+ message: Taxon 'Pseudomonas fluorescens' has no interactions
+ removed_findings: {}
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml: b45144b36c7683c4f2273ab9fb5bfa1d13c50d28ebad3e8594f19e700086eef2
+ tests/test_causal_review_batch56.py: 30171988efbe30351b7e84596c8186cdce497f5a2583ddf560191ba337ee4c82
+ tests/test_participating_taxa.py: ca533428e9ced189980963c393a262fac560f9345144282070a24465efa90323
+ kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml: 2dddd68ddedcbb86e9524066b26f0c3ade41432b515e8bfee9427c5a49a5f1b9
+ kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml: 848044ac5bcc1eeea7cf6c1496f51aba0484b5ab84d09af30dc7ab20743e835d
+ kb/communities/KBase_ORT_Workflow_Community_Model.yaml: b4cfa6d608db1e2d04f70537c425d23def58fb2528394a9226b82f4cc609ebf2
+ reports/causal_graph_review/README.md: d50ea4947db2074889a0bb5d2e86cb1282a5a65f4adc51b42484ad90df5c3d19
+ post_commit_docs_current: Separate publication gate, not asserted before commit.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 390
+ mixed: 125
+ community_level_only: 265
+ taxa: 1505
+ credited_solely_by_the_rule: 1233
+ current:
+ records: 460
+ with_community_level: 390
+ mixed: 124
+ community_level_only: 266
+ taxa: 1505
+ credited_solely_by_the_rule: 1236
+ interpretation: KB1 now represents community observations with explicit participant subsets rather than
+ unverified exact pair assignments. Three formerly pairwise-covered canonical taxa move into the solely-community-level
+ count. No taxonomy or production connectivity-rule changes; the RFMIA source-pair discrepancy is not
+ hidden by adding unsupported participants.
+corpus:
+ records: 460
+ nodes: 1461
+ edges: 654
+ review_status_counts:
+ needs_research: 18
+ pending: 252
+ reviewed: 190
+limitations:
+- All11 original nodes/9 arrows reviewed;9 nodes/3 PARTIAL arrows remain. Two procedural nodes and six
+ unsupported/procedural arrows removed. No new graph structure.
+- Full2013/2019 KB1 primary bodies read;2019 selected figures/tables inspected;2002 field abstract only.
+ No2013 original images or external supplements/raw data.
+- Full RFMIA v1 PDF text/captions read and selected Methods/equations/table/architecture/charts inspected;
+ no mathematical derivation, model rerun, supplementary/raw/code/narrative audit.
+- Full ORT publisher body/Methods/Table1/captions read; no original figure pixels, supplements, raw data/code
+ or KBase execution. Platform paper title/header/opening paragraphs only (no indexed abstract), not full-paper
+ recertification.
+- All920 caches remain byte-identical. Primary-checked short graph fragments do not certify complete cached
+ abstracts. ORT and RFMIA cache discrepancies remain1528; existing1362 selected.txt provenance and1091
+ Linux DOI lookup remain separate limitations.
+- Canonical taxonomy and raw non-graph fields preserved, not recertified. KB1 species identity remains1526;
+ model identities/design/narrative metadata remain1527. Positive cofactor/coculture effects and modeled
+ outputs are preserved with study limits.
+- No Edison dry run, paid request/report or spend. Existing graph repairs only; future extension requires
+ separate one-community research and specific payload/spend authorization.
+- Dedup includes827 all-state issue titles/bodies, broader synonyms and38 ignored/hidden local matches
+ with scoped exclusions described in source-progress.md. Not every historical comment/PR or generated
+ page inspected.
+- Repair1523-1525 stay open until protected-main merge;1526-1528 remain unresolved afterward. This is
+ self-adversarial review, not independent approval.
+- SupportingReference coverage476 and writer artifact1095 remain known limitations. Reference CLI Total
+ checks counts reported issues, not executed checks.
+- RFMIA explicit Methods/Results participants expose two DISCONNECTED warnings for the abstract-only alternative
+ taxa. These are unresolved membership metadata under1527, not a reason to invent interactions or expand
+ participant lists. Total36 network warnings; zero dangling edges/anchors.
diff --git a/reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml b/reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml
new file mode 100644
index 000000000..0f0f75cb6
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml
@@ -0,0 +1,345 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: e9893c06c181d1705eb2917ef865f0579ba19761
+baseline_commit: e9893c06c181d1705eb2917ef865f0579ba19761
+base_tree: f320485bfbcfede39762d87e8538a01464f636a2
+pre_source_baseline_sha256: 3bafb6cbe362af30c6260c3b4e898aec862b7eb94868833e4f213b0f09016097
+issues:
+- 1523
+- 1524
+- 1525
+unresolved_non_graph_issues:
+- 1526
+- 1527
+- 1528
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 827
+ ignored_hidden_local_search: true
+ matching_issues:
+ - 1384
+ - 653
+ - 592
+ - 491
+ - 442
+ - 416
+ - 403
+ - 293
+ - 292
+ - 258
+ matching_local_files: 38
+ limitations: Scoped local exclusions and partial historical-comment/PR coverage documented in source-progress.md.
+reference_cache_original_hashes:
+ references_cache/PMID_12523427.md: b6d85a597fdfefdd242f246cb397cdd65e467e12dd9f336267cd89919ec38534
+ references_cache/PMID_31441646.md: b0aed5b15e4f1bdde34f6910e24150e8670e7d113b1e4d379a73259ca89217d5
+ references_cache/PMID_23479750.md: dbae8f2e9156373b1b4a6043c9ecead8a0a4e2368fc55d36fe7c7408fc4e65b7
+ references_cache/doi_10.1101_2023.08.23.554558.md: 2c82dbe829a7f85718478190f58e4ee9d69c5a46b97b6e67744dfafa6f82b3b9
+ references_cache/PMID_34726691.md: 97bff6553d33d68a1c92063f9f3e8c3ba1b7abe51ff4847fd1181e823b3e169f
+ references_cache/PMID_34726691.txt: f1c22541a5ea79a3a31f5b85e8eb424396a21c6783b2b56106d35b0a18b74c2a
+ references_cache/PMID_29979655.md: e08a9ea0a7a8161ac785bd2dbad73df48d2b2eda69ebee63df7b8918bdf6d4c1
+primary_artifacts:
+ source-progress.md: 93fa1b7fbb20619c2bc7b93ed09fda1df34518379a1deee74724d47ae9864c0b
+ source-extraction.json: 8d88104ce4204d6de08335f706071ce73984c753e5fe05059dd419ce4cf6377c
+ cobalamin-primary.html: 060332e3face6c618198fb71ff9d0e9754b81f53831528ff2082c2b5b2d09848
+ cobalamin-primary.txt: 28730e5e8736e0d59fc764d847d88da93e94b148ad0bcc7634b9595b711111e3
+ ort-primary.html: fae8933afd99b0d6e24aea48c952eb18763566b46451c10ea38db39dbf30269e
+ ort-primary.txt: a23d2b3d56b764c0ea448766a339a863d595f8b1311865096c20594f607fad1a
+ zahmeeth-2023-primary.pdf: 004ce9de311e7bf7b5ecffe07e69eee5a98b5ef815677aa9d9290dc7e6edf792
+ zahmeeth-2023-primary.txt: 0915cb04aa02767d81ccaaa233cd45341fdebb2c77cc1dcf9d19e48d9625c295
+ kb1-2019-primary.pdf: dcfed8d1b6e89ddfd9aab41ed454bbf1d85c091b2642c4b8a586e2b839b6b15f
+ kb1-2019-primary.txt: 33bf0dcf75a02e0bfa8d42d1b7332c038d33947b0438dc2777728121738b9094
+primary_urls:
+- https://pubmed.ncbi.nlm.nih.gov/12523427/
+- https://pmc.ncbi.nlm.nih.gov/articles/PMC3638461/
+- https://pstorage-loughborough-53465.s3.amazonaws.com/22773368/acs.est.9b02339.pdf
+- https://mbite.unl.edu/sites/unl.edu.engineering.computing.mbite/files/media/file/a_Zahmeeth_bioRxiv2023_2.pdf
+- https://academic.oup.com/bioinformatics/article/38/3/778/6415821
+limitations:
+- All11 original nodes/9 arrows reviewed;9 nodes/3 PARTIAL arrows remain. Two procedural nodes and six unsupported/procedural
+ arrows removed. No new graph structure.
