-
In one defined coculture, dual-species biofilms had reduced biomass, cell counts, metabolic activity, EPS, and structural density relative to single-species biofilms, with metabolic and signaling pathways suppressed in both members.
-
+
The PMID:42629020 coculture had reduced aggregate biofilm biomass, cell counts, metabolic activity and extracellular matrix relative to single-species biofilms. Preserve this reported suppressive phenotype without treating aggregate endpoints as demonstrated reciprocal negative fitness effects. This observation does not establish the mechanism of a different strain/condition study.
@@ -672,10 +670,8 @@
Evidence
-
Across 60 S. aureus strains, most strains suppressed C. albicans growth by a contact-dependent mechanism, while matrix composition and antifungal response varied among strain combinations.
-
+
PMID:42413741 reports strain-dependent, contact-associated fungal suppression and variation among dual-species biofilm compositions. This is a reported one-way inhibitory effect, not evidence that both partners suffer reciprocal negative fitness effects or that the mechanism explains PMID:42629020.
Source Taxon: Staphylococcus aureus
@@ -701,16 +697,6 @@
Contact-Dependent Strain-Specific Fungal Suppression
-
-
Downstream Effects:
-
-
-
→ Antagonistic Dual-Species Biofilm Suppression
-
Contact-dependent C. albicans suppression by most S. aureus strains provides a strain-level mechanism for antagonistic dual-species biofilm outcomes.
-
-
-
-
Evidence
@@ -751,8 +737,7 @@
Evidence
Copper-Mediated Nutritional Mutualism
MUTUALISM
-
In plastic-grown biofilms, C. albicans increased copper uptake through Ctr1 while S. aureus increased copper export through CsoR and CopZ; disrupting copper availability reduced dual-species biomass.
-
+
HYPOTHESIZED/PARTIAL: PMID:42359480 interprets its larger dual-species biofilms and proteomic copper-handling observations as nutritional mutualism. Preserve this study-specific interpretation, distinguishing inferred copper handling and aggregate biomass from quantified reciprocal partner benefit or a universal relationship across the six studies.
@@ -793,10 +778,10 @@
Evidence
PMID:42359480
- - SUPPORT (IN_VITRO)
+ - PARTIAL (COMPUTATIONAL)
"C. albicans increased copper uptake via transporter Ctr1, while S. aureus enhanced copper export via regulator CsoR and export chaperone CopZ"
+ Early C. albicans biofilms provide a contact-dependent physical scaffold that increases S. aureus cell numbers during biofilm maturation.
-
+ PMID:33831044 reports a contact-dependent scaffold association and increased bacterial cell numbers within its tested Candida-Staphylococcus system. Retain this source-supported colonization-facilitation observation without importing a hyphal requirement or other conditions from a separate study.
-
C. albicans suppresses S. aureus in planktonic coculture, whereas hyphae-competent biofilms support mutual adaptation, biomass accumulation, cohesion, and resistance.
-
+
PMID:41324029 reports differing outcomes between planktonic and biofilm contexts. Preserve the study-specific suppression and aggregate biofilm observations without classifying every condition as mutualism or turning its morphological comparison into a requirement for the separate PMID:33831044 scaffold study.
@@ -925,16 +907,6 @@
Growth-State and Hyphal Context Dependence
-
-
Downstream Effects:
-
-
-
→ Candida Biofilm Scaffold Supports Staphylococcus Colonization
-
Hyphae-competent biofilm growth creates the Candida scaffold context that supports S. aureus adhesion, proliferation, and mature biofilm architecture.
-
-
-
-
Evidence
@@ -972,11 +944,9 @@
Evidence
-
S. aureus changes the C. albicans transcriptome in dual-species biofilms, including expression programs associated with virulence, biofilm formation, protein binding, and heat-shock responses.
-
+
PMID:34888261 reports Candida transcript differences and gene-ontology associations in the studied dual-species biofilms. Transcript abundance and functional annotations are not demonstrated changes in genotype, infection severity or colonization. No phenotype-enhancing mechanism is inferred from this expression result.
Source Taxon: Staphylococcus aureus
@@ -998,12 +968,6 @@
Staphylococcus-Induced Candida Virulence Response
class="term-link" target="_blank" rel="noopener noreferrer">GO:0010467)
-
- biofilm formation
- (GO:0042710 )
-
-
@@ -1019,36 +983,77 @@
Evidence
PMID:34888261
- - SUPPORT (IN_VITRO)
+ - SUPPORT (COMPUTATIONAL)
"Upregulated genes in dual-species biofilms corresponded to multiple gene ontology terms, including those attributed to virulence, biofilm formation and protein binding"
-
-
+
+
+
+
+
+
+
+
+
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which observations belong to the same tested system, and which claims remain interpretations rather than measured partner effects?
+
+
Six primary abstracts were read as separate studies of a species pair, not one resolved strain/condition system. Remove cross-study causal joins; distinguish aggregate biomass, one-way inhibition, proteomic interpretation and transcript associations. Retain the directly supported scaffold observation and the copper authors mutualism interpretation with explicit qualifications. Available full-text leads were not reviewed here. This is evidence/metadata correction only, without new enhancement procedures, genetic designs or partner mechanisms.
+
+
Attaches to: ecological_interactions#Antagonistic Dual-Species Biofilm Suppression, ecological_interactions#Contact-Dependent Strain-Specific Fungal Suppression, ecological_interactions#Copper-Mediated Nutritional Mutualism, ecological_interactions#Candida Biofilm Scaffold Supports Staphylococcus Colonization, ecological_interactions#Growth-State and Hyphal Context Dependence, ecological_interactions#Study-Specific Candida Transcript Response
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
significantly reduced biomass, cell counts, metabolic activity, and EPS content
+
Supports the measured suppressive biofilm phenotype.
+
"S. aureus pushes C. albicans towards a more virulent genotype"
+
+ Dual-species proteomic analysis revealed non-reciprocal copper handling
+ Supports the reported proteomic interpretation; PARTIAL for nutritional mutualism and not a direct measurement of transferred copper or reciprocal fitness.
+
@@ -1530,7 +1535,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1558,7 +1563,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1666,7 +1671,7 @@ Evidence
(function() {
var intId = "interaction:4";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1694,7 +1699,7 @@ Evidence
(function() {
var intId = "interaction:5";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1702,14 +1707,12 @@ Evidence
processes.push("gene expression");
- processes.push("biofilm formation");
-
- var evidenceCount = 2;
+ var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Staphylococcus-Induced Candida Virulence Response",
+ label: "Study-Specific Candida Transcript Response",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html b/docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html
index 987d26a56..2e368b425 100644
--- a/docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html
+++ b/docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html
@@ -651,7 +651,7 @@ Ecological Interactions
Ecological interaction network for Stordalen Mire Methylotrophic Methanogenesis Community
- 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, 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 (niche partitioning).
@@ -659,18 +659,13 @@
Ecological Interactions
-
-
@@ -678,15 +673,18 @@ Ecological Interactions
-
Methanogenic archaea encode and express methylotrophic genes, revising Stordalen Mire methanogenesis from only hydrogenotrophic and acetoclastic pathways to co-occurring methylotrophic methane production across permafrost thaw stages.
+
Methanogen MAGs encode methylotrophic potential and express associated genes in Stordalen Mire. Integrated field omics support a methylotrophic contribution alongside other methanogenesis routes, but do not quantify pathway-specific methane flux. These observations do not establish syntrophic product-removal feedback between partners.
-
Source Taxon: Stordalen Mire methanogenic archaea
+
Participating Taxa:
+
+ Stordalen Mire methanogenic archaea
+
+
@@ -731,7 +729,7 @@
Evidence
- SUPPORT (COMPUTATIONAL)
"Methanogenesis across increasing permafrost thaw is thus revised"
+ "Of the 36 methanogen MAGs identified as being active in this data set, 10 expressed genes for methylotrophy"
@@ -741,23 +739,10 @@ Evidence
PMID:38063415
- - SUPPORT (COMPUTATIONAL)
-
-
- "co-occurrence of methylotrophy throughout"
-
-
-
-
-
- "Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships"
+ "co-occurrence of methylotrophy throughout"
@@ -767,15 +752,18 @@ Evidence
-
Bacterial MAGs encode and express anaerobic methylotrophic potential across Stordalen Mire, indicating a bacterial route for processing methylated compounds that can interact with methane-generating carbon flow.
+
Bacterial MAGs encode anaerobic methylotrophic potential and associated transcripts occur across the mire. Preserve the broad genomic and expression evidence without asserting traced cross-feeding. The removed acetate-to-methylotrophic-methanogenesis arrow named the wrong recipient route; no replacement exchange mechanism or recipient node is added.
+
-
Source Taxon: Stordalen Mire anaerobic methylotrophic bacteria
+
Participating Taxa:
+ Stordalen Mire anaerobic methylotrophic bacteria
+
+
@@ -802,17 +790,6 @@
Bacterial Anaerobic Methylotrophy
-
-
Downstream Effects:
-
-
-
→ Methanogenic Methylotrophy Across Thaw Gradient
-
Anaerobic bacterial methylotrophs provide a potential indirect route to methane production by forming methanogenic by-products such as acetate.
-
-
-
-
-
Evidence
@@ -827,7 +804,7 @@
Evidence
- SUPPORT (COMPUTATIONAL)
"In addition to methanogenic methylotrophy, >1,700 bacterial MAGs"
+ ">1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential"
@@ -840,7 +817,7 @@ Evidence
- SUPPORT (COMPUTATIONAL)
- "bacterial methylotrophy may be an important and previously underappreciated component"
+ "with expression across 12 phyla"
@@ -850,13 +827,19 @@ Evidence
-
Metabolomics detected diverse methylated compounds, and methanogen orders differed in inferred methylated substrate use, suggesting substrate-based partitioning of methylotrophic activity in bog and fen methanogen communities.
+
HYPOTHESIZED/PARTIAL: metabolite detection and differing methyltransferase expression led the authors to propose methylated-substrate niche partitioning in the fen. Retain this source proposal, not demonstrated substrate uptake, reduced competition or an established bog-and-fen partitioning mechanism.
+
+
Participating Taxa:
+
+ Stordalen Mire methanogenic archaea
+
+
@@ -876,9 +859,8 @@
Methylated-Compound Substrate Niche Partitioning
Downstream Effects:
-
→ Methanogenic Methylotrophy Across Thaw Gradient
-
Substrate-partitioned methyltransferase expression routes methylated oxygen compounds, sulfides, and amines into direct methylotrophic methanogenesis by different methanogen orders.
-
+
→ Methanogenic Methylotrophic Potential and Expression
+
HYPOTHESIZED/PARTIAL: differing inferred substrate preferences could support co-occurring methylotrophic pathways among fen methanogens. The expression and metabolite evidence motivates this existing direction but does not isolate niche partitioning as its cause, measure substrate-specific flux or demonstrate reduced competition.
Evidence
PMID:38063415
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
- "Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds"
+ "Our expression data also hint at methylotrophic niche partitioning that may occur in the fen"
@@ -920,10 +902,9 @@ Evidence
-
Palsa hosted bacterial methylotrophy, while partially thawed bog and fully thawed fen hosted both methanogenic and bacterial methylotrophic activity, indicating functional changes along the permafrost thaw gradient.
+
Field omics support bacterial methylotrophic expression in palsa and both bacterial and methanogenic methylotrophic expression in bog and fen. This is a habitat-associated expression pattern, not measured pathway-specific production rates or evidence that the pattern itself causes the same activities. No niche-partitioning classification is assigned to this gradient observation.
@@ -932,35 +913,7 @@
Thaw-Stage Activity Gradient
-
Biological Processes:
-
-
-
- response to abiotic stimulus
- (GO:0009628 )
-
-
-
-
-
-
-
-
Downstream Effects:
-
-
-
→ Methanogenic Methylotrophy Across Thaw Gradient
-
Partially thawed bog and fully thawed fen habitats housed active methanogenic methylotrophy, while the frozen palsa was described as non-methanogenic.
-
-
-
-
-
→ Bacterial Anaerobic Methylotrophy
-
Bacterial methylotrophy was active across the thaw gradient, including in palsa where methanogenic methylotrophy was not detected.
-
-
-
@@ -973,7 +926,7 @@
Evidence
PMID:38063415
- - SUPPORT (IN_VIVO)
+ - SUPPORT (COMPUTATIONAL)
"the most frozen non-methanogenic palsa found to host bacterial methylotrophy"
@@ -986,7 +939,7 @@ Evidence
PMID:38063415
- - SUPPORT (IN_VIVO)
+ - SUPPORT (COMPUTATIONAL)
"partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities"
@@ -1002,6 +955,60 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How much methane is attributable to each inferred pathway, and which proposed transfers are demonstrated?
+
+
Preserve genomic, transcript and metabolite observations and the qualified fen niche proposal. The source assigns acetate to acetoclastic methanogenesis, not the methylotrophic target of the removed arrow. Neither omics co-occurrence nor the broad 2018 catalog establishes product-removal feedback or traced partner exchange. Habitat patterns remain observations without redundant arrows. Quantitative pathway contribution remains a stated source gap.
+
+
Attaches to: ecological_interactions#Methanogenic Methylotrophic Potential and Expression, ecological_interactions#Bacterial Anaerobic Methylotrophic Potential and Expression, ecological_interactions#Proposed Methylated-Substrate Niche Partitioning, ecological_interactions#Thaw-Stage Methylotrophic Expression Patterns
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
which are substrates for acetoclastic and hydrogenotrophic methanogens, respectively.
+
In the preceding source sentence these substrates are acetate and carbon dioxide, respectively; this bounds the removed route claim.
+
+
+
experimentation is needed to resolve the question of the comparative kinetics of
+
The source explicitly identifies unresolved pathway kinetics and production contributions.
+
+
+
+
@@ -1324,7 +1331,7 @@ Environmental Factors
(function() {
var intId = "interaction:0";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1339,11 +1346,11 @@ Environmental Factors
processes.push("methanogenesis");
- var evidenceCount = 3;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Methanogenic Methylotrophy Across Thaw Gradient",
+ label: "Methanogenic Methylotrophic Potential and Expression",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1352,18 +1359,24 @@ Environmental Factors
});
- var srcKey = "Stordalen Mire methanogenic archaea";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
+
+ "Stordalen Mire methanogenic archaea"
+
+ ];
+ 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 = [];
@@ -1380,7 +1393,7 @@ Environmental Factors
nodes.push({
id: intId,
- label: "Bacterial Anaerobic Methylotrophy",
+ label: "Bacterial Anaerobic Methylotrophic Potential and Expression",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1389,12 +1402,18 @@ Environmental Factors
});
- var srcKey = "Stordalen Mire anaerobic methylotrophic bacteria";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
+
+ "Stordalen Mire anaerobic methylotrophic bacteria"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
@@ -1413,7 +1432,7 @@ Environmental Factors
nodes.push({
id: intId,
- label: "Methylated-Compound Substrate Niche Partitioning",
+ label: "Proposed Methylated-Substrate Niche Partitioning",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1424,24 +1443,31 @@ Environmental Factors
+ var participantKeys = [
+
+ "Stordalen Mire methanogenic archaea"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:3";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("response to abiotic stimulus");
-
-
var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Thaw-Stage Activity Gradient",
+ label: "Thaw-Stage Methylotrophic Expression Patterns",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.html b/docs/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.html
index 3deb0f4d0..05618953a 100644
--- a/docs/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.html
+++ b/docs/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.html
@@ -634,7 +634,7 @@ Ecological Interactions
Ecological interaction network for Streptomyces A2-A5-A11-M7 Pesticide-Bioremediation 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 (mutualism).
+ 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.
@@ -642,8 +642,8 @@
Ecological Interactions
@@ -652,10 +652,8 @@ Ecological Interactions
-
The four strains showed no detectable antagonism in the reported screen, and the A2-A5-A11-M7 mixed culture accumulated more biomass than the corresponding pure cultures in pesticide-supplemented minimal medium. Pairwise directions and exchanged metabolites were not resolved.
-
+
The exact four-strain mixture showed non-antagonism and greater aggregate biomass than the corresponding pure cultures in the reported pesticide experiment. These observations do not measure reciprocal benefit to each member. The 2013 paper includes other mixtures, including a six-member immobilized system whose results are not assigned to this four-member record.
@@ -713,7 +711,7 @@
Evidence
PMID:41678860
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"revealing their metabolic versatility and potential cooperative work, fundamental for the degradation of xenobiotic compounds."
@@ -726,11 +724,9 @@ Evidence
-
Every Streptomyces member of C1 carried at least one gene encoding an herbicide-degradation enzyme, supporting atrazine catabolic capacity distributed across the exact A2-A5-A11-M7 consortium.
-
+
The 2026 source detected at least one herbicide-catabolism-associated gene in each C1 member. This supports distributed genetic potential, not measured expression, enzyme activity or a demonstrated contribution of each member to removal.
@@ -765,8 +761,7 @@
C1 Distributed Atrazine Catabolism
→ C1 Atrazine Growth and Removal
-
Distributed herbicide-catabolism genes provide the mechanistic basis for C1 growth on and removal of atrazine as a sole carbon or nitrogen source.
-
+
HYPOTHESIZED/PARTIAL: the detected catabolic genes could underlie the reported C1 atrazine growth/removal phenotype. The accessible abstract reports gene presence and community outcomes but does not isolate gene activity or member-specific contributions as causal mediators.