+- Full2013/2019 KB1 primary bodies read;2019 selected figures/tables inspected;2002 field abstract only. No2013
+ original images or external supplements/raw data.
+- Full RFMIA v1 PDF text/captions read and selected Methods/equations/table/architecture/charts inspected; no mathematical
+ derivation, model rerun, supplementary/raw/code/narrative audit.
+- Full ORT publisher body/Methods/Table1/captions read; no original figure pixels, supplements, raw data/code or
+ KBase execution. Platform paper title/header/opening paragraphs only (no indexed abstract), not full-paper recertification.
+- All920 caches remain byte-identical. Primary-checked short graph fragments do not certify complete cached abstracts.
+ ORT and RFMIA cache discrepancies remain1528; existing1362 selected.txt provenance and1091 Linux DOI lookup remain
+ separate limitations.
+- Canonical taxonomy and raw non-graph fields preserved, not recertified. KB1 species identity remains1526; model
+ identities/design/narrative metadata remain1527. Positive cofactor/coculture effects and modeled outputs are preserved
+ with study limits.
+- No Edison dry run, paid request/report or spend. Existing graph repairs only; future extension requires separate
+ one-community research and specific payload/spend authorization.
+- Dedup includes827 all-state issue titles/bodies, broader synonyms and38 ignored/hidden local matches with scoped
+ exclusions described in source-progress.md. Not every historical comment/PR or generated page inspected.
+- Repair1523-1525 stay open until protected-main merge;1526-1528 remain unresolved afterward. This is self-adversarial
+ review, not independent approval.
+- SupportingReference coverage476 and writer artifact1095 remain known limitations. Reference CLI Total checks counts
+ reported issues, not executed checks.
+- RFMIA explicit Methods/Results participants expose two DISCONNECTED warnings for the abstract-only alternative
+ taxa. These are unresolved membership metadata under1527, not a reason to invent interactions or expand participant
+ lists. Total36 network warnings; zero dangling edges/anchors.
+records:
+- path: kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml
+ id: CommunityMech:000132
+ original_sha256: 9f951642ed74d82ba8e0581acef30a3b4367e04c786c8065d658c8a5990ea217
+ record_sha256: 2dddd68ddedcbb86e9524066b26f0c3ade41432b515e8bfee9427c5a49a5f1b9
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml
+ scope: Whole record and every original node/arrow; source-bounded existing structure repair.
+ summary: Separate KB-1 community and field endpoints from external-recipient cofactor experiments.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Reductive Dechlorination to Ethene
+ rationale: Preserve consortium dechlorination and separate laboratory/field scope.
+ - node: Acetogen Cobamide Support
+ rationale: Preserve positive community cofactor support without traced exclusive transfer or unverified species
+ identity.
+ - node: Sporomusa DMB-Guided Cobalamin Support
+ rationale: Preserve controlled DMB-guided donor and partner phenotypes without substituting external recipient
+ strains for KB-1 members.
+ removed_node_decisions: []
+ edges_before:
+ - source: Acetogen Cobamide Support
+ target: Reductive Dechlorination to Ethene
+ description: Acetogen-derived cobalamin support supplies the cofactor context required for complete Dehalococcoides
+ reductive dechlorination in KB-1 without exogenous vitamins.
+ - source: Sporomusa DMB-Guided Cobalamin Support
+ target: Reductive Dechlorination to Ethene
+ description: DMB-guided cobalamin support can supply the corrinoid cofactor context required for Dehalococcoides
+ reductive dechlorination.
+ edges_after:
+ - source: Acetogen Cobamide Support
+ target: Reductive Dechlorination to Ethene
+ description: PARTIAL - Acetobacterium-associated cofactor availability can support Dehalococcoides dechlorination
+ in the vitamin-free KB-1 laboratory cultures. Community transfers, cofactor measurements and biosynthetic
+ genes support this route, but do not isolate its exclusive contribution or establish its mediation of the
+ separate field bioaugmentation result.
+ retained_edge_decisions:
+ - source: Acetogen Cobamide Support
+ target: Reductive Dechlorination to Ethene
+ description: PARTIAL - Acetobacterium-associated cofactor availability can support Dehalococcoides dechlorination
+ in the vitamin-free KB-1 laboratory cultures. Community transfers, cofactor measurements and biosynthetic
+ genes support this route, but do not isolate its exclusive contribution or establish its mediation of the
+ separate field bioaugmentation result.
+ rationale: Preserve the supported route with exact-system/model limits; biological or field mediation remains
+ PARTIAL.
+ removed_edge_decisions:
+ - source: Sporomusa DMB-Guided Cobalamin Support
+ target: Reductive Dechlorination to Ethene
+ description: DMB-guided cobalamin support can supply the corrinoid cofactor context required for Dehalococcoides
+ reductive dechlorination.
+ rationale: External recipient strains in controlled coculture do not establish mediation of the KB-1 field/community
+ endpoint.
+ references:
+ - PMID:12523427
+ - PMID:31441646
+ - PMID:23479750
+ issues:
+ - 1523
+ - 1526
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/KB1_Chlorinated_Ethene_Dechlorinating_Consortium/2026-10-06T182704Z-codex-64a338.yaml
+ source_review:
+ scope: Full2013/2019 primary main texts read;2019 Tables1-2/Figures2-5 visual inspection.2002 field abstract
+ only; no external supplements/raw data.
+ detailed_scope_file: source-progress.md
+ cache_provenance_certified: false
+- path: kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml
+ id: CommunityMech:000037
+ original_sha256: 9363499efd03e336a153ea8d17d0e7e05a9a9ca6fb417160b59bc2099d2783a9
+ record_sha256: 848044ac5bcc1eeea7cf6c1496f51aba0484b5ab84d09af30dc7ab20743e835d
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml
+ scope: Whole record and every original node/arrow; source-bounded existing structure repair.
+ summary: Retain model-dependent outputs without workflow causality or imposed-constraint rescue claims.
+ renamed_nodes:
+ Mixed-Bag and Compartmentalized GEM Comparison: Model-Architecture-Dependent Information Flow
+ In Silico Community-Formation Dependencies: Model-Conditional Growth Contrasts
+ node_decisions:
+ - node: Model-Architecture-Dependent Information Flow
+ rationale: Retain architecture-dependent model output without niche partitioning or an analysis-to-result causal
+ arrow.
+ - node: Model-Conditional Growth Contrasts
+ rationale: Preserve dextrin model growth while exposing imposed aerobic constraints and untested biological
+ mediation.
+ - node: Greater Community Information Flow
+ rationale: Preserve computed information metrics without assigning mutualism or universal growth benefit.
+ removed_node_decisions:
+ - node: RFMIA Community Information-Flow Adaptation
+ rationale: Researcher adaptation/construction workflow is not a biological interaction.
+ - node: Idealized Two-Member Community Model Construction
+ rationale: Researcher adaptation/construction workflow is not a biological interaction.
+ edges_before:
+ - source: RFMIA Community Information-Flow Adaptation
+ target: Idealized Two-Member Community Model Construction
+ description: 'The RFMIA framework was applied to idealized two-member microbial communities represented by genome-scale
+ metabolic models.
+
+ '
+ - source: Idealized Two-Member Community Model Construction
+ target: Mixed-Bag and Compartmentalized GEM Comparison
+ description: 'The idealized two-member models supplied the test cases for comparing mixed-bag and compartmentalized
+ community genome-scale model structures.
+
+ '
+ - source: Idealized Two-Member Community Model Construction
+ target: In Silico Community-Formation Dependencies
+ description: 'The paired idealized communities were also used to identify model dependencies that justified
+ community formation relative to isolate simulations.
+
+ '
+ - source: Mixed-Bag and Compartmentalized GEM Comparison
+ target: Greater Community Information Flow
+ description: 'Comparing the alternative GEM frameworks produced the specific result that mixed-bag community
+ models conducted more information flow than compartmentalized ones.
+
+ '
+ - source: In Silico Community-Formation Dependencies
+ target: Greater Community Information Flow
+ description: 'The modeled dependency examples accompanied the broader finding that two-member community models
+ carried more metabolic information flow than isolate models.
+
+ '
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: RFMIA Community Information-Flow Adaptation
+ target: Idealized Two-Member Community Model Construction
+ description: 'The RFMIA framework was applied to idealized two-member microbial communities represented by genome-scale
+ metabolic models.
+
+ '
+ rationale: Research workflow or accompanying model results do not establish a directed biological cause.
+ - source: Idealized Two-Member Community Model Construction
+ target: Mixed-Bag and Compartmentalized GEM Comparison
+ description: 'The idealized two-member models supplied the test cases for comparing mixed-bag and compartmentalized
+ community genome-scale model structures.
+
+ '
+ rationale: Research workflow or accompanying model results do not establish a directed biological cause.
+ - source: Idealized Two-Member Community Model Construction
+ target: In Silico Community-Formation Dependencies
+ description: 'The paired idealized communities were also used to identify model dependencies that justified
+ community formation relative to isolate simulations.
+
+ '
+ rationale: Research workflow or accompanying model results do not establish a directed biological cause.
+ - source: Mixed-Bag and Compartmentalized GEM Comparison
+ target: Greater Community Information Flow
+ description: 'Comparing the alternative GEM frameworks produced the specific result that mixed-bag community
+ models conducted more information flow than compartmentalized ones.
+
+ '
+ rationale: Research workflow or accompanying model results do not establish a directed biological cause.
+ - source: In Silico Community-Formation Dependencies
+ target: Greater Community Information Flow
+ description: 'The modeled dependency examples accompanied the broader finding that two-member community models
+ carried more metabolic information flow than isolate models.
+
+ '
+ rationale: Research workflow or accompanying model results do not establish a directed biological cause.
+ references:
+ - doi:10.1101/2023.08.23.554558
+ issues:
+ - 1524
+ - 1527
+ - 1528
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/KBase_Models_for_Zahmeeth_Original_PLOS/2026-10-06T182704Z-codex-1ab001.yaml
+ source_review:
+ scope: Full v1 author-lab15-page PDF text/captions read;selected Methods/equations/table/model-architecture/charts
+ visual inspection. No code/supplement/model-rerun audit.
+ detailed_scope_file: source-progress.md
+ cache_provenance_certified: false
+- path: kb/communities/KBase_ORT_Workflow_Community_Model.yaml
+ id: CommunityMech:000038
+ original_sha256: 850826c4759b18be1a87bcc88d948cd064fdfbe911c22a4bccb227bdc86d9ab0
+ record_sha256: b4cfa6d608db1e2d04f70537c425d23def58fb2528394a9226b82f4cc609ebf2
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml
+ scope: Whole record and every original node/arrow; source-bounded existing structure repair.
+ summary: Expose ORT gapfilled nitrogen completion and bound modeled substrate routes.
+ renamed_nodes:
+ Coupled Nitrification in Columbia River Sediments: Modeled Coupled Nitrification
+ Nitrate-to-Nitrogen Gas Denitrification: Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ Metabolome-Informed Carbon Source Utilization: Modeled Metabolome-Informed Carbon Utilization
+ node_decisions:
+ - node: Modeled Coupled Nitrification
+ rationale: Preserve sequential nitrifier model roles without demonstrated syntrophy.
+ - node: Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ rationale: Preserve simulated nitrogen output while exposing the missing genomic step and gapfill.
+ - node: Modeled Metabolome-Informed Carbon Utilization
+ rationale: Preserve model chemical breadth without measured flux, per-denitrifier substrate counts or field-limit
+ identification.
+ removed_node_decisions: []
+ edges_before:
+ - source: Coupled Nitrification in Columbia River Sediments
+ target: Nitrate-to-Nitrogen Gas Denitrification
+ description: 'Coupled archaeal and bacterial nitrification produces nitrate that feeds the downstream Steroidobacteraceae
+ denitrifiers.
+
+ '
+ - source: Metabolome-Informed Carbon Source Utilization
+ target: Nitrate-to-Nitrogen Gas Denitrification
+ description: Metabolome-derived organic carbon sources constrain the denitrifier reactions that reduce nitrate
+ through the modeled nitrogen cycle.
+ edges_after:
+ - source: Modeled Coupled Nitrification
+ target: Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ description: PARTIAL - sequential modeled nitrification supplies nitrate for modeled denitrification. This is
+ a substrate route in the proof-of-concept simulation, not proof of an exclusive environmental nitrate source,
+ obligatory partner dependence or genome-supported completion to nitrogen gas.
+ - source: Modeled Metabolome-Informed Carbon Utilization
+ target: Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ description: PARTIAL - modeled carbon uptake contributes substrate and stoichiometric context to the denitrification
+ representation. The exchange calculations support this model-level coupling, not selective demonstration that
+ these example compounds control field denitrification or are consumed by both denitrifiers.
+ retained_edge_decisions:
+ - source: Modeled Coupled Nitrification
+ target: Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ description: PARTIAL - sequential modeled nitrification supplies nitrate for modeled denitrification. This is
+ a substrate route in the proof-of-concept simulation, not proof of an exclusive environmental nitrate source,
+ obligatory partner dependence or genome-supported completion to nitrogen gas.
+ rationale: Preserve the supported route with exact-system/model limits; biological or field mediation remains
+ PARTIAL.
+ - source: Modeled Metabolome-Informed Carbon Utilization
+ target: Modeled Nitrate Reduction with Gapfilled Nitrogen Production
+ description: PARTIAL - modeled carbon uptake contributes substrate and stoichiometric context to the denitrification
+ representation. The exchange calculations support this model-level coupling, not selective demonstration that
+ these example compounds control field denitrification or are consumed by both denitrifiers.
+ rationale: Preserve the supported route with exact-system/model limits; biological or field mediation remains
+ PARTIAL.
+ removed_edge_decisions: []
+ references:
+ - PMID:34726691
+ issues:
+ - 1525
+ - 1527
+ - 1528
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/KBase_ORT_Workflow_Community_Model/2026-10-06T182705Z-codex-10ac84.yaml
+ source_review:
+ scope: Full publisher primary main text/Methods/Table1/captions read;no figure pixels,supplements,raw data/code
+ or KBase execution. Actual PubMed abstract differs from selected.md.