Evidence
-
The exact A2-A5-A11-M7 consortium grew on atrazine supplied as either the sole carbon source or sole nitrogen source while removing the herbicide from liquid cultures.
-
+
The exact A2-A5-A11-M7 consortium showed growth and atrazine removal in the source nutrient-role comparisons. Preserve these observed liquid-culture outcomes without treating parent-compound removal as complete mineralization or measured reciprocal partner benefit.
@@ -834,8 +827,7 @@
C1 Atrazine Growth and Removal
→ C1 Atrazine Phytotoxicity Reversal
-
Atrazine growth and removal by C1 reduces the herbicide toxicity of the treated liquid system.
-
+
HYPOTHESIZED/PARTIAL: atrazine removal could contribute to the reported decrease in phytotoxicity after C1 treatment. The accessible abstract does not establish parent-compound depletion as the sole cause, resolve transformation-product effects or demonstrate complete mineralization.
Evidence
-
Liquid cultures treated with the C1 consortium were detoxified enough to reverse the measured phytotoxicity of atrazine, especially when atrazine was supplied as the carbon source.
-
+
The source phytotoxicity tests found that C1 treatment reversed the measured herbicide toxicity, with differing outcomes across the nutrient-role comparisons. Preserve this positive tested endpoint without attributing it exclusively to parent-compound depletion or generalizing it to all toxicity endpoints.
@@ -925,6 +915,60 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Do the detected genes and atrazine removal independently establish the mechanisms of C1 performance and reduced phytotoxicity?
+
+
Retain the exact four-member observations. Aggregate biomass and compatibility are not reciprocal benefit. Gene detection does not establish expression or flux, and treatment-associated phytotoxicity reversal does not isolate its mediator. Keep the two existing directions qualified; do not transfer six-member immobilized-culture results. The 2026 abstract and bounded 2013 results were read, not full methods or all source formulations.
+
+
Attaches to: ecological_interactions#Non-antagonistic community-level growth enhancement, ecological_interactions#C1 Herbicide-Catabolism Gene Detection, ecological_interactions#C1 Atrazine Growth and Removal, ecological_interactions#C1 Atrazine Phytotoxicity Reversal
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
the presence of at least one of the genes that encode enzymes involved in the herbicide degradation was detected in all C1 members.
+
Supports distribution of herbicide-catabolic potential across all four consortium members.
+
+
+
Phytotoxicity tests demonstrated the ability of C1 to reverse the herbicide toxicity, especially with atrazine as a carbon source.
+
Supports the reported post-treatment phytotoxicity endpoint, not an isolated depletion-mediated causal mechanism.
+
+
+
+
@@ -1675,7 +1719,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1709,7 +1753,7 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1726,7 +1770,7 @@
Evidence
nodes.push({
id: intId,
- label: "C1 Distributed Atrazine Catabolism",
+ label: "C1 Herbicide-Catabolism Gene Detection",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1741,7 +1785,7 @@
Evidence
(function() {
var intId = "interaction:2";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1773,7 +1817,7 @@
Evidence
(function() {
var intId = "interaction:3";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
diff --git a/docs/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.html b/docs/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.html
index 0e5d3a4de..0dd5c4b25 100644
--- a/docs/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.html
+++ b/docs/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.html
@@ -530,8 +530,7 @@
Ecological Interactions
-
Injection of 150 tons of supercritical carbon dioxide into a 1.4 km deep aquifer perturbed the native subsurface microbiome.
-
+
The source reports community-structure changes following supercritical carbon dioxide injection into the deep aquifer. Retain the field perturbation as abiotic input context; the accessible abstract does not isolate the mechanism of the community response.
@@ -555,8 +554,7 @@
scCO2 Injection Reshapes Subsurface Community
→ Post-Injection Carboxydocella Decline
-
Community restructuring after supercritical carbon dioxide injection was associated with a decline in native carboxydotrophic Carboxydocella.
-
+
HYPOTHESIZED/PARTIAL: the injected supercritical carbon dioxide is the upstream field perturbation proposed to alter conditions underlying the subsequent Carboxydocella relative-abundance decrease. The temporal association does not establish that aggregate community restructuring itself caused the decline or isolate the physiological mediator.
Evidence
- The aquifer perturbation reduced the relative abundance of the native, thermophilic, carbon-monoxide-utilizing anaerobe Carboxydocella.
-
+ Carboxydocella decreased in relative abundance after the field injection. Relative abundance does not establish absolute cell loss, mortality or a measured fitness decrease, and the accessible abstract does not isolate the mechanism.
@@ -632,10 +629,9 @@ Evidence
-
Detailed metagenomic profiling recovered genome-level information for the native carboxydotrophic Carboxydocella population before and after the geosequestration experiment.
-
+
The source infers a before/after difference in Carboxydocella CO-oxidation potential from CODH gene analysis. Preserve this genomic interpretation, not a demonstrated physiological switch or a measured oxidation rate.
@@ -654,6 +650,16 @@
Native Carboxydocella Genome Resolution
+
+
Downstream Effects:
+
+
+
→ Potential Subsurface Carbon-Electron Flow Through CO
+
HYPOTHESIZED/PARTIAL: a change in encoded CO-oxidation potential could alter carbon/electron flow through carbon monoxide. The source discusses this implication; the accessible abstract does not report a measured flux or isolate CODH variation as the causal mediator.
+
+
+
+
Evidence
@@ -665,10 +671,10 @@
Evidence
PMID:32633030
- - SUPPORT (IN_VIVO)
+ - SUPPORT (COMPUTATIONAL)
"detailed metagenomic profiling of this experiment, with genome resolution of the native carboxydotrophic Carboxydocella
+
"a switch in CO-oxidation potential by Carboxydocella through analysis of its carbon monoxide dehydrogenase (CODH) gene before and after the geosequestration experiment
"
@@ -679,10 +685,9 @@
Evidence
-
Carbon monoxide dehydrogenase analysis showed that Carboxydocella changed its potential for carbon monoxide oxidation across the scCO2 perturbation.
-
+
HYPOTHESIZED/PARTIAL: the source discusses potential impacts on subsurface carbon and electron flow through carbon monoxide. This is an implication of the genomic comparison, not measured community flux or demonstrated metabolite exchange.
@@ -701,17 +706,6 @@
CODH-Mediated CO-Oxidation Switch
-
-
Downstream Effects:
-
-
-
→ Subsurface Carbon-Electron Flow Through CO
-
A CODH-mediated change in carbon monoxide oxidation can alter subsurface carbon and electron transfer through the CO intermediate.
-
-
-
-
-
Evidence
@@ -723,10 +717,10 @@
Evidence
PMID:32633030
- - SUPPORT (IN_VIVO)
+ - PARTIAL (COMPUTATIONAL)
-
"a switch in CO-oxidation potential by Carboxydocella through analysis of its carbon monoxide dehydrogenase (CODH) gene before and after the geosequestration experiment
+
"subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide (CO)
"
@@ -735,59 +729,52 @@
Evidence
-
-
-
The Carboxydocella CODH switch has implications for the movement of carbon and electrons through the metabolic intermediate carbon monoxide in geosequestration-perturbed deep aquifers.
-
-
-
-
-
+
-
Metabolites:
+
- carbon monoxide
- (CHEBI:17245 )
+
+ Knowledge gaps & discussions (1)
-
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which field responses and genomic interpretations establish absolute population change or functional flux?
+
+
Keep the field association and relative-abundance observation separate from gene-based functional potential. Remove the isolated genome-resolution workflow node, preserving the prior analysis-edge repair. The two remaining directions are hypotheses/partial interpretations rather than isolated causal mediators. The primary abstract was read; a failed publisher request is not proof that full text is absent elsewhere.
+
Attaches to: ecological_interactions#scCO2 Injection Reshapes Subsurface Community, ecological_interactions#Post-Injection Carboxydocella Decline, ecological_interactions#CODH-Associated CO-Oxidation Potential, ecological_interactions#Potential Subsurface Carbon-Electron Flow Through CO
+
+ 1 evidence item(s)
+
+
+
COMPUTATIONAL
+
PARTIAL
-
Evidence
-
-
-
+ subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide (CO)
+
+ Supports the source discussion of potential carbon/electron-flow impacts; the surrounding abstract explicitly qualifies these as potential.
+
-
"subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide (CO)
-"
-
-
+
-
@@ -1084,7 +1071,7 @@ Environmental Factors
nodes.push({
id: intId,
- label: "Native Carboxydocella Genome Resolution",
+ label: "CODH-Associated CO-Oxidation Potential",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1112,35 +1099,7 @@ Environmental Factors
nodes.push({
id: intId,
- label: "CODH-Mediated CO-Oxidation Switch",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:4";
- var intType = "UNKNOWN";
- var metabolites = [];
-
-
- metabolites.push("carbon monoxide");
-
-
- var processes = [];
-
- var evidenceCount = 1;
-
- nodes.push({
- id: intId,
- label: "Subsurface Carbon-Electron Flow Through CO",
+ label: "Potential Subsurface Carbon-Electron Flow Through CO",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1172,7 +1131,7 @@ Environmental Factors
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 = 6;
+ var nodeCount = 5;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/history/records/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture/2026-10-08T020856Z-codex-69aaae.yaml b/history/records/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture/2026-10-08T020856Z-codex-69aaae.yaml
new file mode 100644
index 000000000..1ee6d61f5
--- /dev/null
+++ b/history/records/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture/2026-10-08T020856Z-codex-69aaae.yaml
@@ -0,0 +1,31 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml
+ slug: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+session:
+ id: 2026-10-08T020856Z-codex-69aaae
+ timestamp: '2026-10-08T02:08:56Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1829
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain aggregate suppression, removing reciprocal-competition typing not established
+ by aggregate endpoints.; Retain study-specific contact-associated fungal suppression without
+ reciprocal-competition typing or a cross-study mechanism arrow.; Retain the authors mutualism
+ proposal as HYPOTHESIZED/PARTIAL, separating proteomic inference from aggregate biomass.;
+ Retain the source-supported scaffold facilitation without importing another study requirement.;
+ Retain context-dependent observations without universal mutualism or a cross-study hyphal-requirement
+ arrow.; Retain transcript and ontology associations; remove demonstrated-virulence/genotype
+ and colonization interpretations.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
diff --git a/history/records/Stordalen_Mire_Methylotrophic_Methanogenesis_Community/2026-10-08T020857Z-codex-bf13e7.yaml b/history/records/Stordalen_Mire_Methylotrophic_Methanogenesis_Community/2026-10-08T020857Z-codex-bf13e7.yaml
new file mode 100644
index 000000000..c6d4fd8d4
--- /dev/null
+++ b/history/records/Stordalen_Mire_Methylotrophic_Methanogenesis_Community/2026-10-08T020857Z-codex-bf13e7.yaml
@@ -0,0 +1,30 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml
+ slug: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+session:
+ id: 2026-10-08T020857Z-codex-bf13e7
+ timestamp: '2026-10-08T02:08:57Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1830
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain archaeal encoded potential and transcripts with canonical participant scope;
+ remove unsupported syntrophy and unrelated catalog evidence.; Retain bacterial encoded
+ potential and transcripts with canonical participant scope; remove categorical cross-feeding
+ and the acetate-to-methylotrophic route error.; Retain source-proposed fen niche partitioning
+ and its existing functional direction as HYPOTHESIZED/PARTIAL, not measured uptake or
+ reduced competition.; Retain habitat-associated transcript patterns with computational
+ provenance; remove niche typing and activity-restatement arrows.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
diff --git a/history/records/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium/2026-10-08T020858Z-codex-c3faca.yaml b/history/records/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium/2026-10-08T020858Z-codex-c3faca.yaml
new file mode 100644
index 000000000..f62b619e3
--- /dev/null
+++ b/history/records/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium/2026-10-08T020858Z-codex-c3faca.yaml
@@ -0,0 +1,29 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml
+ slug: Streptomyces_A2_A5_A11_M7_Pesticide_Consortium
+session:
+ id: 2026-10-08T020858Z-codex-c3faca
+ timestamp: '2026-10-08T02:08:58Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1831
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain exact-mixture non-antagonism and aggregate biomass, removing reciprocal-mutualism
+ typing and excluding other source formulations.; Retain herbicide-catabolism gene detection
+ as genetic potential, with the existing outcome direction HYPOTHESIZED/PARTIAL.; Retain
+ observed atrazine growth/removal without mineralization or reciprocal-benefit claims;
+ qualify the existing toxicity direction.; Retain positive tested phytotoxicity reversal
+ without claiming its sole causal mediator or universal detoxification.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
diff --git a/history/records/Subsurface_Carboxydocella_CO_Aquifer_Community/2026-10-08T020859Z-codex-ab9af4.yaml b/history/records/Subsurface_Carboxydocella_CO_Aquifer_Community/2026-10-08T020859Z-codex-ab9af4.yaml
new file mode 100644
index 000000000..ca2818872
--- /dev/null
+++ b/history/records/Subsurface_Carboxydocella_CO_Aquifer_Community/2026-10-08T020859Z-codex-ab9af4.yaml
@@ -0,0 +1,29 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml
+ slug: Subsurface_Carboxydocella_CO_Aquifer_Community
+session:
+ id: 2026-10-08T020859Z-codex-ab9af4
+ timestamp: '2026-10-08T02:08:59Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1832
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain field perturbation input with its existing relative-abundance direction
+ HYPOTHESIZED/PARTIAL, not aggregate restructuring as a proven mediator.; Retain observed
+ relative-abundance decline without inferring absolute loss, mortality or fitness.; Retain
+ CODH-associated genomic potential with computational provenance, not a demonstrated physiological
+ switch.; Retain potential carbon/electron-flow implications and their existing direction
+ as HYPOTHESIZED/PARTIAL, not measured flux.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
diff --git a/kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml b/kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml
index 720ff8417..01b633814 100644
--- a/kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml
+++ b/kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml
@@ -89,11 +89,10 @@ taxonomy:
explanation: Independently supports C. albicans membership in the exact biofilm composition.
ecological_interactions:
- name: Antagonistic Dual-Species Biofilm Suppression
- description: >
- In one defined coculture, dual-species biofilms had reduced biomass, cell
- counts, metabolic activity, EPS, and structural density relative to
- single-species biofilms, with metabolic and signaling pathways suppressed in both members.
- interaction_type: COMPETITION
+ description: The PMID:42629020 coculture had reduced aggregate biofilm biomass, cell counts, metabolic activity
+ and extracellular matrix relative to single-species biofilms. Preserve this reported suppressive phenotype without
+ treating aggregate endpoints as demonstrated reciprocal negative fitness effects. This observation does not
+ establish the mechanism of a different strain/condition study.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biofilm formation
@@ -105,18 +104,17 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: there is an antagonistic effect between C. albicans and S. aureus
- explanation: Supports antagonism in the reported dairy and clinical surface model.
+ explanation: Supports the source authors antagonism interpretation, not demonstrated reciprocal competition
+ from aggregate endpoints alone.
- reference: PMID:42629020
supports: SUPPORT
evidence_source: IN_VITRO
snippet: significantly reduced biomass, cell counts, metabolic activity, and EPS content
explanation: Supports the measured suppressive biofilm phenotype.
- name: Contact-Dependent Strain-Specific Fungal Suppression
- description: >
- Across 60 S. aureus strains, most strains suppressed C. albicans growth by
- a contact-dependent mechanism, while matrix composition and antifungal
- response varied among strain combinations.
- interaction_type: COMPETITION
+ description: PMID:42413741 reports strain-dependent, contact-associated fungal suppression and variation among
+ dual-species biofilm compositions. This is a reported one-way inhibitory effect, not evidence that both partners
+ suffer reciprocal negative fitness effects or that the mechanism explains PMID:42629020.
scope: PAIRWISE
source_taxon:
preferred_term: Staphylococcus aureus
@@ -133,11 +131,6 @@ ecological_interactions:
term:
id: GO:0042710
label: biofilm formation
- downstream:
- - target: Antagonistic Dual-Species Biofilm Suppression
- description: Contact-dependent C. albicans suppression by most S. aureus
- strains provides a strain-level mechanism for antagonistic dual-species
- biofilm outcomes.
evidence:
- reference: PMID:42413741
supports: SUPPORT
@@ -147,13 +140,14 @@ ecological_interactions:
- reference: PMID:42413741
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: dual-species biofilms varied significantly in their bacterial-to-fungal cell ratios and in the composition of the biofilm-associated extracellular matrix
+ snippet: dual-species biofilms varied significantly in their bacterial-to-fungal cell ratios and in the composition
+ of the biofilm-associated extracellular matrix
explanation: Supports variation in community composition and matrix across strain combinations.
- name: Copper-Mediated Nutritional Mutualism
- description: >
- In plastic-grown biofilms, C. albicans increased copper uptake through Ctr1
- while S. aureus increased copper export through CsoR and CopZ; disrupting
- copper availability reduced dual-species biomass.
+ description: 'HYPOTHESIZED/PARTIAL: PMID:42359480 interprets its larger dual-species biofilms and proteomic copper-handling
+ observations as nutritional mutualism. Preserve this study-specific interpretation, distinguishing inferred
+ copper handling and aggregate biomass from quantified reciprocal partner benefit or a universal relationship
+ across the six studies.'
interaction_type: MUTUALISM
scope: COMMUNITY_LEVEL
metabolites:
@@ -168,19 +162,25 @@ ecological_interactions:
label: biofilm formation
evidence:
- reference: PMID:42359480
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: C. albicans increased copper uptake via transporter Ctr1, while S. aureus enhanced copper export via regulator CsoR and export chaperone CopZ
- explanation: Supports complementary copper handling by the two members.
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: Dual-species proteomic analysis revealed non-reciprocal copper handling
+ explanation: Supports the reported proteomic interpretation; PARTIAL for nutritional mutualism and not a direct
+ measurement of transferred copper or reciprocal fitness.
+ computational_provenance:
+ prediction_type: STATISTICAL_INFERENCE
+ parameters: Abstract-reported comparison of dual-species proteomic profiles. Software, statistical model and
+ versions were not verified; this evidence concerns inferred copper handling, not directly traced transfer.
- reference: PMID:42359480
supports: SUPPORT
evidence_source: IN_VITRO
snippet: dual-species biofilms are consistently larger than single-species counterparts
- explanation: Supports cooperative biofilm growth in the copper-economy study.
+ explanation: Supports the reported aggregate biomass difference within this study, not quantified benefit to
+ each partner.
- name: Candida Biofilm Scaffold Supports Staphylococcus Colonization
- description: >
- Early C. albicans biofilms provide a contact-dependent physical scaffold
- that increases S. aureus cell numbers during biofilm maturation.
+ description: PMID:33831044 reports a contact-dependent scaffold association and increased bacterial cell numbers
+ within its tested Candida-Staphylococcus system. Retain this source-supported colonization-facilitation observation
+ without importing a hyphal requirement or other conditions from a separate study.
interaction_type: COLONIZATION_FACILITATION
scope: PAIRWISE
source_taxon:
@@ -215,39 +215,33 @@ ecological_interactions:
snippet: C. albicans provided a scaffold for initial bacterial adhesion
explanation: Supports the physical-scaffold mechanism.
- name: Growth-State and Hyphal Context Dependence
- description: >
- C. albicans suppresses S. aureus in planktonic coculture, whereas
- hyphae-competent biofilms support mutual adaptation, biomass accumulation,
- cohesion, and resistance.
- interaction_type: MUTUALISM
+ description: PMID:41324029 reports differing outcomes between planktonic and biofilm contexts. Preserve the study-specific
+ suppression and aggregate biofilm observations without classifying every condition as mutualism or turning its
+ morphological comparison into a requirement for the separate PMID:33831044 scaffold study.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biofilm formation
term:
id: GO:0042710
label: biofilm formation
- downstream:
- - target: Candida Biofilm Scaffold Supports Staphylococcus Colonization
- description: Hyphae-competent biofilm growth creates the Candida scaffold
- context that supports S. aureus adhesion, proliferation, and mature
- biofilm architecture.
evidence:
- reference: PMID:41324029
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: C. albicans dominated in planktonic co-culture, suppressing S. aureus growth, whereas biofilm conditions favored mutual adaptation
+ snippet: C. albicans dominated in planktonic co-culture, suppressing S. aureus growth, whereas biofilm conditions
+ favored mutual adaptation
explanation: Supports interaction reversal between planktonic and biofilm states.
- reference: PMID:41324029
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: hyphae-competent C. albicans forming dual-species biofilms with S. aureus that accumulated substantial biomass
- explanation: Supports the role of hyphal morphology in cooperative biofilm accumulation.
-- name: Staphylococcus-Induced Candida Virulence Response
- description: >
- S. aureus changes the C. albicans transcriptome in dual-species biofilms,
- including expression programs associated with virulence, biofilm formation,
- protein binding, and heat-shock responses.
- interaction_type: COLONIZATION_FACILITATION
+ snippet: hyphae-competent C. albicans forming dual-species biofilms with S. aureus that accumulated substantial
+ biomass
+ explanation: Supports the reported within-study morphological context and aggregate biomass; it does not establish
+ a requirement in another study.
+- name: Study-Specific Candida Transcript Response
+ description: PMID:34888261 reports Candida transcript differences and gene-ontology associations in the studied
+ dual-species biofilms. Transcript abundance and functional annotations are not demonstrated changes in genotype,
+ infection severity or colonization. No phenotype-enhancing mechanism is inferred from this expression result.
scope: PAIRWISE
source_taxon:
preferred_term: Staphylococcus aureus
@@ -264,21 +258,18 @@ ecological_interactions:
term:
id: GO:0010467
label: gene expression
- - preferred_term: biofilm formation
- term:
- id: GO:0042710
- label: biofilm formation
evidence:
- reference: PMID:34888261
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Upregulated genes in dual-species biofilms corresponded to multiple gene ontology terms, including those attributed to virulence, biofilm formation and protein binding
- explanation: Supports the Candida transcriptional response to S. aureus.
- - reference: PMID:34888261
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: S. aureus pushes C. albicans towards a more virulent genotype
- explanation: Supports the study's interpretation of increased Candida virulence-associated expression.
+ evidence_source: COMPUTATIONAL
+ snippet: Upregulated genes in dual-species biofilms corresponded to multiple gene ontology terms, including
+ those attributed to virulence, biofilm formation and protein binding
+ explanation: Supports the reported transcript and ontology associations, not demonstrated virulence, genotype
+ change or colonization facilitation.
+ computational_provenance:
+ prediction_type: STATISTICAL_INFERENCE
+ parameters: Abstract-reported RNA-seq comparison and gene-ontology interpretation. Exact analysis software
+ and versions were not verified; this is expression/annotation evidence, not a functional phenotype assay.
environmental_factors:
- name: Surface-associated biofilm growth
value: plastic and other biotic or abiotic surfaces
@@ -395,3 +386,45 @@ metals_present:
- COPPER
metal_relevance: SIGNIFICANT
metal_notes: Copper depletion and supplementation both reduced dual-species biofilm biomass in the cited in vitro study.
+discussions:
+- discussion_id: staph_candida_study_boundaries
+ prompt: Which observations belong to the same tested system, and which claims remain interpretations rather than
+ measured partner effects?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Antagonistic Dual-Species Biofilm Suppression
+ - ecological_interactions#Contact-Dependent Strain-Specific Fungal Suppression
+ - ecological_interactions#Copper-Mediated Nutritional Mutualism
+ - ecological_interactions#Candida Biofilm Scaffold Supports Staphylococcus Colonization
+ - ecological_interactions#Growth-State and Hyphal Context Dependence
+ - ecological_interactions#Study-Specific Candida Transcript Response
+ rationale: Six primary abstracts were read as separate studies of a species pair, not one resolved strain/condition
+ system. Remove cross-study causal joins; distinguish aggregate biomass, one-way inhibition, proteomic interpretation
+ and transcript associations. Retain the directly supported scaffold observation and the copper authors mutualism
+ interpretation with explicit qualifications. Available full-text leads were not reviewed here. This is evidence/metadata
+ correction only, without new enhancement procedures, genetic designs or partner mechanisms.
+ evidence:
+ - reference: PMID:42629020
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: significantly reduced biomass, cell counts, metabolic activity, and EPS content
+ explanation: Supports the measured suppressive biofilm phenotype.
+ - reference: PMID:42359480
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: Dual-species proteomic analysis revealed non-reciprocal copper handling
+ explanation: Supports the reported proteomic interpretation; PARTIAL for nutritional mutualism and not a direct
+ measurement of transferred copper or reciprocal fitness.
+curation_history:
+- timestamp: '2026-10-08T02:08:52Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain aggregate suppression, removing reciprocal-competition typing not established by aggregate endpoints.;
+ Retain study-specific contact-associated fungal suppression without reciprocal-competition typing or a cross-study
+ mechanism arrow.; Retain the authors mutualism proposal as HYPOTHESIZED/PARTIAL, separating proteomic inference
+ from aggregate biomass.; Retain the source-supported scaffold facilitation without importing another study requirement.;
+ Retain context-dependent observations without universal mutualism or a cross-study hyphal-requirement arrow.;
+ Retain transcript and ontology associations; remove demonstrated-virulence/genotype and colonization interpretations.
+ Issue#1829; reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
+ llm_assisted: true
diff --git a/kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml b/kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml
index d4cf0f407..07451d48a 100644
--- a/kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml
+++ b/kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml
@@ -124,18 +124,12 @@ taxonomy:
snippet: with expression across 12 phyla
explanation: Supports transcriptional activity of bacterial anaerobic methylotrophy.
ecological_interactions:
-- name: Methanogenic Methylotrophy Across Thaw Gradient
- description: Methanogenic archaea encode and express methylotrophic genes,
- revising Stordalen Mire methanogenesis from only hydrogenotrophic and
- acetoclastic pathways to co-occurring methylotrophic methane production
- across permafrost thaw stages.
- interaction_type: SYNTROPHY
+- name: Methanogenic Methylotrophic Potential and Expression
+ description: Methanogen MAGs encode methylotrophic potential and express associated genes in Stordalen Mire. Integrated
+ field omics support a methylotrophic contribution alongside other methanogenesis routes, but do not quantify
+ pathway-specific methane flux. These observations do not establish syntrophic product-removal feedback between
+ partners.
scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: Stordalen Mire methanogenic archaea
- term:
- id: NCBITaxon:2157
- label: Archaea
metabolites:
- preferred_term: methane
term:
@@ -154,33 +148,38 @@ ecological_interactions:
- reference: PMID:38063415
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: Methanogenesis across increasing permafrost thaw is thus revised
- explanation: Supports the revised methanogenesis model across the thaw gradient.
+ snippet: Of the 36 methanogen MAGs identified as being active in this data set, 10 expressed genes for methylotrophy
+ explanation: Supports methylotrophy-associated transcript evidence in methanogen MAGs, not direct methane flux
+ or thermodynamic dependence.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: 'Genome-resolved field omics: DRAM annotation with manual methylotrophy-gene assessment and mapped
+ transcript expression. The source uses homology, synteny and selected phylogenetic checks; bacterial phylogenetic
+ validation was restricted to selected phyla. Encoded/expression potential is not direct flux. Exact claim-specific
+ full pipeline reproduction was not performed.'
- reference: PMID:38063415
- supports: SUPPORT
- evidence_source: COMPUTATIONAL
- snippet: co-occurrence of methylotrophy throughout
- explanation: Supports methylotrophy as a co-occurring methanogenesis mode.
- - reference: PMID:30013118
supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: Microbial and geochemical data highlight lineages that correlate with
- the production of greenhouse gases and indicate novel syntrophic relationships
- explanation: Woodcroft et al. 2018 establish novel syntrophic relationships and
- lineage-greenhouse-gas correlations in a permafrost thaw gradient, supporting
- the SYNTROPHY framing of methanogenic methylotrophy at the community level.
- Partial because the abstract does not name Stordalen Mire specifically.
-- name: Bacterial Anaerobic Methylotrophy
- description: Bacterial MAGs encode and express anaerobic methylotrophic
- potential across Stordalen Mire, indicating a bacterial route for processing
- methylated compounds that can interact with methane-generating carbon flow.
- interaction_type: CROSS_FEEDING
- scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: Stordalen Mire anaerobic methylotrophic bacteria
+ snippet: co-occurrence of methylotrophy throughout
+ explanation: Supports the source integrated-omics interpretation of co-occurring pathways; their quantitative
+ methane contributions remain unresolved.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: 'Genome-resolved field omics: DRAM annotation with manual methylotrophy-gene assessment and mapped
+ transcript expression. The source uses homology, synteny and selected phylogenetic checks; bacterial phylogenetic
+ validation was restricted to selected phyla. Encoded/expression potential is not direct flux. Exact claim-specific
+ full pipeline reproduction was not performed.'
+ participating_taxa:
+ - preferred_term: Stordalen Mire methanogenic archaea
term:
- id: NCBITaxon:2
- label: Bacteria
+ id: NCBITaxon:2157
+ label: Archaea
+- name: Bacterial Anaerobic Methylotrophic Potential and Expression
+ description: Bacterial MAGs encode anaerobic methylotrophic potential and associated transcripts occur across
+ the mire. Preserve the broad genomic and expression evidence without asserting traced cross-feeding. The removed
+ acetate-to-methylotrophic-methanogenesis arrow named the wrong recipient route; no replacement exchange mechanism
+ or recipient node is added.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: methanol
term:
@@ -191,27 +190,39 @@ ecological_interactions:
term:
id: GO:0009056
label: catabolic process
- downstream:
- - target: Methanogenic Methylotrophy Across Thaw Gradient
- description: >
- Anaerobic bacterial methylotrophs provide a potential indirect route to
- methane production by forming methanogenic by-products such as acetate.
evidence:
- reference: PMID:38063415
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: In addition to methanogenic methylotrophy, >1,700 bacterial MAGs
- explanation: Supports bacterial methylotrophy alongside methanogenic methylotrophy.
+ snippet: '>1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential'
+ explanation: Supports broad encoded bacterial potential, not a measured exchanged-metabolite flux.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: 'Genome-resolved field omics: DRAM annotation with manual methylotrophy-gene assessment and mapped
+ transcript expression. The source uses homology, synteny and selected phylogenetic checks; bacterial phylogenetic
+ validation was restricted to selected phyla. Encoded/expression potential is not direct flux. Exact claim-specific
+ full pipeline reproduction was not performed.'
- reference: PMID:38063415
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: bacterial methylotrophy may be an important and previously underappreciated component
- explanation: Supports bacterial methylotrophy as a meaningful community process.
-- name: Methylated-Compound Substrate Niche Partitioning
- description: Metabolomics detected diverse methylated compounds, and
- methanogen orders differed in inferred methylated substrate use, suggesting
- substrate-based partitioning of methylotrophic activity in bog and fen
- methanogen communities.
+ snippet: with expression across 12 phyla
+ explanation: Supports detected transcription across bacterial phyla without demonstrating recipient use of bacterial
+ products.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: 'Genome-resolved field omics: DRAM annotation with manual methylotrophy-gene assessment and mapped
+ transcript expression. The source uses homology, synteny and selected phylogenetic checks; bacterial phylogenetic
+ validation was restricted to selected phyla. Encoded/expression potential is not direct flux. Exact claim-specific
+ full pipeline reproduction was not performed.'
+ participating_taxa:
+ - preferred_term: Stordalen Mire anaerobic methylotrophic bacteria
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+- name: Proposed Methylated-Substrate Niche Partitioning
+ description: 'HYPOTHESIZED/PARTIAL: metabolite detection and differing methyltransferase expression led the authors
+ to propose methylated-substrate niche partitioning in the fen. Retain this source proposal, not demonstrated
+ substrate uptake, reduced competition or an established bog-and-fen partitioning mechanism.'
interaction_type: NICHE_PARTITIONING
scope: COMMUNITY_LEVEL
metabolites:
@@ -220,56 +231,65 @@ ecological_interactions:
id: CHEBI:17790
label: methanol
downstream:
- - target: Methanogenic Methylotrophy Across Thaw Gradient
- description: >
- Substrate-partitioned methyltransferase expression routes methylated
- oxygen compounds, sulfides, and amines into direct methylotrophic
- methanogenesis by different methanogen orders.
+ - target: Methanogenic Methylotrophic Potential and Expression
+ description: 'HYPOTHESIZED/PARTIAL: differing inferred substrate preferences could support co-occurring methylotrophic
+ pathways among fen methanogens. The expression and metabolite evidence motivates this existing direction but
+ does not isolate niche partitioning as its cause, measure substrate-specific flux or demonstrate reduced competition.'
evidence:
- reference: PMID:38063415
supports: SUPPORT
evidence_source: COMPUTATIONAL
snippet: Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire
- explanation: Supports availability of methylated substrates in the community environment.
+ explanation: Supports detected environmental methylated compounds, not uptake by a particular methanogen or
+ reduced competition.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: Source-reported metabolomic compound identification by LC-MS/NMR interpreted alongside genome-resolved
+ omics. Metabolite presence does not assign uptake to a particular population; raw spectra were not reanalyzed.
- reference: PMID:38063415
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of
- methylated oxygen compounds
- explanation: Supports substrate differentiation among methanogenic groups.
-- name: Thaw-Stage Activity Gradient
- description: Palsa hosted bacterial methylotrophy, while partially thawed bog
- and fully thawed fen hosted both methanogenic and bacterial methylotrophic
- activity, indicating functional changes along the permafrost thaw gradient.
- interaction_type: NICHE_PARTITIONING
- scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: response to abiotic stimulus
+ snippet: Our expression data also hint at methylotrophic niche partitioning that may occur in the fen
+ explanation: Explicitly supports the authors qualified fen niche interpretation, not demonstrated competition
+ reduction.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: Source integration of methanogen gene assignments and mapped transcript expression with environmental
+ metabolites. Substrate preferences and fen niche partitioning are interpretations, not direct uptake or
+ competition measurements.
+ participating_taxa:
+ - preferred_term: Stordalen Mire methanogenic archaea
term:
- id: GO:0009628
- label: response to abiotic stimulus
- downstream:
- - target: Methanogenic Methylotrophy Across Thaw Gradient
- description: >
- Partially thawed bog and fully thawed fen habitats housed active
- methanogenic methylotrophy, while the frozen palsa was described as
- non-methanogenic.
- - target: Bacterial Anaerobic Methylotrophy
- description: >
- Bacterial methylotrophy was active across the thaw gradient, including in
- palsa where methanogenic methylotrophy was not detected.