+ detailed_scope_file: source-progress.md
+ cache_provenance_certified: false
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 5844aa4c4..08a553078 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -206,9 +206,9 @@ kb/communities/Infant_Gut_Strain_Persistence_Maternal_Community.yaml CommunityMe
kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml CommunityMech:000036 09de6c3346c0253626f8175162e663538a44860465124483cf12f75ba655c0bd 5 3 88.0 reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml reviewed
kb/communities/Jala_Maize_PGPB_SynCom.yaml CommunityMech:000099 f1f84af4838a5c066a06690f4e5ab55130ac29dcd6bf28db302b5ce116627652 4 2 90.0 reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml reviewed
kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml CommunityMech:000356 2a203d55521c6c2f51365d762a7294e4daa222232e808468239c89b2405d8456 2 1 75.0 reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml reviewed
-kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml CommunityMech:000132 9f951642ed74d82ba8e0581acef30a3b4367e04c786c8065d658c8a5990ea217 3 2 100.0 pending
-kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml CommunityMech:000037 9363499efd03e336a153ea8d17d0e7e05a9a9ca6fb417160b59bc2099d2783a9 5 5 100.0 pending
-kb/communities/KBase_ORT_Workflow_Community_Model.yaml CommunityMech:000038 850826c4759b18be1a87bcc88d948cd064fdfbe911c22a4bccb227bdc86d9ab0 3 2 100.0 pending
+kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml CommunityMech:000132 2dddd68ddedcbb86e9524066b26f0c3ade41432b515e8bfee9427c5a49a5f1b9 3 1 80.0 reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml reviewed
+kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml CommunityMech:000037 848044ac5bcc1eeea7cf6c1496f51aba0484b5ab84d09af30dc7ab20743e835d 3 0 59.2 reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml reviewed
+kb/communities/KBase_ORT_Workflow_Community_Model.yaml CommunityMech:000038 b4cfa6d608db1e2d04f70537c425d23def58fb2528394a9226b82f4cc609ebf2 3 2 90.0 reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml reviewed
kb/communities/KBase_Synthetic_Bacterial_Community_R2A.yaml CommunityMech:000039 e3457fd6a6f0d72ebea718b86fa7e33e989af6bad87f7b553b8b41a8228b331a 3 2 100.0 pending
kb/communities/Kefir_Flavor_Lentilactobacillus_Kluyveromyces_Coculture.yaml CommunityMech:000332 4485382b7e341df884ca34ff9bf9bd7d3bf0c8f36cd99f91e9714461c67e7234 6 0 75.0 pending
kb/communities/Klebsiella_Arthrobacter_KZ_Phenanthrene_Cadmium_SynCom.yaml CommunityMech:000344 1d9b711fa86c876ec1657a114242ebba6cb14cd8be5323a25baeae6511c9b520 1 0 65.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 40aa8e637..f043e5dd6 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": 1463,
- "edges": 660,
+ "nodes": 1461,
+ "edges": 654,
"records_without_nodes": 8,
- "records_without_edges": 154,
+ "records_without_edges": 155,
"review_status_counts": {
"needs_research": 18,
- "pending": 255,
- "reviewed": 187
+ "pending": 252,
+ "reviewed": 190
},
"structural_defects": [],
"network_audit": [
@@ -724,6 +724,102 @@
"message": "Taxon 'RUG023 sp. (MAG SPH2)' has no interactions",
"severity": "warning"
},
+ {
+ "record": "KBase_Models_for_Zahmeeth_Original_PLOS",
+ "type": "DISCONNECTED",
+ "taxon": "Klebsiella",
+ "taxon_id": "NCBITaxon:570",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Klebsiella",
+ "term": {
+ "id": "NCBITaxon:570",
+ "label": "Klebsiella"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Klebsiella",
+ "gtdb_taxon": "Klebsiella",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella",
+ "ncbi_source_id": "NCBITaxon:570",
+ "majority_fraction": 1.0,
+ "support_genomes": 44527,
+ "total_genomes": 44529,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 2 GTDB taxa under the NCBI taxon]"
+ }
+ },
+ "functional_role": [
+ "CROSS_FEEDER"
+ ],
+ "evidence": [
+ {
+ "reference": "doi:10.1101/2023.08.23.554558",
+ "supports": "SUPPORT",
+ "evidence_source": "COMPUTATIONAL",
+ "snippet": "another of Bacteroides thetaiotaomicron (B. theta) and Klebsiella",
+ "explanation": "Establishes Klebsiella as a member of the computational community models."
+ }
+ ]
+ },
+ "message": "Taxon 'Klebsiella' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "KBase_Models_for_Zahmeeth_Original_PLOS",
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonas fluorescens",
+ "taxon_id": "NCBITaxon:294",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonas fluorescens",
+ "term": {
+ "id": "NCBITaxon:294",
+ "label": "Pseudomonas fluorescens"
+ },
+ "gtdb_grounding_status": "AMBIGUOUS",
+ "gtdb_candidates": [
+ "GTDB:s__Pseudomonas_E_alvandae",
+ "GTDB:s__Pseudomonas_E_asgharzadehiana",
+ "GTDB:s__Pseudomonas_E_azotoformans_A",
+ "GTDB:s__Pseudomonas_E_brassicacearum",
+ "GTDB:s__Pseudomonas_E_crudilactis",
+ "GTDB:s__Pseudomonas_E_edaphica",
+ "GTDB:s__Pseudomonas_E_fluorescens",
+ "GTDB:s__Pseudomonas_E_fluorescens_AP",
+ "GTDB:s__Pseudomonas_E_fluorescens_AQ",
+ "GTDB:s__Pseudomonas_E_fluorescens_B",
+ "GTDB:s__Pseudomonas_E_fluorescens_H",
+ "GTDB:s__Pseudomonas_E_fluorescens_S",
+ "GTDB:s__Pseudomonas_E_kilonensis",
+ "GTDB:s__Pseudomonas_E_lactis",
+ "GTDB:s__Pseudomonas_E_lactucae",
+ "GTDB:s__Pseudomonas_E_paracarnis",
+ "GTDB:s__Pseudomonas_E_petroselini",
+ "GTDB:s__Pseudomonas_E_poae",
+ "GTDB:s__Pseudomonas_E_protegens",
+ "GTDB:s__Pseudomonas_E_reactans",
+ "GTDB:s__Pseudomonas_E_salomonii",
+ "GTDB:s__Pseudomonas_E_simiae",
+ "GTDB:s__Pseudomonas_E_sp002874965"
+ ]
+ },
+ "functional_role": [
+ "CROSS_FEEDER"
+ ],
+ "evidence": [
+ {
+ "reference": "doi:10.1101/2023.08.23.554558",
+ "supports": "SUPPORT",
+ "evidence_source": "COMPUTATIONAL",
+ "snippet": "idealized two-member microbial communities, one of E. coli and Pseudomonas fluorescens",
+ "explanation": "Establishes P. fluorescens as a member of the computational community models."
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonas fluorescens' has no interactions",
+ "severity": "warning"
+ },
{
"record": "Mangrove_Benzene_MFC_Bioanode_Consortium",
"type": "DISCONNECTED",
diff --git a/reports/causal_graph_review/validation-20261006-batch56.json b/reports/causal_graph_review/validation-20261006-batch56.json
new file mode 100644
index 000000000..1cf83a8ac
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch56.json
@@ -0,0 +1,922 @@
+{
+ "base_commit": "e9893c06c181d1705eb2917ef865f0579ba19761",
+ "scope": [
+ "kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml",
+ "kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml",
+ "kb/communities/KBase_ORT_Workflow_Community_Model.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "KB1_Chlorinated_Ethene_Dechlorinating_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KB1_Chlorinated_Ethene_Dechlorinating_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "KB1_Chlorinated_Ethene_Dechlorinating_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch56/KB1_Chlorinated_Ethene_Dechlorinating_Consortium-strict.tsv",
+ "kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KB1_Chlorinated_Ethene_Dechlorinating_Consortium-strict.log",
+ "log_sha256": "576612a392425185656cc7d16f66ba00c1073a7eff1d913280732ac11c8987ac",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch56/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-batch56/KB1_Chlorinated_Ethene_Dechlorinating_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "KB1_Chlorinated_Ethene_Dechlorinating_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KB1_Chlorinated_Ethene_Dechlorinating_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "KB1_Chlorinated_Ethene_Dechlorinating_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KB1_Chlorinated_Ethene_Dechlorinating_Consortium-references.log",
+ "log_sha256": "10f632e0f0268b6dabe6634acd748a2c27635e1c0d76c451a7b5fbe4689a4e19",
+ "output_tail": "Validating kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "KB1_Chlorinated_Ethene_Dechlorinating_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KB1_Chlorinated_Ethene_Dechlorinating_Consortium-snippets.log",
+ "log_sha256": "f77044cea09a90a006f3fc48666f62a208521829981c6819a3a36631506c4ec1",
+ "output_tail": "# 16 evidence snippets scanned across 1 files\n MATCH 16\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": "KB1_Chlorinated_Ethene_Dechlorinating_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KB1_Chlorinated_Ethene_Dechlorinating_Consortium-rank.log",
+ "log_sha256": "fb9390799470ef2f06c4c4046dda79241c72912a3754738dbf1f541bf82cc49c",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000132\",\n \"name\": \"KB-1 Chlorinated Ethene Dechlorinating Consortium\",\n \"score\": 80.0,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "KB1_Chlorinated_Ethene_Dechlorinating_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/KB1_Chlorinated_Ethene_Dechlorinating_Consortium/2026-10-06T182704Z-codex-64a338.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KB1_Chlorinated_Ethene_Dechlorinating_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "KBase_Models_for_Zahmeeth_Original_PLOS-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_Models_for_Zahmeeth_Original_PLOS-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "KBase_Models_for_Zahmeeth_Original_PLOS-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch56/KBase_Models_for_Zahmeeth_Original_PLOS-strict.tsv",
+ "kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_Models_for_Zahmeeth_Original_PLOS-strict.log",
+ "log_sha256": "ccdfc6c2f01d0a687dcc4865bc4a28f61080f4dacf937718ec90c67988442af3",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch56/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-batch56/KBase_Models_for_Zahmeeth_Original_PLOS-strict.tsv\n"
+ },
+ {
+ "check": "KBase_Models_for_Zahmeeth_Original_PLOS-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_Models_for_Zahmeeth_Original_PLOS-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "KBase_Models_for_Zahmeeth_Original_PLOS-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_Models_for_Zahmeeth_Original_PLOS-references.log",
+ "log_sha256": "cb4266f3fffbd34c087151866017768c78a96e5ba9831e7055b119b45f53ed8e",
+ "output_tail": "Validating kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.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/KBase_Models_for_Zahmeeth_Original_PLOS.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": "KBase_Models_for_Zahmeeth_Original_PLOS-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_Models_for_Zahmeeth_Original_PLOS-snippets.log",
+ "log_sha256": "1835af07ebf0373785ca2d25de18c6984a3cbcfdec0d2610f1d8437504408710",
+ "output_tail": "# 10 evidence snippets scanned across 1 files\n MATCH 10\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": "KBase_Models_for_Zahmeeth_Original_PLOS-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_Models_for_Zahmeeth_Original_PLOS-rank.log",
+ "log_sha256": "c232b0248bf4b89dbed65d02a8f5665af7a9e6dae24bdb608dc47221224f5d25",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000037\",\n \"name\": \"KBase Models for Zahmeeth Original PLOS\",\n \"score\": 59.2,\n \"taxonomy\": 4,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 2,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\",\n \"disconnected_taxa\"\n ],\n \"path\": \"kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "KBase_Models_for_Zahmeeth_Original_PLOS-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/KBase_Models_for_Zahmeeth_Original_PLOS/2026-10-06T182704Z-codex-1ab001.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_Models_for_Zahmeeth_Original_PLOS-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "KBase_ORT_Workflow_Community_Model-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/KBase_ORT_Workflow_Community_Model.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_ORT_Workflow_Community_Model-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "KBase_ORT_Workflow_Community_Model-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch56/KBase_ORT_Workflow_Community_Model-strict.tsv",
+ "kb/communities/KBase_ORT_Workflow_Community_Model.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_ORT_Workflow_Community_Model-strict.log",
+ "log_sha256": "58548eb5aa8c728adade4cf19a8c34632b9df8910ef20cb44f3a1304b6942633",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch56/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-batch56/KBase_ORT_Workflow_Community_Model-strict.tsv\n"
+ },
+ {
+ "check": "KBase_ORT_Workflow_Community_Model-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/KBase_ORT_Workflow_Community_Model.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_ORT_Workflow_Community_Model-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "KBase_ORT_Workflow_Community_Model-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/KBase_ORT_Workflow_Community_Model.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_ORT_Workflow_Community_Model-references.log",
+ "log_sha256": "661eee137e0e8179b35bf606af69a85a777d2493957be2b662102a52e1c60d2e",
+ "output_tail": "Validating kb/communities/KBase_ORT_Workflow_Community_Model.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/KBase_ORT_Workflow_Community_Model.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": "KBase_ORT_Workflow_Community_Model-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/KBase_ORT_Workflow_Community_Model.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_ORT_Workflow_Community_Model-snippets.log",
+ "log_sha256": "aec1f2712a64b5cd549f668dd69d5e1ab54d6d5693d8f53bbce26317b755b383",
+ "output_tail": "# 11 evidence snippets scanned across 1 files\n MATCH 11\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": "KBase_ORT_Workflow_Community_Model-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/KBase_ORT_Workflow_Community_Model.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_ORT_Workflow_Community_Model-rank.log",
+ "log_sha256": "3a023e32e02acc1bd9502a0e38605ceb0f5d080bc8bc392b93255b944b316236",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000038\",\n \"name\": \"KBase ORT Workflow Community Model\",\n \"score\": 90.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/KBase_ORT_Workflow_Community_Model.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "KBase_ORT_Workflow_Community_Model-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/KBase_ORT_Workflow_Community_Model/2026-10-06T182705Z-codex-10ac84.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/KBase_ORT_Workflow_Community_Model-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-batch56/inventory.log",
+ "log_sha256": "3dd0f3a0907b4225c9cfe5e32ac88534a4960f220344f02377c7c9d9a2765d75",
+ "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\": 1461,\n \"edges\": 654,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 155,\n \"review_status_counts\": {\n \"needs_research\": 18,\n \"pending\": 252,\n \"reviewed\": 190\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-batch56/network.log",
+ "log_sha256": "0955d3471f474fec8dcceb846ff932573d11c9833de73b2b2822241553762186",
+ "output_tail": "{\n \"preferred_term\": \"Legionella MAGs\",\n \"term\": {\n \"id\": \"NCBITaxon:445\",\n \"label\": \"Legionella\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n },\n \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n \"evidence\": [\n {\n \"reference\": \"PMID:41457319\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"COMPUTATIONAL\",\n \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n }\n ]\n },\n \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\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}\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/rank-all.log",
+ "log_sha256": "9d79ea15e18ca814f177d7a5521c204f3f71474c83e1b95c5b8c3f6673e58fb1",
+ "output_tail": "ities/Soybean_N_Fixation_sfSynCom.yaml\tCommunityMech:000064\tSoybean N-Fixation Simplified SynCom\t4\t4\t0\t3\t2\t3\t\t0\t0\n402\t100.0\tkb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml\tCommunityMech:000267\tSphingobium-Rhodococcus Lignin-Dimer Valorization Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n403\t100.0\tkb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml\tCommunityMech:000326\tStaphylococcus-Candida Context-Dependent Biofilm Coculture\t2\t2\t0\t6\t2\t13\t\t0\t0\n404\t100.0\tkb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml\tCommunityMech:000254\tStordalen Mire Methylotrophic Methanogenesis Community\t3\t3\t0\t4\t4\t9\t\t0\t0\n405\t100.0\tkb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml\tCommunityMech:000335\tStreptomyces A2-A5-A11-M7 Pesticide-Bioremediation Consortium\t4\t4\t0\t4\t2\t5\t\t0\t0\n406\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t5\t2\t5\t\t0\t0\n407\t100.0\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t4\t\t0\t0\n408\t100.0\tkb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml\tCommunityMech:000222\tSulfide Spring Autotrophic CPR-Hosting Biofilm\t3\t3\t0\t3\t2\t4\t\t0\t0\n409\t100.0\tkb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml\tCommunityMech:000127\tSynComBac10 Chicken Intestinal SynCom\t3\t3\t0\t3\t2\t3\t\t0\t0\n410\t100.0\tkb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\tCommunityMech:000314\tSynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community\t5\t5\t0\t3\t2\t3\t\t0\t0\n411\t100.0\tkb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\tCommunityMech:000278\tSynCom BsBv Cigar Tobacco Leaf Fermentation\t2\t2\t0\t3\t2\t3\t\t0\t0\n412\t100.0\tkb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\tCommunityMech:000285\tSynCom + Chlorella sorokiniana Biogas-slurry Coupling System\t2\t2\t0\t5\t3\t5\t\t0\t0\n413\t100.0\tkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\tCommunityMech:000302\tSynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\t2\t2\t0\t3\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n417\t100.0\tkb/communities/Synechococcus_Bacillus_SPC.yaml\tCommunityMech:000065\tSynechococcus-Bacillus Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n418\t100.0\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n419\t100.0\tkb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\tCommunityMech:000198\tSynechococcus-Halomonas Light-Driven PHB Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\tCommunityMech:000167\tSynechococcus-Pseudomonas