+ id: NCBITaxon:2157
+ label: Archaea
+- name: Thaw-Stage Methylotrophic Expression Patterns
+ description: Field omics support bacterial methylotrophic expression in palsa and both bacterial and methanogenic
+ methylotrophic expression in bog and fen. This is a habitat-associated expression pattern, not measured pathway-specific
+ production rates or evidence that the pattern itself causes the same activities. No niche-partitioning classification
+ is assigned to this gradient observation.
+ scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:38063415
supports: SUPPORT
- evidence_source: IN_VIVO
+ evidence_source: COMPUTATIONAL
snippet: the most frozen non-methanogenic palsa found to host bacterial methylotrophy
- explanation: Supports palsa-stage bacterial methylotrophic activity.
+ explanation: Supports the source habitat-associated omics interpretation, not direct pathway-rate measurements
+ or a separate causal driver.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: Source comparison of annotated methylotrophy-associated transcripts across palsa, bog and fen
+ field samples. Expression is used as an activity indicator, not a measured methane production rate.
- reference: PMID:38063415
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: partially thawed bog and fully thawed fen seen to house both methanogenic and
- bacterial methylotrophic activities
- explanation: Supports bog and fen stages with both methanogenic and bacterial methylotrophy.
+ evidence_source: COMPUTATIONAL
+ snippet: partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic
+ activities
+ explanation: Supports the source habitat-associated omics interpretation, not direct pathway-rate measurements
+ or a separate causal driver.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: Source comparison of annotated methylotrophy-associated transcripts across palsa, bog and fen
+ field samples. Expression is used as an activity indicator, not a measured methane production rate.
environmental_factors:
- name: Permafrost thaw stage
value: palsa, bog, and fen thaw-gradient habitats
@@ -393,3 +413,41 @@ metal_relevance: NOT_APPLICABLE
metal_notes: This community is curated for permafrost wetland carbon cycling and
methane emissions; no metal or rare earth element process is curated as a
primary function.
+discussions:
+- discussion_id: mire_omics_flux_and_route_limits
+ prompt: How much methane is attributable to each inferred pathway, and which proposed transfers are demonstrated?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Methanogenic Methylotrophic Potential and Expression
+ - ecological_interactions#Bacterial Anaerobic Methylotrophic Potential and Expression
+ - ecological_interactions#Proposed Methylated-Substrate Niche Partitioning
+ - ecological_interactions#Thaw-Stage Methylotrophic Expression Patterns
+ rationale: Preserve genomic, transcript and metabolite observations and the qualified fen niche proposal. The
+ source assigns acetate to acetoclastic methanogenesis, not the methylotrophic target of the removed arrow. Neither
+ omics co-occurrence nor the broad 2018 catalog establishes product-removal feedback or traced partner exchange.
+ Habitat patterns remain observations without redundant arrows. Quantitative pathway contribution remains a stated
+ source gap.
+ evidence:
+ - reference: PMID:38063415
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: which are substrates for acetoclastic and hydrogenotrophic methanogens, respectively.
+ explanation: In the preceding source sentence these substrates are acetate and carbon dioxide, respectively;
+ this bounds the removed route claim.
+ - reference: PMID:38063415
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: experimentation is needed to resolve the question of the comparative kinetics of
+ explanation: The source explicitly identifies unresolved pathway kinetics and production contributions.
+curation_history:
+- timestamp: '2026-10-08T02:08:53Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain archaeal encoded potential and transcripts with canonical participant scope; remove unsupported
+ syntrophy and unrelated catalog evidence.; Retain bacterial encoded potential and transcripts with canonical
+ participant scope; remove categorical cross-feeding and the acetate-to-methylotrophic route error.; Retain source-proposed
+ fen niche partitioning and its existing functional direction as HYPOTHESIZED/PARTIAL, not measured uptake or
+ reduced competition.; Retain habitat-associated transcript patterns with computational provenance; remove niche
+ typing and activity-restatement arrows. Issue#1830; reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
+ llm_assisted: true
diff --git a/kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml b/kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml
index fa81c8850..0b07e905a 100644
--- a/kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml
+++ b/kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml
@@ -96,12 +96,10 @@ taxonomy:
explanation: Identifies M7 as a member of the exact consortium.
ecological_interactions:
- name: Non-antagonistic community-level growth enhancement
- description: >
- The four strains showed no detectable antagonism in the reported screen, and
- the A2-A5-A11-M7 mixed culture accumulated more biomass than the corresponding
- pure cultures in pesticide-supplemented minimal medium. Pairwise directions
- and exchanged metabolites were not resolved.
- interaction_type: MUTUALISM
+ description: The exact four-strain mixture showed non-antagonism and greater aggregate biomass than the corresponding
+ pure cultures in the reported pesticide experiment. These observations do not measure reciprocal benefit to
+ each member. The 2013 paper includes other mixtures, including a six-member immobilized system whose results
+ are not assigned to this four-member record.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: chlorpyrifos
@@ -121,19 +119,21 @@ ecological_interactions:
- reference: PMID:23865051
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Results revealed that the strains did not have any antagonistic effects and showed tolerance against the pesticides mixture. In fact, the growth of mixed cultures was significantly higher than in pure cultures.
- explanation: Supports compatible assembly and community-level growth enhancement while leaving the pairwise mechanism unresolved.
+ snippet: Results revealed that the strains did not have any antagonistic effects and showed tolerance against
+ the pesticides mixture. In fact, the growth of mixed cultures was significantly higher than in pure cultures.
+ explanation: Supports the reported screen and aggregate growth comparison; not quantified reciprocal benefit
+ or the performance of every source formulation.
- reference: PMID:41678860
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: revealing their metabolic versatility and potential cooperative work, fundamental for the degradation of xenobiotic compounds.
- explanation: Supports the authors' interpretation that cooperative activity contributes to the consortium phenotype.
-- name: C1 Distributed Atrazine Catabolism
- description: >
- Every Streptomyces member of C1 carried at least one gene encoding an
- herbicide-degradation enzyme, supporting atrazine catabolic capacity
- distributed across the exact A2-A5-A11-M7 consortium.
- interaction_type: MUTUALISM
+ snippet: revealing their metabolic versatility and potential cooperative work, fundamental for the degradation
+ of xenobiotic compounds.
+ explanation: Preserves the source authors potential-cooperation interpretation without classifying all members
+ as mutualistic.
+- name: C1 Herbicide-Catabolism Gene Detection
+ description: The 2026 source detected at least one herbicide-catabolism-associated gene in each C1 member. This
+ supports distributed genetic potential, not measured expression, enzyme activity or a demonstrated contribution
+ of each member to removal.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: atrazine
@@ -147,21 +147,20 @@ ecological_interactions:
label: xenobiotic metabolic process
downstream:
- target: C1 Atrazine Growth and Removal
- description: >
- Distributed herbicide-catabolism genes provide the mechanistic basis for
- C1 growth on and removal of atrazine as a sole carbon or nitrogen source.
+ description: 'HYPOTHESIZED/PARTIAL: the detected catabolic genes could underlie the reported C1 atrazine growth/removal
+ phenotype. The accessible abstract reports gene presence and community outcomes but does not isolate gene
+ activity or member-specific contributions as causal mediators.'
evidence:
- reference: PMID:41678860
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: the presence of at least one of the genes that encode enzymes involved in the herbicide degradation was detected in all C1 members.
+ snippet: the presence of at least one of the genes that encode enzymes involved in the herbicide degradation
+ was detected in all C1 members.
explanation: Supports distribution of herbicide-catabolic potential across all four consortium members.
- name: C1 Atrazine Growth and Removal
- description: >
- The exact A2-A5-A11-M7 consortium grew on atrazine supplied as either the
- sole carbon source or sole nitrogen source while removing the herbicide from
- liquid cultures.
- interaction_type: MUTUALISM
+ description: The exact A2-A5-A11-M7 consortium showed growth and atrazine removal in the source nutrient-role
+ comparisons. Preserve these observed liquid-culture outcomes without treating parent-compound removal as complete
+ mineralization or measured reciprocal partner benefit.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: atrazine
@@ -175,21 +174,20 @@ ecological_interactions:
label: xenobiotic metabolic process
downstream:
- target: C1 Atrazine Phytotoxicity Reversal
- description: >
- Atrazine growth and removal by C1 reduces the herbicide toxicity of the
- treated liquid system.
+ description: 'HYPOTHESIZED/PARTIAL: atrazine removal could contribute to the reported decrease in phytotoxicity
+ after C1 treatment. The accessible abstract does not establish parent-compound depletion as the sole cause,
+ resolve transformation-product effects or demonstrate complete mineralization.'
evidence:
- reference: PMID:41678860
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: These results demonstrated the ability of C1 to remove atrazine and use it as a carbon or nitrogen source
+ snippet: These results demonstrated the ability of C1 to remove atrazine and use it as a carbon or nitrogen
+ source
explanation: Supports C1 atrazine removal under both nutrient-role treatments.
- name: C1 Atrazine Phytotoxicity Reversal
- description: >
- Liquid cultures treated with the C1 consortium were detoxified enough to
- reverse the measured phytotoxicity of atrazine, especially when atrazine was
- supplied as the carbon source.
- interaction_type: MUTUALISM
+ description: The source phytotoxicity tests found that C1 treatment reversed the measured herbicide toxicity,
+ with differing outcomes across the nutrient-role comparisons. Preserve this positive tested endpoint without
+ attributing it exclusively to parent-compound depletion or generalizing it to all toxicity endpoints.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: atrazine
@@ -205,8 +203,10 @@ ecological_interactions:
- reference: PMID:41678860
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Phytotoxicity tests demonstrated the ability of C1 to reverse the herbicide toxicity, especially with atrazine as a carbon source.
- explanation: Supports detoxification as a downstream C1 community output.
+ snippet: Phytotoxicity tests demonstrated the ability of C1 to reverse the herbicide toxicity, especially with
+ atrazine as a carbon source.
+ explanation: Supports the reported post-treatment phytotoxicity endpoint, not an isolated depletion-mediated
+ causal mechanism.
environmental_factors:
- name: Atrazine concentration
value: 25 and 50
@@ -404,3 +404,42 @@ external_resources:
explanation: Explicitly identifies the exact composition in the atrazine study.
metal_relevance: NOT_APPLICABLE
metal_notes: The curated exact composition is represented for pesticide degradation; metal-remediation studies using different Streptomyces combinations are not attributed to this record.
+discussions:
+- discussion_id: c1_gene_presence_and_outcome_mediation
+ prompt: Do the detected genes and atrazine removal independently establish the mechanisms of C1 performance and
+ reduced phytotoxicity?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Non-antagonistic community-level growth enhancement
+ - ecological_interactions#C1 Herbicide-Catabolism Gene Detection
+ - ecological_interactions#C1 Atrazine Growth and Removal
+ - ecological_interactions#C1 Atrazine Phytotoxicity Reversal
+ rationale: Retain the exact four-member observations. Aggregate biomass and compatibility are not reciprocal benefit.
+ Gene detection does not establish expression or flux, and treatment-associated phytotoxicity reversal does not
+ isolate its mediator. Keep the two existing directions qualified; do not transfer six-member immobilized-culture
+ results. The 2026 abstract and bounded 2013 results were read, not full methods or all source formulations.
+ evidence:
+ - reference: PMID:41678860
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: the presence of at least one of the genes that encode enzymes involved in the herbicide degradation
+ was detected in all C1 members.
+ explanation: Supports distribution of herbicide-catabolic potential across all four consortium members.
+ - reference: PMID:41678860
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Phytotoxicity tests demonstrated the ability of C1 to reverse the herbicide toxicity, especially with
+ atrazine as a carbon source.
+ explanation: Supports the reported post-treatment phytotoxicity endpoint, not an isolated depletion-mediated
+ causal mechanism.
+curation_history:
+- timestamp: '2026-10-08T02:08:54Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain exact-mixture non-antagonism and aggregate biomass, removing reciprocal-mutualism typing and excluding
+ other source formulations.; Retain herbicide-catabolism gene detection as genetic potential, with the existing
+ outcome direction HYPOTHESIZED/PARTIAL.; Retain observed atrazine growth/removal without mineralization or reciprocal-benefit
+ claims; qualify the existing toxicity direction.; Retain positive tested phytotoxicity reversal without claiming
+ its sole causal mediator or universal detoxification. Issue#1831; reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
+ llm_assisted: true
diff --git a/kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml b/kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml
index dfdae75bc..9b23a63be 100644
--- a/kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml
+++ b/kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml
@@ -49,9 +49,9 @@ taxonomy:
decline.
ecological_interactions:
- name: scCO2 Injection Reshapes Subsurface Community
- description: >
- Injection of 150 tons of supercritical carbon dioxide into a 1.4 km deep
- aquifer perturbed the native subsurface microbiome.
+ description: The source reports community-structure changes following supercritical carbon dioxide injection into
+ the deep aquifer. Retain the field perturbation as abiotic input context; the accessible abstract does not isolate
+ the mechanism of the community response.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: carbon dioxide
@@ -60,20 +60,21 @@ ecological_interactions:
label: carbon dioxide
downstream:
- target: Post-Injection Carboxydocella Decline
- description: >
- Community restructuring after supercritical carbon dioxide injection was
- associated with a decline in native carboxydotrophic Carboxydocella.
+ description: 'HYPOTHESIZED/PARTIAL: the injected supercritical carbon dioxide is the upstream field perturbation
+ proposed to alter conditions underlying the subsequent Carboxydocella relative-abundance decrease. The temporal
+ association does not establish that aggregate community restructuring itself caused the decline or isolate
+ the physiological mediator.'
evidence:
- reference: PMID:32633030
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: changes to the microbial community structure of a deep aquifer
- (1.4 km) receiving 150 tons of injected supercritical CO2
+ snippet: changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 tons of injected
+ supercritical CO2
explanation: Supports the scCO2 injection effect on community structure.
- name: Post-Injection Carboxydocella Decline
- description: >
- The aquifer perturbation reduced the relative abundance of the native,
- thermophilic, carbon-monoxide-utilizing anaerobe Carboxydocella.
+ description: Carboxydocella decreased in relative abundance after the field injection. Relative abundance does
+ not establish absolute cell loss, mortality or a measured fitness decrease, and the accessible abstract does
+ not isolate the mechanism.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: carbon monoxide
@@ -84,37 +85,17 @@ ecological_interactions:
- reference: PMID:32633030
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- the thermophilic CO-utilizing anaerobe Carboxydocella, which decreased
- in relative abundance post-scCO2 injection
- explanation: >
- Supports the Carboxydocella decline after supercritical carbon dioxide
- injection.
-- name: Native Carboxydocella Genome Resolution
- description: >
- Detailed metagenomic profiling recovered genome-level information for the
- native carboxydotrophic Carboxydocella population before and after the
- geosequestration experiment.
- scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: carbon monoxide
- term:
- id: CHEBI:17245
- label: carbon monoxide
- evidence:
- - reference: PMID:32633030
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >
- detailed metagenomic profiling of this experiment, with genome resolution
- of the native carboxydotrophic Carboxydocella
- explanation: >
- Supports genome-resolved analysis of the native Carboxydocella
- carboxydotroph.
-- name: CODH-Mediated CO-Oxidation Switch
- description: >
- Carbon monoxide dehydrogenase analysis showed that Carboxydocella changed
- its potential for carbon monoxide oxidation across the scCO2 perturbation.
+ snippet: 'the thermophilic CO-utilizing anaerobe Carboxydocella, which decreased in relative abundance post-scCO2
+ injection
+
+ '
+ explanation: 'Supports the Carboxydocella decline after supercritical carbon dioxide injection.
+
+ '
+- name: CODH-Associated CO-Oxidation Potential
+ description: The source infers a before/after difference in Carboxydocella CO-oxidation potential from CODH gene
+ analysis. Preserve this genomic interpretation, not a demonstrated physiological switch or a measured oxidation
+ rate.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: carbon monoxide
@@ -122,25 +103,29 @@ ecological_interactions:
id: CHEBI:17245
label: carbon monoxide
downstream:
- - target: Subsurface Carbon-Electron Flow Through CO
- description: >
- A CODH-mediated change in carbon monoxide oxidation can alter subsurface
- carbon and electron transfer through the CO intermediate.
+ - target: Potential Subsurface Carbon-Electron Flow Through CO
+ description: 'HYPOTHESIZED/PARTIAL: a change in encoded CO-oxidation potential could alter carbon/electron flow
+ through carbon monoxide. The source discusses this implication; the accessible abstract does not report a
+ measured flux or isolate CODH variation as the causal mediator.'
evidence:
- reference: PMID:32633030
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >
- a switch in CO-oxidation potential by Carboxydocella through analysis of
- its carbon monoxide dehydrogenase (CODH) gene before and after the
- geosequestration experiment
- explanation: >
- Supports the CODH-driven CO-oxidation function and its switch.
-- name: Subsurface Carbon-Electron Flow Through CO
- description: >
- The Carboxydocella CODH switch has implications for the movement of carbon
- and electrons through the metabolic intermediate carbon monoxide in
- geosequestration-perturbed deep aquifers.
+ evidence_source: COMPUTATIONAL
+ snippet: 'a switch in CO-oxidation potential by Carboxydocella through analysis of its carbon monoxide dehydrogenase
+ (CODH) gene before and after the geosequestration experiment
+
+ '
+ explanation: Supports the source gene-based interpretation of functional potential, not directly measured CO
+ oxidation or physiological switching.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: Abstract-reported genome-resolved metagenomics and before/after CODH gene comparison. Software,
+ gene-comparison method and versions were not verified; physiological rates and carbon/electron flux were
+ not measured in the abstract.