Phototrophic PHA and DNT Coculture\t2\t2\t0\t4\t2\t8\t\t0\t0\n421\t100.0\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n422\t100.0\tkb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\tCommunityMech:000211\tSynechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n424\t100.0\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t8\t\t0\t0\n425\t100.0\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t5\t\t0\t0\n426\t100.0\tkb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml\tCommunityMech:000189\tSyntrophomonas-Methanococcus Butyrate Growth Coordination Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n427\t100.0\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n428\t100.0\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\t\t0\t0\n429\t100.0\tkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml\tCommunityMech:000187\tSyntrophus-Methanospirillum Gentianae Benzoate Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n431\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n432\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\n433\t100.0\tkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml\tCommunityMech:000259\tThalassiosira-Marinobacter Marine Snow Coculture\t2\t2\t0\t4\t2\t10\t\t0\t0\n434\t100.0\tkb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml\tCommunityMech:000162\tThalassiosira-Ruegeria Phycosphere Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n435\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\n436\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\n437\t100.0\tkb/communities/Thermophilic_Pyrite_QS_Consortium.yaml\tCommunityMech:000073\tThermophilic Pyrite Quorum Sensing Consortium\t3\t3\t0\t6\t2\t14\t\t0\t0\n438\t100.0\tkb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\tCommunityMech:000186\tThermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\t2\t2\t0\t3\t2\t8\t\t0\t0\n439\t100.0\tkb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml\tCommunityMech:000239\tThiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community\t3\t3\t0\t3\t2\t3\t\t0\t0\n440\t100.0\tkb/communities/Tinto_River_Iron_Cycling_Community.yaml\tCommunityMech:000074\tTinto River Iron Cycling Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\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\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\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-batch56/render.log",
+ "log_sha256": "6be0aa44b842cf20124dff133fa9a99278f1ea711beb810ef315ceae7e34e48a",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch56/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch56/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch56/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-batch56/render-repeat.log",
+ "log_sha256": "6be0aa44b842cf20124dff133fa9a99278f1ea711beb810ef315ceae7e34e48a",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch56/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch56/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch56/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch56/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json, pathlib, runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch55')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda: paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/connectivity-survey.log",
+ "log_sha256": "0cba7b1ce46ae54af280c908931b05bb57eb071fc18ccf86db6282c4c686b3e5",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 390, \"mixed\": 125, \"community_level_only\": 265, \"taxa\": 1505, \"credited_solely_by_the_rule\": 1233}, \"current\": {\"records\": 460, \"with_community_level\": 390, \"mixed\": 124, \"community_level_only\": 266, \"taxa\": 1505, \"credited_solely_by_the_rule\": 1236}}\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_batch11.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_batch6.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch9.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-batch56/regressions.log",
+ "log_sha256": "c8b10e103983d439a4945811fc04843ba45f5c43bf40378bac5cf3c10977214e",
+ "output_tail": "........................................................................ [ 13%]\n........................................................................ [ 27%]\n........................................................................ [ 41%]\n........................................................................ [ 54%]\n........................................................................ [ 68%]\n........................................................................ [ 82%]\n........................................................................ [ 95%]\n...................... [100%]\n526 passed in 185.75s (0:03:05)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/black.log",
+ "log_sha256": "b9cf511501d306d2bd8355ccb165c8ddc0a6fdd62d7c72c4a7b1795cf8934c8c",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n2 files would be left unchanged.\n"
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ },
+ {
+ "check": "primary-graph-fragments",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import hashlib,json,pathlib,yaml\nroot=pathlib.Path('/private/tmp/communitymech-batch56')\ndoc=yaml.safe_load(pathlib.Path('kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml').read_text())\nprimary=' '.join((root/'zahmeeth-2023-primary.txt').read_text().split())\nrfmia=[e['snippet'] for n in doc['ecological_interactions'] for e in n['evidence']]\nassert all(' '.join(q.split()) in primary for q in rfmia)\ndoc=yaml.safe_load(pathlib.Path('kb/communities/KBase_ORT_Workflow_Community_Model.yaml').read_text())\nprimary=' '.join((root/'ort-primary.txt').read_text().split())\nort=list(dict.fromkeys(e['snippet'] for n in doc['ecological_interactions'] for e in n['evidence']))\nassert all(' '.join(q.split()) in primary for q in ort)\nassert 'neither of these genomes encoded a gene' in primary\nprint(json.dumps({'rfmia_verified_graph_fragments':len(rfmia),'ort_verified_graph_fragments':len(ort),'complete_cache_provenance_certified':False}))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/primary-graph-fragments.log",
+ "log_sha256": "dfcb8f1e787ba29677dc904d4471f892df03b31445e06c7abed6f054a68f8e5a",
+ "output_tail": "{\"rfmia_verified_graph_fragments\": 3, \"ort_verified_graph_fragments\": 2, \"complete_cache_provenance_certified\": false}\n"
+ },
+ {
+ "check": "final-ledger-regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch56.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch56/final-ledger-regressions.log",
+ "log_sha256": "40b951cae52565860314b0637b01b87ec8f152cb33777b78996e501a0f6a1bcc",
+ "output_tail": "....... [100%]\n7 passed in 0.74s\n"
+ }
+ ],
+ "limitations": [
+ "All11 original nodes/9 arrows reviewed;9 nodes/3 PARTIAL arrows remain. Two procedural nodes and six unsupported/procedural arrows removed. No new graph structure.",
+ "Full2013/2019 KB1 primary bodies read;2019 selected figures/tables inspected;2002 field abstract only. No2013 original images or external supplements/raw data.",
+ "Full RFMIA v1 PDF text/captions read and selected Methods/equations/table/architecture/charts inspected; no mathematical derivation, model rerun, supplementary/raw/code/narrative audit.",
+ "Full ORT publisher body/Methods/Table1/captions read; no original figure pixels, supplements, raw data/code or KBase execution. Platform paper title/header/opening paragraphs only (no indexed abstract), not full-paper recertification.",
+ "All920 caches remain byte-identical. Primary-checked short graph fragments do not certify complete cached abstracts. ORT and RFMIA cache discrepancies remain1528; existing1362 selected.txt provenance and1091 Linux DOI lookup remain separate limitations.",
+ "Canonical taxonomy and raw non-graph fields preserved, not recertified. KB1 species identity remains1526; model identities/design/narrative metadata remain1527. Positive cofactor/coculture effects and modeled outputs are preserved with study limits.",
+ "No Edison dry run, paid request/report or spend. Existing graph repairs only; future extension requires separate one-community research and specific payload/spend authorization.",
+ "Dedup includes827 all-state issue titles/bodies, broader synonyms and38 ignored/hidden local matches with scoped exclusions described in source-progress.md. Not every historical comment/PR or generated page inspected.",
+ "Repair1523-1525 stay open until protected-main merge;1526-1528 remain unresolved afterward. This is self-adversarial review, not independent approval.",
+ "SupportingReference coverage476 and writer artifact1095 remain known limitations. Reference CLI Total checks counts reported issues, not executed checks.",
+ "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate.",
+ "RFMIA explicit Methods/Results participants expose two DISCONNECTED warnings for the abstract-only alternative taxa. These are unresolved membership metadata under1527, not a reason to invent interactions or expand participant lists. Total36 network warnings; zero dangling edges/anchors."
+ ],
+ "snippet_counts_by_record": {
+ "kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml": {
+ "MATCH": 16,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml": {
+ "MATCH": 10,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/KBase_ORT_Workflow_Community_Model.yaml": {
+ "MATCH": 11,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 33,
+ "unchanged_record_files": 457,
+ "unchanged_cache_files": 920,
+ "primary_artifacts": {
+ "source-progress.md": "93fa1b7fbb20619c2bc7b93ed09fda1df34518379a1deee74724d47ae9864c0b",
+ "source-extraction.json": "8d88104ce4204d6de08335f706071ce73984c753e5fe05059dd419ce4cf6377c",
+ "cobalamin-primary.html": "060332e3face6c618198fb71ff9d0e9754b81f53831528ff2082c2b5b2d09848",
+ "cobalamin-primary.txt": "28730e5e8736e0d59fc764d847d88da93e94b148ad0bcc7634b9595b711111e3",
+ "ort-primary.html": "fae8933afd99b0d6e24aea48c952eb18763566b46451c10ea38db39dbf30269e",
+ "ort-primary.txt": "a23d2b3d56b764c0ea448766a339a863d595f8b1311865096c20594f607fad1a",
+ "zahmeeth-2023-primary.pdf": "004ce9de311e7bf7b5ecffe07e69eee5a98b5ef815677aa9d9290dc7e6edf792",
+ "zahmeeth-2023-primary.txt": "0915cb04aa02767d81ccaaa233cd45341fdebb2c77cc1dcf9d19e48d9625c295",
+ "kb1-2019-primary.pdf": "dcfed8d1b6e89ddfd9aab41ed454bbf1d85c091b2642c4b8a586e2b839b6b15f",
+ "kb1-2019-primary.txt": "33bf0dcf75a02e0bfa8d42d1b7332c038d33947b0438dc2777728121738b9094"
+ },
+ "cache_provenance_caveat": "All cache bytes preserved; MATCH does not certify the mismatching ORT/RFMIA abstracts. See1528.",
+ "network_delta": {
+ "existing_findings_preserved": 34,
+ "added_findings": {
+ "KBase_Models_for_Zahmeeth_Original_PLOS": [
+ {
+ "type": "DISCONNECTED",
+ "taxon": "Klebsiella",
+ "taxon_id": "NCBITaxon:570",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Klebsiella",
+ "term": {
+ "id": "NCBITaxon:570",
+ "label": "Klebsiella"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Klebsiella",
+ "gtdb_taxon": "Klebsiella",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella",
+ "ncbi_source_id": "NCBITaxon:570",
+ "majority_fraction": 1.0,
+ "support_genomes": 44527,
+ "total_genomes": 44529,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 2 GTDB taxa under the NCBI taxon]"
+ }
+ },
+ "functional_role": [
+ "CROSS_FEEDER"
+ ],
+ "evidence": [
+ {
+ "reference": "doi:10.1101/2023.08.23.554558",
+ "supports": "SUPPORT",
+ "evidence_source": "COMPUTATIONAL",
+ "snippet": "another of Bacteroides thetaiotaomicron (B. theta) and Klebsiella",
+ "explanation": "Establishes Klebsiella as a member of the computational community models."
+ }
+ ]
+ },
+ "message": "Taxon 'Klebsiella' has no interactions"
+ },
+ {
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonas fluorescens",
+ "taxon_id": "NCBITaxon:294",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonas fluorescens",
+ "term": {
+ "id": "NCBITaxon:294",
+ "label": "Pseudomonas fluorescens"
+ },
+ "gtdb_grounding_status": "AMBIGUOUS",
+ "gtdb_candidates": [
+ "GTDB:s__Pseudomonas_E_alvandae",
+ "GTDB:s__Pseudomonas_E_asgharzadehiana",
+ "GTDB:s__Pseudomonas_E_azotoformans_A",
+ "GTDB:s__Pseudomonas_E_brassicacearum",
+ "GTDB:s__Pseudomonas_E_crudilactis",
+ "GTDB:s__Pseudomonas_E_edaphica",
+ "GTDB:s__Pseudomonas_E_fluorescens",
+ "GTDB:s__Pseudomonas_E_fluorescens_AP",
+ "GTDB:s__Pseudomonas_E_fluorescens_AQ",
+ "GTDB:s__Pseudomonas_E_fluorescens_B",
+ "GTDB:s__Pseudomonas_E_fluorescens_H",
+ "GTDB:s__Pseudomonas_E_fluorescens_S",
+ "GTDB:s__Pseudomonas_E_kilonensis",
+ "GTDB:s__Pseudomonas_E_lactis",
+ "GTDB:s__Pseudomonas_E_lactucae",
+ "GTDB:s__Pseudomonas_E_paracarnis",
+ "GTDB:s__Pseudomonas_E_petroselini",
+ "GTDB:s__Pseudomonas_E_poae",
+ "GTDB:s__Pseudomonas_E_protegens",
+ "GTDB:s__Pseudomonas_E_reactans",
+ "GTDB:s__Pseudomonas_E_salomonii",
+ "GTDB:s__Pseudomonas_E_simiae",
+ "GTDB:s__Pseudomonas_E_sp002874965"
+ ]
+ },
+ "functional_role": [
+ "CROSS_FEEDER"
+ ],
+ "evidence": [
+ {
+ "reference": "doi:10.1101/2023.08.23.554558",
+ "supports": "SUPPORT",
+ "evidence_source": "COMPUTATIONAL",
+ "snippet": "idealized two-member microbial communities, one of E. coli and Pseudomonas fluorescens",
+ "explanation": "Establishes P. fluorescens as a member of the computational community models."
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonas fluorescens' has no interactions"
+ }
+ ]
+ },
+ "removed_findings": {}
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1447,
+ "arrows": 646
+ },
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 390,
+ "mixed": 125,
+ "community_level_only": 265,
+ "taxa": 1505,
+ "credited_solely_by_the_rule": 1233
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 390,
+ "mixed": 124,
+ "community_level_only": 266,
+ "taxa": 1505,
+ "credited_solely_by_the_rule": 1236
+ }
+ },
+ "interpretation": "KB1 now represents community observations with explicit participant subsets rather than unverified exact pair assignments. Three formerly pairwise-covered canonical taxa move into the solely-community-level count. No taxonomy or production connectivity-rule changes; the RFMIA source-pair discrepancy is not hidden by adding unsupported participants."
+ },
+ "network_warning_count": 36,
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1461,
+ "edges": 654,
+ "records_without_nodes": 8,
+ "records_without_edges": 155,
+ "review_status_counts": {
+ "needs_research": 18,
+ "pending": 252,
+ "reviewed": 190
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml": "b45144b36c7683c4f2273ab9fb5bfa1d13c50d28ebad3e8594f19e700086eef2",
+ "tests/test_causal_review_batch56.py": "30171988efbe30351b7e84596c8186cdce497f5a2583ddf560191ba337ee4c82",
+ "tests/test_participating_taxa.py": "ca533428e9ced189980963c393a262fac560f9345144282070a24465efa90323",
+ "kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml": "2dddd68ddedcbb86e9524066b26f0c3ade41432b515e8bfee9427c5a49a5f1b9",
+ "kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml": "848044ac5bcc1eeea7cf6c1496f51aba0484b5ab84d09af30dc7ab20743e835d",
+ "kb/communities/KBase_ORT_Workflow_Community_Model.yaml": "b4cfa6d608db1e2d04f70537c425d23def58fb2528394a9226b82f4cc609ebf2",
+ "reports/causal_graph_review/README.md": "d50ea4947db2074889a0bb5d2e86cb1282a5a65f4adc51b42484ad90df5c3d19"
+ },
+ "status": "verified_kb1_and_kbase_graph_repair",
+ "source_scope_label_correction": {
+ "previous_ledger_sha256": "f7eeb7de7e8dd4e7a72fbb3636424eed884178f9eaae5091ba9c87d85458f990",
+ "reason": "Platform title/header/opening paragraphs were inspected; no indexed abstract exists. Corrected the label, not scientific data. Final ledger regression rerun below."