+- name: Potential Subsurface Carbon-Electron Flow Through CO
+ description: 'HYPOTHESIZED/PARTIAL: the source discusses potential impacts on subsurface carbon and electron flow
+ through carbon monoxide. This is an implication of the genomic comparison, not measured community flux or demonstrated
+ metabolite exchange.'
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: carbon monoxide
@@ -149,14 +134,19 @@ ecological_interactions:
label: carbon monoxide
evidence:
- reference: PMID:32633030
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >
- subsurface flow of carbon and electrons from oxidation of the metabolic
- intermediate carbon monoxide (CO)
- explanation: >
- Supports carbon monoxide oxidation as a route for subsurface carbon and
- electron flow.
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: 'subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide
+ (CO)
+
+ '
+ explanation: Supports the source discussion of potential carbon/electron-flow impacts; the surrounding abstract
+ explicitly qualifies these as potential.
+ computational_provenance:
+ prediction_type: OTHER
+ parameters: Abstract-reported genome-resolved metagenomics and before/after CODH gene comparison. Software,
+ gene-comparison method and versions were not verified; physiological rates and carbon/electron flux were
+ not measured in the abstract.
environmental_factors:
- name: Supercritical CO2 injection
value: 150 tons of injected scCO2
@@ -207,7 +197,39 @@ curation_history:
- timestamp: '2026-10-02T06:04:09Z'
curator: codex
action: REPAIR_CAUSAL_GRAPH
- changes: Removed two Subsurface Carboxydocella analysis edges that treated a
- post-scCO2 abundance response and native genome resolution as upstream of
- metagenome profiling and CODH before-versus-after comparison.
+ changes: Removed two Subsurface Carboxydocella analysis edges that treated a post-scCO2 abundance response and
+ native genome resolution as upstream of metagenome profiling and CODH before-versus-after comparison.
llm_assisted: true
+- timestamp: '2026-10-08T02:08:55Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain field perturbation input with its existing relative-abundance direction HYPOTHESIZED/PARTIAL,
+ not aggregate restructuring as a proven mediator.; Retain observed relative-abundance decline without inferring
+ absolute loss, mortality or fitness.; Retain CODH-associated genomic potential with computational provenance,
+ not a demonstrated physiological switch.; Retain potential carbon/electron-flow implications and their existing
+ direction as HYPOTHESIZED/PARTIAL, not measured flux. Issue#1832; reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
+ llm_assisted: true
+discussions:
+- discussion_id: aquifer_relative_abundance_and_functional_potential
+ prompt: Which field responses and genomic interpretations establish absolute population change or functional flux?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#scCO2 Injection Reshapes Subsurface Community
+ - ecological_interactions#Post-Injection Carboxydocella Decline
+ - ecological_interactions#CODH-Associated CO-Oxidation Potential
+ - ecological_interactions#Potential Subsurface Carbon-Electron Flow Through CO
+ rationale: Keep the field association and relative-abundance observation separate from gene-based functional potential.
+ Remove the isolated genome-resolution workflow node, preserving the prior analysis-edge repair. The two remaining
+ directions are hypotheses/partial interpretations rather than isolated causal mediators. The primary abstract
+ was read; a failed publisher request is not proof that full text is absent elsewhere.
+ evidence:
+ - reference: PMID:32633030
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: 'subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide
+ (CO)
+
+ '
+ explanation: Supports the source discussion of potential carbon/electron-flow impacts; the surrounding abstract
+ explicitly qualifies these as potential.
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 560a8ca1a..0cfef3086 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -1260,3 +1260,27 @@ non-graph #1827 stays open. Prior #847 concerns interaction typing, not
environmental grounding; the new issue and review metadata were corrected
without changing old histories. Self-review is not independent approval or
corpus completion.
+
+## Batch106: Study Boundaries And Omics Interpretation
+
+[Decisions](decisions/20261008-four-records-batch106.yaml),
+[validation](validation-20261008-batch106.json),
+[cache provenance](cache-provenance-20261008-batch106.json) and
+[self-adversarial review](adversarial-review-20261008-batch106.yaml) cover
+Staphylococcus-Candida, Stordalen Mire, the four-member Streptomyces pesticide
+consortium and the subsurface Carboxydocella aquifer record.
+Eighteen of nineteen nodes and five qualified existing directions remain.
+One analysis-workflow node and five cross-study, wrong-route or restatement
+arrows are removed. Study-specific observations and source hypotheses remain
+distinct from reciprocal fitness effects, traced exchange and measured flux.
+The mire fen niche proposal and both pesticide directions remain explicitly
+hypothetical; gene detection is not demonstrated expression or causal mediation.
+The prior aquifer analysis-edge repair and existing cache repairs are preserved.
+All caches and non-graph raw blocks remain unchanged, not recertified.
+Source review includes nine whole primary abstracts and bounded mire2023 and
+pesticide2013 main-text spans, not whole-paper or raw-data certification.
+Available Staphylococcus-Candida full-text leads were not reviewed; no global
+full-text absence is asserted. No new topology, Edison spend or pathogen
+enhancement procedures are introduced. Repairs #1829-#1832 await protected-main
+merge; non-graph #1833 stays open. Self-review is not independent approval or
+corpus completion.
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch106.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch106.yaml
new file mode 100644
index 000000000..4f92bbe72
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch106.yaml
@@ -0,0 +1,257 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 20d6692b687fa6826bc25f8673543215c18aa310
+scope:
+- kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml
+- kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml
+- kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml
+- kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch106.json
+findings:
+- issue: 1829
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate study-specific Staphylococcus-Candida observations and remove cross-study causal joins
+ disposition: Close only after protected-main merge.
+- issue: 1830
+ severity: P2
+ status: addressed_in_this_change
+ finding: Bound Stordalen methylotrophy graphs to omics evidence and correct the acetate-route arrow
+ disposition: Close only after protected-main merge.
+- issue: 1831
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate Streptomyces aggregate performance from mutualism and gene-mediated causation
+ disposition: Close only after protected-main merge.
+- issue: 1832
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate Carboxydocella genome-analysis workflow from ecological response and functional potential
+ disposition: Close only after protected-main merge.
+- issue: 1833
+ severity: P2
+ status: open_non_graph_follow_up
+ finding: Audit non-graph role and substrate extrapolations in Stordalen and Staphylococcus-Candida records
+ disposition: Separate non-graph curation required.
+adversarial_checks:
+- 'Whole original targets and all changed graph/discussion diffs reviewed. All19 original nodes and10 directions
+ have dispositions: retain18nodes and5qualified existing directions, remove1analysis-workflow node and5cross-study/wrong-route/restatement
+ arrows, rename8nodes. No new topology or provider spend.'
+- 'Challenge removal versus lost evidence: retain the six separate Staphylococcus-Candida observations, mire encoded
+ potential/expression/metabolite findings, exact four-member pesticide outcomes and aquifer relative-abundance/genomic-potential
+ findings. Retain qualified source hypotheses rather than deleting all topology or rejecting positive results.'
+- 'Staphylococcus-Candida: species composition is not one fixed experimental system. Remove cross-study mechanism/requirement
+ arrows; aggregate biomass and one-way inhibition do not demonstrate reciprocal competition. Preserve copper authors
+ mutualism as HYPOTHESIZED/PARTIAL and direct scaffold facilitation. RNA/ontology associations do not establish
+ virulence, altered genotype or colonization. No new pathogen enhancement procedures, genetic designs, strain-selection
+ advice or partner mechanisms.'
+- 'Mire: source distinguishes acetate-to-acetoclastic routing from methylotrophic methanogenesis. Remove the wrong-route
+ arrow without importing another mechanism. Product-removal feedback and traced exchange are not established by
+ omics co-occurrence. Retain source-proposed fen niche partitioning and its existing direction HYPOTHESIZED/PARTIAL,
+ not reduced competition or direct uptake. Preserve genomic/transcript/metabolite support and canonical identity-only
+ scope; the gradient remains an observation, not its own causal driver.'
+- 'Pesticide: non-antagonism and greater mixed biomass do not establish reciprocal benefit. Preserve exact A2-A5-A11-M7
+ observations without transferring six-member immobilized-culture results. Gene detection supports potential, not
+ expression/flux; removal is not mineralization. Keep both existing directions HYPOTHESIZED/PARTIAL because the
+ accessible abstract does not isolate gene activity or parent depletion as mediators. Positive phytotoxicity endpoints
+ remain.'
+- 'Aquifer: remove the genome-resolution workflow node and preserve prior analysis-edge repair. Field perturbation
+ is the upstream abiotic input, not aggregate restructuring as a demonstrated mediator. Relative abundance is not
+ absolute loss or fitness. CODH analysis supports inferred potential, not a physiological switch; carbon/electron
+ flow is a source implication, not measured flux. Keep both existing directions qualified and do not invent methods.'
+- 'Twenty-nine graph and seven discussion quotations match fresh primary text and unchanged caches. Eleven independent
+ primary retrievals: nine whole abstracts plus bounded mire2023/pesticide2013 main-text coverage. Available Staphylococcus-Candida
+ PMCID leads were not read; copper cache PMCID differs from fresh metadata. Failed aquifer/pesticide publisher
+ requests were Internal Error, not verified HTTP403. No global full-text absence claim, bypass, cache import, supplement/figure-pixel
+ or raw-data certification.'
+- Four guarded writes and four append-only histories;456 other records/all923 caches and prior history/decision
+ files byte-identical. Non-graph raw blocks unchanged. Identity-only mire scopes do not change the global census
+ because the whole-community gradient observation remains. No census threshold, schema or runtime-rule changes.
+ The pre-write guard rejected unsupported discussion provenance fields; provenance remains on interaction evidence
+ without changing the shared schema.
+- Eight focused tests and959 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks
+ and four histories validate. Network equals56 baseline warnings with zero structural defects. Deterministic rendering
+ and exact HTML parser cover456pages/1372descriptions/545arrows, not screenshots. Plain just-lint passed; explicit-runtime
+ no-incremental mypy additionally checked.
+- Repairs1829-1832 addressed but remain open until protected-main merge; non-graph1833 remains open. Prior691/763
+ and aquifer analysis repairs preserved. The caches requested by764 are present, so no duplicate cache issue/import.
+ Existing license949, loader1703, DOIcache1091, denied and unansweredEdison scopes are not resolved. Self-review
+ is not independent approval; no artificial CI, protection bypass or premature cleanup.
+- Corpus338reviewed/72pending/50needs_research is not completion. Postcommit docs-current and exact-head publication
+ require separate receipts, not preasserted here.
+verification:
+ combined_regressions: 959 passed in 793.39s (0:13:13)
+ new_regression_tests: 8
+ total_recorded_gate_outputs: 41
+ primary_graph_snippet_proof:
+ graph_quotations: 29
+ new_discussion_quotations: 7
+ fresh_primary_literal_matches: 36
+ all_cached_literal_matches: 36
+ retained_nodes: 18
+ removed_nodes: 1
+ retained_arrows: 5
+ removed_arrows: 5
+ new_nodes_or_directions: 0
+ scope: All reviewed quotations match fresh primary text and unchanged existing caches literally after normalization;
+ entailment separately reviewed. Staphylococcus-Candida, mire2018, pesticide2026 and aquifer abstracts; mire2023
+ and pesticide2013 have bounded main-text coverage. No cache text or audit exception.
+ references: Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091
+ remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total
+ checks counts issues,not executed checks. Loader1703 not certified.
+ snippet_counts_by_record:
+ kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml:
+ MATCH: 31
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml:
+ MATCH: 26
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml:
+ MATCH: 24
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml:
+ MATCH: 9
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 8960
+ categories:
+ MATCH: 8824
+ RENDERING: 20
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 39
+ NOCONTENT: 76
+ caveat: Both-root informational audit exit0 is not clean-corpus certification; literal matches are not entailment.
+ network:
+ existing_findings_preserved: 56
+ added_findings: {}
+ removed_findings: {}
+ interpretation: One analysis-workflow node and five cross-study/wrong-route/restatement arrows removed;18 observations
+ and five qualified existing directions retained. All56existing warnings unchanged and zero structural defects.
+ No audit rules changed.
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml: af866c82bb491b74c48f353aeb02c43bda4dd426af2f03dea2a24613dcf6e065
+ tests/test_causal_review_batch106.py: 14c625feb3e733b49012ba53b53c8efedd3ad639cc28f68cf3ad3dc81cc8117a
+ tests/test_participating_taxa.py: 4b0f435e5401b563a03420068c3a9893e5731546950db84dce2505f4fd99812b
+ tests/test_community_level_connectivity_credit.py: 383a0f5904085a5cda800b5102923fc99301831f5769d8d4821e000773d2ea4c
+ reports/causal_graph_review/cache-provenance-20261008-batch106.json: d8a73c0adb6e7239ee5719d2767c24e1dfcdd10314ef888572f14e8a4138846e
+ kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml: b56a50fee784e1e8d6c07167f9faeccef0dc6ec979cc7f3b79861cb7034bc68e
+ kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml: 3f9b3c0e30a8f745ccaa24400d3523ef7306000486ab5e1b5c05a0cf3f877e27
+ kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml: 4ef09a74970615b914a26247da7f2919234df7487a087c51923c41dea1a9042c
+ kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml: 0f750d563e028d6b70a47ac876aec68e29bef5b87eae6ec06ba34630e43e6bd9
+ unchanged_records: 456
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 817
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Qualify existing observation/mechanism boundaries and participant scope; retain five qualified
+ directions, remove one workflow node and five unsupported/restatement arrows. No new mechanisms or directions.
+ post_commit_docs_current: Separate publication gate, not preasserted.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 403
+ mixed: 128
+ community_level_only: 275
+ taxa: 1544
+ credited_solely_by_the_rule: 1270
+ current:
+ records: 460
+ with_community_level: 403
+ mixed: 128
+ community_level_only: 275
+ taxa: 1544
+ credited_solely_by_the_rule: 1270
+ delta:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ interpretation: Mire archaeal/bacterial nodes gain identity-only canonical scope. Its gradient observation still
+ encompasses the community, so the global census is unchanged. No census threshold or runtime rule changes.
+corpus:
+ records: 460
+ nodes: 1386
+ edges: 553
+ review_status_counts:
+ needs_research: 50
+ pending: 72
+ reviewed: 338
+lint_limitation: Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked.
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary Python3.13 lint environment reuses validation runtime and locked mypy1.19.1/stubs/scikit-learn1.8.0/pacmap0.9.1
+ for static checks; not a complete embedding runtime. Project dependencies unchanged.
+limitations:
+- 'Fresh both-root baseline before source reads: 460 records, 923 caches, 56 existing warnings, zero structural
+ defects. Four whole records and all19 original nodes/10 directions reviewed;18 nodes and five qualified existing
+ directions retained, one workflow node and five arrows removed, eight renames. No new topology or Edison submission/spend.'
+- 'Eleven primary sources independently retrieved. All nine abstract-only retrievals were read whole, including
+ the six Staphylococcus-Candida studies, 2018 mire catalog, 2026 pesticide study and aquifer study. Available full-text
+ leads were not fetched for Staphylococcus-Candida: fresh PMCID leads exist for three and the pre-existing copper
+ cache lists PMC13306210 despite missing fresh PMCID metadata. This is an abstract-bounded metadata correction,
+ not an assertion of full-text absence.'
+- Fresh EuropePMC full-body XML retrieved for mire2023 and pesticide2013. Mire abstract1-33, results/discussion238-477
+ and methods528-676 read; pesticide2013 results182-246 read. Other spans were indexed or not read, not whole-paper
+ review. No figure-pixel, supplement, raw-data or full-pipeline certification. Mire CC BY4.0 and pesticide2013
+ CC BY3.0 metadata retained.
+- Existing six Staphylococcus-Candida caches, pesticide2026, both aquifer caches and both lindane abstract caches
+ read whole. Large mire2023, mire2018 and pesticide2013 caches used for bounded context and normalized claim matching,
+ not exhaustive duplicated full-text review. Wiley aquifer and Elsevier pesticide2026 web requests returned Internal
+ Error with no HTTP code reported; no bypass or global full-text-absence assertion. No cache imports, license949/loader1703/DOI-case1091
+ certification.
+- 'Staphylococcus-Candida: retain six separate-study observations; remove cross-study arrows and categorical reciprocal
+ competition/universal mutualism. Preserve the copper authors mutualism interpretation as HYPOTHESIZED/PARTIAL
+ and source-supported scaffold facilitation. Transcript/ontology associations are not demonstrated virulence, genotype
+ change or colonization. No new growth, biofilm, survival, resistance, virulence or colonization enhancement procedures,
+ genetic designs, strain-selection advice or partner mechanisms.'
+- 'Mire: preserve encoded potential, transcripts and metabolite observations with canonical identity-only archaeal/bacterial
+ scope and computational provenance. Remove unestablished syntrophic product-removal feedback and traced cross-feeding.
+ Acetate supports an acetoclastic route, not the removed methylotrophic target; no replacement mechanism/node added.
+ Preserve source-proposed fen niche partitioning and its existing direction as HYPOTHESIZED/PARTIAL; no measured
+ substrate flux or competition reduction. Remove redundant habitat arrows and unrelated catalog support for specific
+ syntrophy.'