+ },
+ "reference_validator_caveat": "CLI Total checks counts reported issues, not executed checks. Exit0 and MATCH do not certify source provenance or scientific support. Retained graph fragments were checked against primary sources; mismatching cached abstracts/nongraph excerpts remain1528. Coverage476, Linux DOI lookup1091 and selected.txt trust1362 remain limitations.",
+ "pre_research_baseline": {
+ "base_commit": "e9893c06c181d1705eb2917ef865f0579ba19761",
+ "base_tree": "f320485bfbcfede39762d87e8538a01464f636a2",
+ "research_worktree": "/private/tmp/communitymech-causal-batch55",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch56/baseline-rank.log",
+ "sha256": "ced9f8fea391d04515d476080b62fdcc346daeca017d369dab1307dc378f4c95",
+ "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\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\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\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"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch56/baseline-just-network.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"
+ },
+ {
+ "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-batch56/baseline-network.log",
+ "sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "output_tail": " \"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}\n"
+ },
+ {
+ "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-batch56/baseline-downstream.log",
+ "sha256": "d9120a51f5ddc8110ff553d5a34126cf12268bd3081eed2887141365e08fdff8",
+ "output_tail": "la_Methane_Sequestration_Coculture.yaml:161: downstream:\nkb/communities/Methylomicrobium_Chlorella_Methane_Sequestration_Coculture.yaml:258: downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:104: downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:127: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:157: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:203: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:199: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:267: downstream:\nkb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml:336: downstream:\nkb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:76: downstream:\nkb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:95: downstream:\nkb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:122: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:281: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:401: downstream:\nkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:223: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:342: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:381: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:135: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\nkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml:247: downstream:\nkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml:344: downstream:\nkb/communities/AMD_Acidophile_Heterotroph_Network.yaml:364: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:207: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "3bafb6cbe362af30c6260c3b4e898aec862b7eb94868833e4f213b0f09016097"
+ }
+}
diff --git a/tests/test_causal_review_batch56.py b/tests/test_causal_review_batch56.py
new file mode 100644
index 000000000..7dc4f53a5
--- /dev/null
+++ b/tests/test_causal_review_batch56.py
@@ -0,0 +1,136 @@
+"""Pin source-system boundaries, model assumptions and the complete graph ledger."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-three-records-batch56.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ return ledger, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in ledger["records"]]
+
+
+def test_explicit_participants_preserve_exact_canonical_subsets():
+ _, docs = records()
+ scopes = [[[0, 1, 2], [0, 1], [2]], [[0, 2]] * 3, [[0, 1], [2, 3], [0, 1, 2, 3]]]
+ for doc, subsets in zip(docs, scopes, strict=True):
+ for node, indexes in zip(doc["ecological_interactions"], subsets, strict=True):
+ assert node["scope"] == "COMMUNITY_LEVEL"
+ assert not {"interaction_type", "source_taxon", "target_taxon"} & node.keys()
+ assert node["participating_taxa"] == [
+ {
+ "preferred_term": doc["taxonomy"][i]["taxon_term"]["preferred_term"],
+ "term": doc["taxonomy"][i]["taxon_term"]["term"],
+ }
+ for i in indexes
+ ]
+ denitrifiers = docs[2]["ecological_interactions"][1]["participating_taxa"]
+ assert len({p["preferred_term"] for p in denitrifiers}) == 2
+ assert {p["term"]["id"] for p in denitrifiers} == {"NCBITaxon:2689614"}
+
+
+def test_kb1_retains_positive_cofactor_support_and_field_endpoint():
+ _, (doc, _, _) = records()
+ outcome, acetogen, _ = doc["ecological_interactions"]
+ assert "ethene accounted" in outcome["description"]
+ assert "consortium outcomes" in outcome["description"]
+ assert "positive community experiments" in acetogen["description"]
+ assert "DMB did not rescue" in acetogen["description"]
+ assert "#1526" in acetogen["description"]
+ arrow = acetogen["downstream"][0]
+ assert arrow["target"] == outcome["name"]
+ assert arrow["description"].startswith("PARTIAL - ")
+ assert "separate field" in arrow["description"]
+ assert all(e["supports"] == "SUPPORT" for e in acetogen["evidence"])
+
+
+def test_sporomusa_positive_rescue_does_not_substitute_external_recipients():
+ _, (doc, _, _) = records()
+ sporo = doc["ecological_interactions"][2]
+ assert "BAV1, GT and FL2" in sporo["description"]
+ assert "restored partner dechlorination and growth" in sporo["description"]
+ assert "FL2 still produced both VC and ethene" in sporo["description"]
+ assert "donor only" in sporo["description"]
+ assert "downstream" not in sporo
+ assert all(p["term"]["id"] != "GO:0015889" for p in sporo["biological_processes"])
+
+
+def test_rfmia_imposed_constraint_is_not_independent_rescue_or_measured_mutualism():
+ _, (_, doc, _) = records()
+ architecture, dependency, information = doc["ecological_interactions"]
+ assert architecture["name"] == "Model-Architecture-Dependent Information Flow"
+ assert "not observed niche partitioning" in architecture["description"]
+ assert "Community models grew on dextrin" in dependency["description"]
+ assert "manually set to zero" in dependency["description"]
+ assert "not independently predicted partner rescue" in dependency["description"]
+ assert "concentration" not in dependency["metabolites"][0]
+ assert "computed information-theoretic outputs" in information["description"]
+ for node in doc["ecological_interactions"]:
+ assert "abstract names different pairs" in node["description"]
+ assert "downstream" not in node and "biological_processes" not in node
+ assert all(e["evidence_source"] == "COMPUTATIONAL" for e in node["evidence"])
+
+
+def test_ort_nitrogen_completion_is_explicitly_gapfilled():
+ _, (_, _, doc) = records()
+ nitrification, denitrification, carbon = doc["ecological_interactions"]
+ assert "Neither MAG encoded nitrogen-gas production" in denitrification["description"]
+ assert "N2O-to-N2 reaction was added by gapfilling" in denitrification["description"]
+ assert "dissolved nitrogen" in denitrification["description"]
+ assert "not experimentally measured partner transfer" in nitrification["description"]
+ assert "not assigned to every denitrifier" in carbon["description"]
+ assert len(denitrification["metabolites"]) == 2
+ assert all(
+ "concentration" not in m
+ for n in doc["ecological_interactions"]
+ for m in n.get("metabolites", [])
+ )
+ for node in [nitrification, carbon]:
+ arrow = node["downstream"][0]
+ assert arrow["target"] == denitrification["name"]
+ assert arrow["description"].startswith("PARTIAL - ")
+ assert "no high-resolution empirical time series" in doc["discussions"][-1]["rationale"]
+
+
+def test_every_original_node_and_arrow_has_exactly_one_decision():
+ ledger, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1523, 1524, 1525]
+ assert ledger["unresolved_non_graph_issues"] == [1526, 1527, 1528]
+ for index, (row, doc) in enumerate(zip(ledger["records"], docs, strict=True)):
+ assert row["status"] == "reviewed"
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert len(row["node_decisions"]) + len(row["removed_node_decisions"]) == [3, 5, 3][index]
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ assert {d["node"] for d in row["node_decisions"]} == names
+ rename = row["renamed_nodes"]
+ before = {
+ (rename.get(e["source"], e["source"]), rename.get(e["target"], e["target"]))
+ for e in row["edges_before"]
+ }
+ kept = {(e["source"], e["target"]) for e in row["retained_edge_decisions"]}
+ removed = {
+ (rename.get(e["source"], e["source"]), rename.get(e["target"], e["target"]))
+ for e in row["removed_edge_decisions"]
+ }
+ assert before == kept | removed and not kept & removed
+ assert len(kept) == [1, 0, 2][index]
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ for discussion in doc["discussions"]:
+ assert discussion["status"] == "OPEN"
+ assert all(a.split("#", 1)[1] in names for a in discussion["attaches_to"])
+
+
+def test_source_scope_does_not_certify_mismatching_cache_provenance():
+ ledger, _ = records()
+ for path, digest in ledger["reference_cache_original_hashes"].items():
+ assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == digest
+ assert all(not r["source_review"]["cache_provenance_certified"] for r in ledger["records"])
+ assert ledger["issue_deduplication"]["ignored_hidden_local_search"] is True
+ assert "field abstract only" in ledger["records"][0]["source_review"]["scope"]
+ assert "No code/supplement/model-rerun" in ledger["records"][1]["source_review"]["scope"]
+ assert "no figure pixels" in ledger["records"][2]["source_review"]["scope"]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 2895c1c44..936d2a2e2 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -300,6 +300,9 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Ion_Adsorption_REE_Indigenous_Community.yaml",
"Jala_Maize_PGPB_SynCom.yaml",
"Jiangshui_LAB_Directed_Fermentation_SynCom.yaml",
+ "KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml",
+ "KBase_Models_for_Zahmeeth_Original_PLOS.yaml",
+ "KBase_ORT_Workflow_Community_Model.yaml",
"Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml",
"Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml",
"MSC1_Dominant_Core.yaml",