+- 'Pesticide: retain the exact four-member non-antagonism, aggregate growth, gene detection, removal and phytotoxicity
+ results. Remove reciprocal-mutualism typing and qualify both existing directions; gene presence is not expression/flux,
+ removal is not mineralization or an isolated toxicity mediator. Do not transfer six-member immobilized-culture
+ results or claim universal consortium superiority. Existing22840534/31430718 caches requested by open764 are present;
+ no duplicate cache issue/import.'
+- 'Aquifer: remove only the genome-resolution workflow node and preserve prior2026-10-02 analysis-edge removal.
+ Retain field perturbation and relative-abundance observation without absolute loss or fitness claims. Gene-based
+ CO-oxidation potential and carbon/electron-flow implications receive computational provenance and HYPOTHESIZED/PARTIAL
+ causal descriptions. No invented methods or measured flux.'
+- Graph issues1829-1832 addressed here and remain open until protected-main merge; non-graph1833 remains open. Fresh
+ all-state title/body dedup matches294/691/763/764. Hidden/ignored local search excludes.git/docs/site/references_cache
+ with relevant caches separately covered. PRs/comments not exhaustively searched. Non-graph role, abundance, placeholder
+ taxonomy, habitat-note and substrate extrapolations remain separately scoped and byte-preserved, not certified.
+- Four guarded writes and append-only histories;456 other records and all923 caches unchanged. Every unrelated raw
+ block preserved. No schema/runtime/audit rule changes. Self-adversarial review is not independent approval or
+ corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication not preasserted.
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch106.json b/reports/causal_graph_review/cache-provenance-20261008-batch106.json
new file mode 100644
index 000000000..895a50a1d
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch106.json
@@ -0,0 +1,320 @@
+{
+ "changes": [],
+ "unchanged_cache_files": 923,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch106/aquifer-metadata.json": "b1e4de41d816a090b77f9a2ca105b576b50eac63d370d36b1c486a2886547ad7",
+ "/private/tmp/communitymech-batch106/aquifer-primary.txt": "204b98e38f62e044ddf34cb884576998ee008424c92b85f77172bb23d52be88f",
+ "/private/tmp/communitymech-batch106/baseline.json": "64492fd221761056719dff3b6beecd8945d2d14600caaf9d60ecbd173cc7d331",
+ "/private/tmp/communitymech-batch106/dedup-local-current.txt": "1399ae89b6a64f403353e6fa84ce230524c8614229de31ed93d22ec19eb0cc52",
+ "/private/tmp/communitymech-batch106/issue-dedup-current.json": "9efea81e5ca9f4e0e80e6c6113e687d07db1cc050e5be4ead759b93498826e48",
+ "/private/tmp/communitymech-batch106/mire-metadata.json": "fcc216c196bd49dd3cf84bd9c073ce8cba637be5f111c1664aa20b1a73b0dc96",
+ "/private/tmp/communitymech-batch106/mire-primary.txt": "b1dec101dafc02dd1487614a0ad47a44405b881f00549598428acdbd51d06d27",
+ "/private/tmp/communitymech-batch106/mire-primary.xml": "66955fd4d62846fc1506c264ead507e7517656051e8673a840fc9e43c286c4aa",
+ "/private/tmp/communitymech-batch106/mire_catalog-metadata.json": "776df37f829b35905e2ae1476b3dbdef5c9f186aa3717f562ec056b64f91a581",
+ "/private/tmp/communitymech-batch106/mire_catalog-primary.txt": "a4f2d9c07fd09a8e2028e0c81df1351cbff2534d36287e97d335e34378069de9",
+ "/private/tmp/communitymech-batch106/pesticide-metadata.json": "2d6cbd20b17100bfe7acbcc5a53c68abf86105b7eefd66ab75d1cc88411f609d",
+ "/private/tmp/communitymech-batch106/pesticide-primary.txt": "470b762cd60cf273dd9cf0e26aacb3fd595f1d5813744900be8a208e82089693",
+ "/private/tmp/communitymech-batch106/pesticide_2013-metadata.json": "7b53440cb84eec4ff6a2271daa7f0c142e00dec4f94c6f50317c3bf03ecead64",
+ "/private/tmp/communitymech-batch106/pesticide_2013-primary.txt": "ea8455cbe6d9abfd92e384a97ccaed46df18e2da8c64f52d847bcc9e7dd93716",
+ "/private/tmp/communitymech-batch106/pesticide_2013-primary.xml": "f0fc6037eb356cb4ef5fc38c97b48462d110741ff2dacfa81433f7b880fcbe66",
+ "/private/tmp/communitymech-batch106/primary-manifest.json": "c3267231491957e9cc73ff03a2c7ff90cc84ac01d787bc075d54d9ddf0949d14",
+ "/private/tmp/communitymech-batch106/staph_antagonism-metadata.json": "b5213ddb96b1ac893ec0e16bbbdf1ed142ff408654d9ba71eec169456136558a",
+ "/private/tmp/communitymech-batch106/staph_antagonism-primary.txt": "ab8b5a878459d775ee0017a963d82e5da8a3cd0909e72228ca9bcfc9ee5ddb0e",
+ "/private/tmp/communitymech-batch106/staph_context-metadata.json": "21f5fd0102eae97b6b080bc6f46df36792139b57b7e6d62c754cae7297267694",
+ "/private/tmp/communitymech-batch106/staph_context-primary.txt": "6ff06f5bc10d3c823d533519b1b423f2d652f9808cc5a293cac656fef4e5088a",
+ "/private/tmp/communitymech-batch106/staph_copper-metadata.json": "a4b6f1ed90c3e6dfe5d54ff1738d6f38929cc7348dc43b2104bb8b4de2660948",
+ "/private/tmp/communitymech-batch106/staph_copper-primary.txt": "9179a1dc45c8e1e0299399b551d82c100b63fbdefc50c35f812719c7f3567f19",
+ "/private/tmp/communitymech-batch106/staph_scaffold-metadata.json": "ac827088cb44ab0d62e021f0b2d50605548626eb046ed5aa63b7ff8a596fc634",
+ "/private/tmp/communitymech-batch106/staph_scaffold-primary.txt": "a1680570bae29f12f7be2e87d324b904bb1fc9d6ecbbdd7e79c97592530fad71",
+ "/private/tmp/communitymech-batch106/staph_strains-metadata.json": "325d880f6dac07b7bc9fad948d1a99df1f9465ad6af210187e44e2927c906b67",
+ "/private/tmp/communitymech-batch106/staph_strains-primary.txt": "a382e518b14dc08353628d08345a783e51e4e8cd388fa265238414717d8e96c9",
+ "/private/tmp/communitymech-batch106/staph_transcript-metadata.json": "1c49f6bdfd62416fb1094e34c9c4313113ef7d658c5580ba51b1ffc4887e8ac7",
+ "/private/tmp/communitymech-batch106/staph_transcript-primary.txt": "4351cb6288a362b7c92528a584eea87bb137fb2cdaa324477fe43e4ea6084267",
+ "references_cache/PMID_23865051.md": "b6f2d840482ad523fff23c79452a547fbfc54f3638a6f937b1948351b5a86505",
+ "references_cache/PMID_32633030.md": "99909ac1a677b513c9caad23462b6eb03d61612d4abf1be65171c023a06cc86c",
+ "references_cache/PMID_33831044.txt": "9883828c4225a2a4249a01163fb84eaa0dbe263630ed1aba05aa2e8d7a64b375",
+ "references_cache/PMID_34888261.txt": "36613735b96dbc704cae754bf4da56b8c6d55258fc897b889b654a088b1a271e",
+ "references_cache/PMID_38063415.md": "597b8ba99a589ed0ce36f84eece15513ad3752f6dc73b2a23f14bb2fd3203ac8",
+ "references_cache/PMID_41324029.txt": "0d421c030c68a206de344912b7dc58c42f4fac96496720b88dd20ef81eaa58a4",
+ "references_cache/PMID_41678860.md": "e3f673e77ae22dff910a26fcababaa9db6f80279ce9c2252438017663dbab77f",
+ "references_cache/PMID_42359480.txt": "c6c60a230f8dcb6f62e8d5f1b57e7796e2c156922e48cf15c2b2ff85ff98dd72",
+ "references_cache/PMID_42413741.txt": "9e677b5066a30ba1bef805f2ed01c5020ef7e4cd3d2d85df088b52f327a0f752",
+ "references_cache/PMID_42629020.txt": "6630c1c1bf989211e851c339c4ff31db1ff91a23df7ffaf1f8bf701154d0595d"
+ },
+ "source_access": {
+ "retrieval_manifest": {
+ "staph_antagonism": {
+ "reference": "PMID:42629020",
+ "title": "Interspecies interactions in dual-species biofilms formed by Staphylococcus aureus and Candida albicans: Phenotypic and transcriptomic insights.",
+ "pmid": "42629020",
+ "pmcid": null,
+ "doi": "10.1016/j.foodres.2026.119768",
+ "publication_types": {
+ "pubType": [
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42629020+AND+SRC%3AMED&format=json&resultType=core",
+ "source": "/private/tmp/communitymech-batch106/staph_antagonism-metadata.json",
+ "source_sha256": "b5213ddb96b1ac893ec0e16bbbdf1ed142ff408654d9ba71eec169456136558a",
+ "metadata": "/private/tmp/communitymech-batch106/staph_antagonism-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/staph_antagonism-primary.txt",
+ "body_sha256": "ab8b5a878459d775ee0017a963d82e5da8a3cd0909e72228ca9bcfc9ee5ddb0e",
+ "body_lines": 14,
+ "scope": "Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism enhancement.",
+ "license": "See publisher",
+ "fulltext_error": null
+ },
+ "staph_strains": {
+ "reference": "PMID:42413741",
+ "title": "Staphylococcus aureus strain heterogeneity modulates virulence traits associated to dual-species biofilms with Candida albicans.",
+ "pmid": "42413741",
+ "pmcid": null,
+ "doi": "10.1016/j.micpath.2026.108686",
+ "publication_types": {
+ "pubType": [
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42413741+AND+SRC%3AMED&format=json&resultType=core",
+ "source": "/private/tmp/communitymech-batch106/staph_strains-metadata.json",
+ "source_sha256": "325d880f6dac07b7bc9fad948d1a99df1f9465ad6af210187e44e2927c906b67",
+ "metadata": "/private/tmp/communitymech-batch106/staph_strains-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/staph_strains-primary.txt",
+ "body_sha256": "a382e518b14dc08353628d08345a783e51e4e8cd388fa265238414717d8e96c9",
+ "body_lines": 19,
+ "scope": "Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism enhancement.",
+ "license": "See publisher",
+ "fulltext_error": null
+ },
+ "staph_copper": {
+ "reference": "PMID:42359480",
+ "title": "Copper-driven mutualism of <i>Candida albicans</i> and <i>Staphylococcus aureus</i> interkingdom biofilms.",
+ "pmid": "42359480",
+ "pmcid": null,
+ "doi": "10.1099/mic.0.001725",
+ "publication_types": {
+ "pubType": [
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42359480+AND+SRC%3AMED&format=json&resultType=core",
+ "source": "/private/tmp/communitymech-batch106/staph_copper-metadata.json",
+ "source_sha256": "a4b6f1ed90c3e6dfe5d54ff1738d6f38929cc7348dc43b2104bb8b4de2660948",
+ "metadata": "/private/tmp/communitymech-batch106/staph_copper-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/staph_copper-primary.txt",
+ "body_sha256": "9179a1dc45c8e1e0299399b551d82c100b63fbdefc50c35f812719c7f3567f19",
+ "body_lines": 15,
+ "scope": "Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism enhancement.",
+ "license": "See publisher",
+ "fulltext_error": null
+ },
+ "staph_scaffold": {
+ "reference": "PMID:33831044",
+ "title": "Targeting Candida albicans in dual-species biofilms with antifungal treatment reduces Staphylococcus aureus and MRSA in vitro.",
+ "pmid": "33831044",
+ "pmcid": "PMC8031443",
+ "doi": "10.1371/journal.pone.0249547",
+ "publication_types": {
+ "pubType": [
+ "Research Support, Non-U.S. Gov't",
+ "research-article",
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A33831044+AND+SRC%3AMED&format=json&resultType=core",
+ "source": "/private/tmp/communitymech-batch106/staph_scaffold-metadata.json",
+ "source_sha256": "ac827088cb44ab0d62e021f0b2d50605548626eb046ed5aa63b7ff8a596fc634",
+ "metadata": "/private/tmp/communitymech-batch106/staph_scaffold-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/staph_scaffold-primary.txt",
+ "body_sha256": "a1680570bae29f12f7be2e87d324b904bb1fc9d6ecbbdd7e79c97592530fad71",
+ "body_lines": 22,
+ "scope": "Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism enhancement.",
+ "license": "See publisher",
+ "fulltext_error": null
+ },
+ "staph_context": {
+ "reference": "PMID:41324029",
+ "title": "A comprehensive study on the dual species biofilm formation of clinical <i>Staphylococcus aureus</i> and <i>Candida albicans</i> strains from the same origins.",
+ "pmid": "41324029",
+ "pmcid": "PMC12664092",
+ "doi": "10.1016/j.bioflm.2025.100324",
+ "publication_types": {
+ "pubType": [
+ "research-article",
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A41324029+AND+SRC%3AMED&format=json&resultType=core",
+ "source": "/private/tmp/communitymech-batch106/staph_context-metadata.json",
+ "source_sha256": "21f5fd0102eae97b6b080bc6f46df36792139b57b7e6d62c754cae7297267694",
+ "metadata": "/private/tmp/communitymech-batch106/staph_context-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/staph_context-primary.txt",
+ "body_sha256": "6ff06f5bc10d3c823d533519b1b423f2d652f9808cc5a293cac656fef4e5088a",
+ "body_lines": 17,
+ "scope": "Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism enhancement.",
+ "license": "See publisher",
+ "fulltext_error": null
+ },
+ "staph_transcript": {
+ "reference": "PMID:34888261",
+ "title": "Investigating the Transcriptome of Candida albicans in a Dual-Species Staphylococcus aureus Biofilm Model.",
+ "pmid": "34888261",
+ "pmcid": "PMC8650683",
+ "doi": "10.3389/fcimb.2021.791523",
+ "publication_types": {
+ "pubType": [
+ "Research Support, Non-U.S. Gov't",
+ "research-article",
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A34888261+AND+SRC%3AMED&format=json&resultType=core",
+ "source": "/private/tmp/communitymech-batch106/staph_transcript-metadata.json",
+ "source_sha256": "1c49f6bdfd62416fb1094e34c9c4313113ef7d658c5580ba51b1ffc4887e8ac7",
+ "metadata": "/private/tmp/communitymech-batch106/staph_transcript-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/staph_transcript-primary.txt",
+ "body_sha256": "4351cb6288a362b7c92528a584eea87bb137fb2cdaa324477fe43e4ea6084267",
+ "body_lines": 13,
+ "scope": "Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism enhancement.",
+ "license": "See publisher",
+ "fulltext_error": null
+ },
+ "mire": {
+ "reference": "PMID:38063415",
+ "title": "Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost.",
+ "pmid": "38063415",
+ "pmcid": "PMC10805028",
+ "doi": "10.1128/msystems.00698-23",
+ "publication_types": {
+ "pubType": [
+ "Research Support, Non-U.S. Gov't",
+ "research-article",
+ "Research Support, U.S. Gov't, Non-P.H.S.",
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10805028/fullTextXML",
+ "source": "/private/tmp/communitymech-batch106/mire-primary.xml",
+ "source_sha256": "66955fd4d62846fc1506c264ead507e7517656051e8673a840fc9e43c286c4aa",
+ "metadata": "/private/tmp/communitymech-batch106/mire-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/mire-primary.txt",
+ "body_sha256": "b1dec101dafc02dd1487614a0ad47a44405b881f00549598428acdbd51d06d27",
+ "body_lines": 782,
+ "scope": "Complete main body retrieved, not yet read; no figure-pixel/supplement/raw-data review implied.",
+ "license": "Copyright \u00a9 2023 Ellenbogen et al.2023Ellenbogen et al.https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.",
+ "fulltext_error": null
+ },
+ "mire_catalog": {
+ "reference": "PMID:30013118",
+ "title": "Genome-centric view of carbon processing in thawing permafrost.",
+ "pmid": "30013118",
+ "pmcid": null,
+ "doi": "10.1038/s41586-018-0338-1",
+ "publication_types": {
+ "pubType": [
+ "Research Support, Non-U.S. Gov't",
+ "Research Support, U.S. Gov't, Non-P.H.S.",
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A30013118+AND+SRC%3AMED&format=json&resultType=core",
+ "source": "/private/tmp/communitymech-batch106/mire_catalog-metadata.json",
+ "source_sha256": "776df37f829b35905e2ae1476b3dbdef5c9f186aa3717f562ec056b64f91a581",
+ "metadata": "/private/tmp/communitymech-batch106/mire_catalog-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/mire_catalog-primary.txt",
+ "body_sha256": "a4f2d9c07fd09a8e2028e0c81df1351cbff2534d36287e97d335e34378069de9",
+ "body_lines": 11,
+ "scope": "Abstract only in this retrieval; no global full-text absence claim.",
+ "license": "See publisher",
+ "fulltext_error": null
+ },
+ "pesticide": {
+ "reference": "PMID:41678860",
+ "title": "Defined microbial consortium with bioremediation potential: atrazine removal, phytotoxicity, and detection of genes involved in herbicide catabolism.",
+ "pmid": "41678860",
+ "pmcid": null,
+ "doi": "10.1016/j.chemosphere.2026.144856",
+ "publication_types": {
+ "pubType": [
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A41678860+AND+SRC%3AMED&format=json&resultType=core",
+ "source": "/private/tmp/communitymech-batch106/pesticide-metadata.json",
+ "source_sha256": "2d6cbd20b17100bfe7acbcc5a53c68abf86105b7eefd66ab75d1cc88411f609d",
+ "metadata": "/private/tmp/communitymech-batch106/pesticide-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/pesticide-primary.txt",
+ "body_sha256": "470b762cd60cf273dd9cf0e26aacb3fd595f1d5813744900be8a208e82089693",
+ "body_lines": 15,
+ "scope": "Abstract only in this retrieval; no global full-text absence claim.",
+ "license": "See publisher",
+ "fulltext_error": null
+ },
+ "pesticide_2013": {
+ "reference": "PMID:23865051",
+ "title": "Enhanced removal of a pesticides mixture by single cultures and consortia of free and immobilized Streptomyces strains.",
+ "pmid": "23865051",
+ "pmcid": "PMC3705853",
+ "doi": "10.1155/2013/392573",
+ "publication_types": {
+ "pubType": [
+ "Research Support, Non-U.S. Gov't",
+ "research-article",
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3705853/fullTextXML",
+ "source": "/private/tmp/communitymech-batch106/pesticide_2013-primary.xml",
+ "source_sha256": "f0fc6037eb356cb4ef5fc38c97b48462d110741ff2dacfa81433f7b880fcbe66",
+ "metadata": "/private/tmp/communitymech-batch106/pesticide_2013-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/pesticide_2013-primary.txt",
+ "body_sha256": "ea8455cbe6d9abfd92e384a97ccaed46df18e2da8c64f52d847bcc9e7dd93716",
+ "body_lines": 323,
+ "scope": "Complete main body retrieved, not yet read; no figure-pixel/supplement/raw-data review implied.",
+ "license": "Copyright \u00a9 2013 Mar\u00eda S. Fuentes et al.2013https://creativecommons.org/licenses/by/3.0/This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.",
+ "fulltext_error": null
+ },
+ "aquifer": {
+ "reference": "PMID:32633030",
+ "title": "Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph.",
+ "pmid": "32633030",
+ "pmcid": null,
+ "doi": "10.1111/1758-2229.12868",
+ "publication_types": {
+ "pubType": [
+ "Research Support, Non-U.S. Gov't",
+ "Journal Article"
+ ]
+ },
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A32633030+AND+SRC%3AMED&format=json&resultType=core",
+ "source": "/private/tmp/communitymech-batch106/aquifer-metadata.json",
+ "source_sha256": "b1e4de41d816a090b77f9a2ca105b576b50eac63d370d36b1c486a2886547ad7",
+ "metadata": "/private/tmp/communitymech-batch106/aquifer-metadata.json",
+ "extracted_body": "/private/tmp/communitymech-batch106/aquifer-primary.txt",
+ "body_sha256": "204b98e38f62e044ddf34cb884576998ee008424c92b85f77172bb23d52be88f",
+ "body_lines": 10,
+ "scope": "Abstract only in this retrieval; no global full-text absence claim.",
+ "license": "See publisher",
+ "fulltext_error": null
+ }
+ },
+ "actual_read_scope": [
+ "Eleven primary sources independently retrieved. All nine abstract-only retrievals were read whole, including the six Staphylococcus-Candida studies, 2018 mire catalog, 2026 pesticide study and aquifer study. Available full-text leads were not fetched for Staphylococcus-Candida: fresh PMCID leads exist for three and the pre-existing copper cache lists PMC13306210 despite missing fresh PMCID metadata. This is an abstract-bounded metadata correction, not an assertion of full-text absence.",
+ "Fresh EuropePMC full-body XML retrieved for mire2023 and pesticide2013. Mire abstract1-33, results/discussion238-477 and methods528-676 read; pesticide2013 results182-246 read. Other spans were indexed or not read, not whole-paper review. No figure-pixel, supplement, raw-data or full-pipeline certification. Mire CC BY4.0 and pesticide2013 CC BY3.0 metadata retained.",
+ "Existing six Staphylococcus-Candida caches, pesticide2026, both aquifer caches and both lindane abstract caches read whole. Large mire2023, mire2018 and pesticide2013 caches used for bounded context and normalized claim matching, not exhaustive duplicated full-text review. Wiley aquifer and Elsevier pesticide2026 web requests returned Internal Error with no HTTP code reported; no bypass or global full-text-absence assertion. No cache imports, license949/loader1703/DOI-case1091 certification."
+ ]
+ },
+ "limitations": [
+ "Fresh both-root baseline before source reads: 460 records, 923 caches, 56 existing warnings, zero structural defects. Four whole records and all19 original nodes/10 directions reviewed;18 nodes and five qualified existing directions retained, one workflow node and five arrows removed, eight renames. No new topology or Edison submission/spend.",
+ "Eleven primary sources independently retrieved. All nine abstract-only retrievals were read whole, including the six Staphylococcus-Candida studies, 2018 mire catalog, 2026 pesticide study and aquifer study. Available full-text leads were not fetched for Staphylococcus-Candida: fresh PMCID leads exist for three and the pre-existing copper cache lists PMC13306210 despite missing fresh PMCID metadata. This is an abstract-bounded metadata correction, not an assertion of full-text absence.",
+ "Fresh EuropePMC full-body XML retrieved for mire2023 and pesticide2013. Mire abstract1-33, results/discussion238-477 and methods528-676 read; pesticide2013 results182-246 read. Other spans were indexed or not read, not whole-paper review. No figure-pixel, supplement, raw-data or full-pipeline certification. Mire CC BY4.0 and pesticide2013 CC BY3.0 metadata retained.",
+ "Existing six Staphylococcus-Candida caches, pesticide2026, both aquifer caches and both lindane abstract caches read whole. Large mire2023, mire2018 and pesticide2013 caches used for bounded context and normalized claim matching, not exhaustive duplicated full-text review. Wiley aquifer and Elsevier pesticide2026 web requests returned Internal Error with no HTTP code reported; no bypass or global full-text-absence assertion. No cache imports, license949/loader1703/DOI-case1091 certification.",
+ "Staphylococcus-Candida: retain six separate-study observations; remove cross-study arrows and categorical reciprocal competition/universal mutualism. Preserve the copper authors mutualism interpretation as HYPOTHESIZED/PARTIAL and source-supported scaffold facilitation. Transcript/ontology associations are not demonstrated virulence, genotype change or colonization. No new growth, biofilm, survival, resistance, virulence or colonization enhancement procedures, genetic designs, strain-selection advice or partner mechanisms.",
+ "Mire: preserve encoded potential, transcripts and metabolite observations with canonical identity-only archaeal/bacterial scope and computational provenance. Remove unestablished syntrophic product-removal feedback and traced cross-feeding. Acetate supports an acetoclastic route, not the removed methylotrophic target; no replacement mechanism/node added. Preserve source-proposed fen niche partitioning and its existing direction as HYPOTHESIZED/PARTIAL; no measured substrate flux or competition reduction. Remove redundant habitat arrows and unrelated catalog support for specific syntrophy.",
+ "Pesticide: retain the exact four-member non-antagonism, aggregate growth, gene detection, removal and phytotoxicity results. Remove reciprocal-mutualism typing and qualify both existing directions; gene presence is not expression/flux, removal is not mineralization or an isolated toxicity mediator. Do not transfer six-member immobilized-culture results or claim universal consortium superiority. Existing22840534/31430718 caches requested by open764 are present; no duplicate cache issue/import.",
+ "Aquifer: remove only the genome-resolution workflow node and preserve prior2026-10-02 analysis-edge removal. Retain field perturbation and relative-abundance observation without absolute loss or fitness claims. Gene-based CO-oxidation potential and carbon/electron-flow implications receive computational provenance and HYPOTHESIZED/PARTIAL causal descriptions. No invented methods or measured flux.",
+ "Graph issues1829-1832 addressed here and remain open until protected-main merge; non-graph1833 remains open. Fresh all-state title/body dedup matches294/691/763/764. Hidden/ignored local search excludes.git/docs/site/references_cache with relevant caches separately covered. PRs/comments not exhaustively searched. Non-graph role, abundance, placeholder taxonomy, habitat-note and substrate extrapolations remain separately scoped and byte-preserved, not certified.",
+ "Four guarded writes and append-only histories;456 other records and all923 caches unchanged. Every unrelated raw block preserved. No schema/runtime/audit rule changes. Self-adversarial review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication not preasserted."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
new file mode 100644
index 000000000..bbc00718a
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
@@ -0,0 +1,1042 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 20d6692b687fa6826bc25f8673543215c18aa310
+baseline_commit: 20d6692b687fa6826bc25f8673543215c18aa310
+base_tree: eea2b5739e61f7587840dfa918f79ec5474bdb23
+pre_source_baseline_sha256: 64492fd221761056719dff3b6beecd8945d2d14600caaf9d60ecbd173cc7d331
+issues:
+- 1829
+- 1830
+- 1831
+- 1832
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1833
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 1081
+ matching_issues:
+ - 294
+ - 691
+ - 763
+ - 764
+ ignored_hidden_local_search: true
+source_access:
+ retrieval_manifest:
+ staph_antagonism:
+ reference: PMID:42629020
+ title: 'Interspecies interactions in dual-species biofilms formed by Staphylococcus aureus and Candida albicans:
+ Phenotypic and transcriptomic insights.'
+ pmid: '42629020'
+ pmcid: null
+ doi: 10.1016/j.foodres.2026.119768
+ publication_types:
+ pubType:
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42629020+AND+SRC%3AMED&format=json&resultType=core
+ source: /private/tmp/communitymech-batch106/staph_antagonism-metadata.json
+ source_sha256: b5213ddb96b1ac893ec0e16bbbdf1ed142ff408654d9ba71eec169456136558a
+ metadata: /private/tmp/communitymech-batch106/staph_antagonism-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/staph_antagonism-primary.txt
+ body_sha256: ab8b5a878459d775ee0017a963d82e5da8a3cd0909e72228ca9bcfc9ee5ddb0e
+ body_lines: 14
+ scope: Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body
+ absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism
+ enhancement.
+ license: See publisher
+ fulltext_error: null
+ staph_strains:
+ reference: PMID:42413741
+ title: Staphylococcus aureus strain heterogeneity modulates virulence traits associated to dual-species biofilms
+ with Candida albicans.
+ pmid: '42413741'
+ pmcid: null
+ doi: 10.1016/j.micpath.2026.108686
+ publication_types:
+ pubType:
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42413741+AND+SRC%3AMED&format=json&resultType=core
+ source: /private/tmp/communitymech-batch106/staph_strains-metadata.json
+ source_sha256: 325d880f6dac07b7bc9fad948d1a99df1f9465ad6af210187e44e2927c906b67
+ metadata: /private/tmp/communitymech-batch106/staph_strains-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/staph_strains-primary.txt
+ body_sha256: a382e518b14dc08353628d08345a783e51e4e8cd388fa265238414717d8e96c9
+ body_lines: 19
+ scope: Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body
+ absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism
+ enhancement.
+ license: See publisher
+ fulltext_error: null
+ staph_copper:
+ reference: PMID:42359480
+ title: Copper-driven mutualism of <i>Candida albicans</i> and <i>Staphylococcus aureus</i>
+ interkingdom biofilms.
+ pmid: '42359480'
+ pmcid: null
+ doi: 10.1099/mic.0.001725
+ publication_types:
+ pubType:
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42359480+AND+SRC%3AMED&format=json&resultType=core
+ source: /private/tmp/communitymech-batch106/staph_copper-metadata.json
+ source_sha256: a4b6f1ed90c3e6dfe5d54ff1738d6f38929cc7348dc43b2104bb8b4de2660948
+ metadata: /private/tmp/communitymech-batch106/staph_copper-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/staph_copper-primary.txt
+ body_sha256: 9179a1dc45c8e1e0299399b551d82c100b63fbdefc50c35f812719c7f3567f19
+ body_lines: 15
+ scope: Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body
+ absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism
+ enhancement.
+ license: See publisher
+ fulltext_error: null
+ staph_scaffold:
+ reference: PMID:33831044
+ title: Targeting Candida albicans in dual-species biofilms with antifungal treatment reduces Staphylococcus
+ aureus and MRSA in vitro.
+ pmid: '33831044'
+ pmcid: PMC8031443
+ doi: 10.1371/journal.pone.0249547
+ publication_types:
+ pubType:
+ - Research Support, Non-U.S. Gov't
+ - research-article
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A33831044+AND+SRC%3AMED&format=json&resultType=core
+ source: /private/tmp/communitymech-batch106/staph_scaffold-metadata.json
+ source_sha256: ac827088cb44ab0d62e021f0b2d50605548626eb046ed5aa63b7ff8a596fc634
+ metadata: /private/tmp/communitymech-batch106/staph_scaffold-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/staph_scaffold-primary.txt
+ body_sha256: a1680570bae29f12f7be2e87d324b904bb1fc9d6ecbbdd7e79c97592530fad71
+ body_lines: 22
+ scope: Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body
+ absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism
+ enhancement.
+ license: See publisher
+ fulltext_error: null
+ staph_context:
+ reference: PMID:41324029
+ title: A comprehensive study on the dual species biofilm formation of clinical <i>Staphylococcus aureus</i>
+ and <i>Candida albicans</i> strains from the same origins.
+ pmid: '41324029'
+ pmcid: PMC12664092
+ doi: 10.1016/j.bioflm.2025.100324
+ publication_types:
+ pubType:
+ - research-article
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A41324029+AND+SRC%3AMED&format=json&resultType=core
+ source: /private/tmp/communitymech-batch106/staph_context-metadata.json
+ source_sha256: 21f5fd0102eae97b6b080bc6f46df36792139b57b7e6d62c754cae7297267694
+ metadata: /private/tmp/communitymech-batch106/staph_context-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/staph_context-primary.txt
+ body_sha256: 6ff06f5bc10d3c823d533519b1b423f2d652f9808cc5a293cac656fef4e5088a
+ body_lines: 17
+ scope: Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body
+ absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism
+ enhancement.
+ license: See publisher
+ fulltext_error: null
+ staph_transcript:
+ reference: PMID:34888261
+ title: Investigating the Transcriptome of Candida albicans in a Dual-Species Staphylococcus aureus
+ Biofilm Model.
+ pmid: '34888261'
+ pmcid: PMC8650683
+ doi: 10.3389/fcimb.2021.791523
+ publication_types:
+ pubType:
+ - Research Support, Non-U.S. Gov't
+ - research-article
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A34888261+AND+SRC%3AMED&format=json&resultType=core
+ source: /private/tmp/communitymech-batch106/staph_transcript-metadata.json
+ source_sha256: 1c49f6bdfd62416fb1094e34c9c4313113ef7d658c5580ba51b1ffc4887e8ac7
+ metadata: /private/tmp/communitymech-batch106/staph_transcript-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/staph_transcript-primary.txt
+ body_sha256: 4351cb6288a362b7c92528a584eea87bb137fb2cdaa324477fe43e4ea6084267
+ body_lines: 13
+ scope: Abstract-only retrieval for this bounded review; PMCID metadata retained where present. No full-body
+ absence claim. Pathogen-associated sources are limited to evidence correction, not procedure or mechanism
+ enhancement.
+ license: See publisher
+ fulltext_error: null
+ mire:
+ reference: PMID:38063415
+ title: 'Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost.'
+ pmid: '38063415'
+ pmcid: PMC10805028
+ doi: 10.1128/msystems.00698-23
+ publication_types:
+ pubType:
+ - Research Support, Non-U.S. Gov't
+ - research-article
+ - Research Support, U.S. Gov't, Non-P.H.S.
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10805028/fullTextXML
+ source: /private/tmp/communitymech-batch106/mire-primary.xml
+ source_sha256: 66955fd4d62846fc1506c264ead507e7517656051e8673a840fc9e43c286c4aa
+ metadata: /private/tmp/communitymech-batch106/mire-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/mire-primary.txt
+ body_sha256: b1dec101dafc02dd1487614a0ad47a44405b881f00549598428acdbd51d06d27
+ body_lines: 782
+ scope: Complete main body retrieved, not yet read; no figure-pixel/supplement/raw-data review implied.
+ license: "Copyright \xA9 2023 Ellenbogen et al.2023Ellenbogen et al.https://creativecommons.org/licenses/by/4.0/This\
+ \ is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International\
+ \ license."
+ fulltext_error: null
+ mire_catalog:
+ reference: PMID:30013118
+ title: Genome-centric view of carbon processing in thawing permafrost.
+ pmid: '30013118'
+ pmcid: null
+ doi: 10.1038/s41586-018-0338-1
+ publication_types:
+ pubType:
+ - Research Support, Non-U.S. Gov't
+ - Research Support, U.S. Gov't, Non-P.H.S.
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A30013118+AND+SRC%3AMED&format=json&resultType=core
+ source: /private/tmp/communitymech-batch106/mire_catalog-metadata.json
+ source_sha256: 776df37f829b35905e2ae1476b3dbdef5c9f186aa3717f562ec056b64f91a581
+ metadata: /private/tmp/communitymech-batch106/mire_catalog-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/mire_catalog-primary.txt
+ body_sha256: a4f2d9c07fd09a8e2028e0c81df1351cbff2534d36287e97d335e34378069de9
+ body_lines: 11
+ scope: Abstract only in this retrieval; no global full-text absence claim.
+ license: See publisher
+ fulltext_error: null
+ pesticide:
+ reference: PMID:41678860
+ title: 'Defined microbial consortium with bioremediation potential: atrazine removal, phytotoxicity, and detection
+ of genes involved in herbicide catabolism.'
+ pmid: '41678860'
+ pmcid: null
+ doi: 10.1016/j.chemosphere.2026.144856
+ publication_types:
+ pubType:
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A41678860+AND+SRC%3AMED&format=json&resultType=core
+ source: /private/tmp/communitymech-batch106/pesticide-metadata.json
+ source_sha256: 2d6cbd20b17100bfe7acbcc5a53c68abf86105b7eefd66ab75d1cc88411f609d
+ metadata: /private/tmp/communitymech-batch106/pesticide-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/pesticide-primary.txt
+ body_sha256: 470b762cd60cf273dd9cf0e26aacb3fd595f1d5813744900be8a208e82089693
+ body_lines: 15
+ scope: Abstract only in this retrieval; no global full-text absence claim.
+ license: See publisher
+ fulltext_error: null
+ pesticide_2013:
+ reference: PMID:23865051
+ title: Enhanced removal of a pesticides mixture by single cultures and consortia of free and immobilized Streptomyces
+ strains.
+ pmid: '23865051'
+ pmcid: PMC3705853
+ doi: 10.1155/2013/392573
+ publication_types:
+ pubType:
+ - Research Support, Non-U.S. Gov't
+ - research-article
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3705853/fullTextXML
+ source: /private/tmp/communitymech-batch106/pesticide_2013-primary.xml
+ source_sha256: f0fc6037eb356cb4ef5fc38c97b48462d110741ff2dacfa81433f7b880fcbe66
+ metadata: /private/tmp/communitymech-batch106/pesticide_2013-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/pesticide_2013-primary.txt
+ body_sha256: ea8455cbe6d9abfd92e384a97ccaed46df18e2da8c64f52d847bcc9e7dd93716
+ body_lines: 323
+ scope: Complete main body retrieved, not yet read; no figure-pixel/supplement/raw-data review implied.
+ license: "Copyright \xA9 2013 Mar\xEDa S. Fuentes et al.2013https://creativecommons.org/licenses/by/3.0/This\
+ \ is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted\
+ \ use, distribution, and reproduction in any medium, provided the original work is properly cited."
+ fulltext_error: null
+ aquifer:
+ reference: PMID:32633030
+ title: Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph.
+ pmid: '32633030'
+ pmcid: null
+ doi: 10.1111/1758-2229.12868
+ publication_types:
+ pubType:
+ - Research Support, Non-U.S. Gov't
+ - Journal Article
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A32633030+AND+SRC%3AMED&format=json&resultType=core
+ source: /private/tmp/communitymech-batch106/aquifer-metadata.json
+ source_sha256: b1e4de41d816a090b77f9a2ca105b576b50eac63d370d36b1c486a2886547ad7
+ metadata: /private/tmp/communitymech-batch106/aquifer-metadata.json
+ extracted_body: /private/tmp/communitymech-batch106/aquifer-primary.txt
+ body_sha256: 204b98e38f62e044ddf34cb884576998ee008424c92b85f77172bb23d52be88f
+ body_lines: 10
+ scope: Abstract only in this retrieval; no global full-text absence claim.
+ license: See publisher
+ fulltext_error: null
+ actual_read_scope:
+ - 'Eleven primary sources independently retrieved. All nine abstract-only retrievals were read whole, including
+ the six Staphylococcus-Candida studies, 2018 mire catalog, 2026 pesticide study and aquifer study. Available
+ full-text leads were not fetched for Staphylococcus-Candida: fresh PMCID leads exist for three and the pre-existing
+ copper cache lists PMC13306210 despite missing fresh PMCID metadata. This is an abstract-bounded metadata correction,
+ not an assertion of full-text absence.'
+ - Fresh EuropePMC full-body XML retrieved for mire2023 and pesticide2013. Mire abstract1-33, results/discussion238-477
+ and methods528-676 read; pesticide2013 results182-246 read. Other spans were indexed or not read, not whole-paper
+ review. No figure-pixel, supplement, raw-data or full-pipeline certification. Mire CC BY4.0 and pesticide2013
+ CC BY3.0 metadata retained.
+ - Existing six Staphylococcus-Candida caches, pesticide2026, both aquifer caches and both lindane abstract caches
+ read whole. Large mire2023, mire2018 and pesticide2013 caches used for bounded context and normalized claim
+ matching, not exhaustive duplicated full-text review. Wiley aquifer and Elsevier pesticide2026 web requests
+ returned Internal Error with no HTTP code reported; no bypass or global full-text-absence assertion. No cache
+ imports, license949/loader1703/DOI-case1091 certification.
+primary_artifacts:
+ /private/tmp/communitymech-batch106/aquifer-metadata.json: b1e4de41d816a090b77f9a2ca105b576b50eac63d370d36b1c486a2886547ad7
+ /private/tmp/communitymech-batch106/aquifer-primary.txt: 204b98e38f62e044ddf34cb884576998ee008424c92b85f77172bb23d52be88f
+ /private/tmp/communitymech-batch106/baseline.json: 64492fd221761056719dff3b6beecd8945d2d14600caaf9d60ecbd173cc7d331
+ /private/tmp/communitymech-batch106/dedup-local-current.txt: 1399ae89b6a64f403353e6fa84ce230524c8614229de31ed93d22ec19eb0cc52
+ /private/tmp/communitymech-batch106/issue-dedup-current.json: 9efea81e5ca9f4e0e80e6c6113e687d07db1cc050e5be4ead759b93498826e48
+ /private/tmp/communitymech-batch106/mire-metadata.json: fcc216c196bd49dd3cf84bd9c073ce8cba637be5f111c1664aa20b1a73b0dc96
+ /private/tmp/communitymech-batch106/mire-primary.txt: b1dec101dafc02dd1487614a0ad47a44405b881f00549598428acdbd51d06d27
+ /private/tmp/communitymech-batch106/mire-primary.xml: 66955fd4d62846fc1506c264ead507e7517656051e8673a840fc9e43c286c4aa
+ /private/tmp/communitymech-batch106/mire_catalog-metadata.json: 776df37f829b35905e2ae1476b3dbdef5c9f186aa3717f562ec056b64f91a581
+ /private/tmp/communitymech-batch106/mire_catalog-primary.txt: a4f2d9c07fd09a8e2028e0c81df1351cbff2534d36287e97d335e34378069de9
+ /private/tmp/communitymech-batch106/pesticide-metadata.json: 2d6cbd20b17100bfe7acbcc5a53c68abf86105b7eefd66ab75d1cc88411f609d
+ /private/tmp/communitymech-batch106/pesticide-primary.txt: 470b762cd60cf273dd9cf0e26aacb3fd595f1d5813744900be8a208e82089693
+ /private/tmp/communitymech-batch106/pesticide_2013-metadata.json: 7b53440cb84eec4ff6a2271daa7f0c142e00dec4f94c6f50317c3bf03ecead64
+ /private/tmp/communitymech-batch106/pesticide_2013-primary.txt: ea8455cbe6d9abfd92e384a97ccaed46df18e2da8c64f52d847bcc9e7dd93716
+ /private/tmp/communitymech-batch106/pesticide_2013-primary.xml: f0fc6037eb356cb4ef5fc38c97b48462d110741ff2dacfa81433f7b880fcbe66
+ /private/tmp/communitymech-batch106/primary-manifest.json: c3267231491957e9cc73ff03a2c7ff90cc84ac01d787bc075d54d9ddf0949d14
+ /private/tmp/communitymech-batch106/staph_antagonism-metadata.json: b5213ddb96b1ac893ec0e16bbbdf1ed142ff408654d9ba71eec169456136558a
+ /private/tmp/communitymech-batch106/staph_antagonism-primary.txt: ab8b5a878459d775ee0017a963d82e5da8a3cd0909e72228ca9bcfc9ee5ddb0e
+ /private/tmp/communitymech-batch106/staph_context-metadata.json: 21f5fd0102eae97b6b080bc6f46df36792139b57b7e6d62c754cae7297267694
+ /private/tmp/communitymech-batch106/staph_context-primary.txt: 6ff06f5bc10d3c823d533519b1b423f2d652f9808cc5a293cac656fef4e5088a
+ /private/tmp/communitymech-batch106/staph_copper-metadata.json: a4b6f1ed90c3e6dfe5d54ff1738d6f38929cc7348dc43b2104bb8b4de2660948
+ /private/tmp/communitymech-batch106/staph_copper-primary.txt: 9179a1dc45c8e1e0299399b551d82c100b63fbdefc50c35f812719c7f3567f19
+ /private/tmp/communitymech-batch106/staph_scaffold-metadata.json: ac827088cb44ab0d62e021f0b2d50605548626eb046ed5aa63b7ff8a596fc634
+ /private/tmp/communitymech-batch106/staph_scaffold-primary.txt: a1680570bae29f12f7be2e87d324b904bb1fc9d6ecbbdd7e79c97592530fad71
+ /private/tmp/communitymech-batch106/staph_strains-metadata.json: 325d880f6dac07b7bc9fad948d1a99df1f9465ad6af210187e44e2927c906b67
+ /private/tmp/communitymech-batch106/staph_strains-primary.txt: a382e518b14dc08353628d08345a783e51e4e8cd388fa265238414717d8e96c9
+ /private/tmp/communitymech-batch106/staph_transcript-metadata.json: 1c49f6bdfd62416fb1094e34c9c4313113ef7d658c5580ba51b1ffc4887e8ac7
+ /private/tmp/communitymech-batch106/staph_transcript-primary.txt: 4351cb6288a362b7c92528a584eea87bb137fb2cdaa324477fe43e4ea6084267
+ references_cache/PMID_23865051.md: b6f2d840482ad523fff23c79452a547fbfc54f3638a6f937b1948351b5a86505
+ references_cache/PMID_32633030.md: 99909ac1a677b513c9caad23462b6eb03d61612d4abf1be65171c023a06cc86c
+ references_cache/PMID_33831044.txt: 9883828c4225a2a4249a01163fb84eaa0dbe263630ed1aba05aa2e8d7a64b375
+ references_cache/PMID_34888261.txt: 36613735b96dbc704cae754bf4da56b8c6d55258fc897b889b654a088b1a271e
+ references_cache/PMID_38063415.md: 597b8ba99a589ed0ce36f84eece15513ad3752f6dc73b2a23f14bb2fd3203ac8
+ references_cache/PMID_41324029.txt: 0d421c030c68a206de344912b7dc58c42f4fac96496720b88dd20ef81eaa58a4
+ references_cache/PMID_41678860.md: e3f673e77ae22dff910a26fcababaa9db6f80279ce9c2252438017663dbab77f
+ references_cache/PMID_42359480.txt: c6c60a230f8dcb6f62e8d5f1b57e7796e2c156922e48cf15c2b2ff85ff98dd72
+ references_cache/PMID_42413741.txt: 9e677b5066a30ba1bef805f2ed01c5020ef7e4cd3d2d85df088b52f327a0f752
+ references_cache/PMID_42629020.txt: 6630c1c1bf989211e851c339c4ff31db1ff91a23df7ffaf1f8bf701154d0595d
+primary_graph_snippet_count: 29
+snippet_checks:
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Antagonistic Dual-Species Biofilm Suppression
+ evidence_index: 0
+ reference: PMID:42629020
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_antagonism-primary.txt
+ cache_artifact: references_cache/PMID_42629020.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Antagonistic Dual-Species Biofilm Suppression
+ evidence_index: 1
+ reference: PMID:42629020
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_antagonism-primary.txt
+ cache_artifact: references_cache/PMID_42629020.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Contact-Dependent Strain-Specific Fungal Suppression
+ evidence_index: 0
+ reference: PMID:42413741
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_strains-primary.txt
+ cache_artifact: references_cache/PMID_42413741.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Contact-Dependent Strain-Specific Fungal Suppression
+ evidence_index: 1
+ reference: PMID:42413741
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_strains-primary.txt
+ cache_artifact: references_cache/PMID_42413741.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Copper-Mediated Nutritional Mutualism
+ evidence_index: 0
+ reference: PMID:42359480
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_copper-primary.txt
+ cache_artifact: references_cache/PMID_42359480.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Copper-Mediated Nutritional Mutualism
+ evidence_index: 1
+ reference: PMID:42359480
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_copper-primary.txt
+ cache_artifact: references_cache/PMID_42359480.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Candida Biofilm Scaffold Supports Staphylococcus Colonization
+ evidence_index: 0
+ reference: PMID:33831044
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_scaffold-primary.txt
+ cache_artifact: references_cache/PMID_33831044.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Candida Biofilm Scaffold Supports Staphylococcus Colonization
+ evidence_index: 1
+ reference: PMID:33831044
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_scaffold-primary.txt
+ cache_artifact: references_cache/PMID_33831044.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Candida Biofilm Scaffold Supports Staphylococcus Colonization
+ evidence_index: 2
+ reference: PMID:33831044
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_scaffold-primary.txt
+ cache_artifact: references_cache/PMID_33831044.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Growth-State and Hyphal Context Dependence
+ evidence_index: 0
+ reference: PMID:41324029
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_context-primary.txt
+ cache_artifact: references_cache/PMID_41324029.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Growth-State and Hyphal Context Dependence
+ evidence_index: 1
+ reference: PMID:41324029
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_context-primary.txt
+ cache_artifact: references_cache/PMID_41324029.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: Study-Specific Candida Transcript Response
+ evidence_index: 0
+ reference: PMID:34888261
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_transcript-primary.txt
+ cache_artifact: references_cache/PMID_34888261.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: Methanogenic Methylotrophic Potential and Expression
+ evidence_index: 0
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: Methanogenic Methylotrophic Potential and Expression
+ evidence_index: 1
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: Bacterial Anaerobic Methylotrophic Potential and Expression
+ evidence_index: 0
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: Bacterial Anaerobic Methylotrophic Potential and Expression
+ evidence_index: 1
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: Proposed Methylated-Substrate Niche Partitioning
+ evidence_index: 0
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: Proposed Methylated-Substrate Niche Partitioning
+ evidence_index: 1
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: Thaw-Stage Methylotrophic Expression Patterns
+ evidence_index: 0
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: Thaw-Stage Methylotrophic Expression Patterns
+ evidence_index: 1
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Streptomyces_A2_A5_A11_M7_Pesticide_Consortium
+ node: Non-antagonistic community-level growth enhancement
+ evidence_index: 0
+ reference: PMID:23865051
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/pesticide_2013-primary.txt
+ cache_artifact: references_cache/PMID_23865051.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Streptomyces_A2_A5_A11_M7_Pesticide_Consortium
+ node: Non-antagonistic community-level growth enhancement
+ evidence_index: 1
+ reference: PMID:41678860
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/pesticide-primary.txt
+ cache_artifact: references_cache/PMID_41678860.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Streptomyces_A2_A5_A11_M7_Pesticide_Consortium
+ node: C1 Herbicide-Catabolism Gene Detection
+ evidence_index: 0
+ reference: PMID:41678860
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/pesticide-primary.txt
+ cache_artifact: references_cache/PMID_41678860.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Streptomyces_A2_A5_A11_M7_Pesticide_Consortium
+ node: C1 Atrazine Growth and Removal
+ evidence_index: 0
+ reference: PMID:41678860
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/pesticide-primary.txt
+ cache_artifact: references_cache/PMID_41678860.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Streptomyces_A2_A5_A11_M7_Pesticide_Consortium
+ node: C1 Atrazine Phytotoxicity Reversal
+ evidence_index: 0
+ reference: PMID:41678860
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/pesticide-primary.txt
+ cache_artifact: references_cache/PMID_41678860.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Subsurface_Carboxydocella_CO_Aquifer_Community
+ node: scCO2 Injection Reshapes Subsurface Community
+ evidence_index: 0
+ reference: PMID:32633030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/aquifer-primary.txt
+ cache_artifact: references_cache/PMID_32633030.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Subsurface_Carboxydocella_CO_Aquifer_Community
+ node: Post-Injection Carboxydocella Decline
+ evidence_index: 0
+ reference: PMID:32633030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/aquifer-primary.txt
+ cache_artifact: references_cache/PMID_32633030.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Subsurface_Carboxydocella_CO_Aquifer_Community
+ node: CODH-Associated CO-Oxidation Potential
+ evidence_index: 0
+ reference: PMID:32633030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/aquifer-primary.txt
+ cache_artifact: references_cache/PMID_32633030.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Subsurface_Carboxydocella_CO_Aquifer_Community
+ node: Potential Subsurface Carbon-Electron Flow Through CO
+ evidence_index: 0
+ reference: PMID:32633030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/aquifer-primary.txt
+ cache_artifact: references_cache/PMID_32633030.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+discussion_snippet_checks:
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: staph_candida_study_boundaries
+ evidence_index: 0
+ reference: PMID:42629020
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_antagonism-primary.txt
+ cache_artifact: references_cache/PMID_42629020.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture
+ node: staph_candida_study_boundaries
+ evidence_index: 1
+ reference: PMID:42359480
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/staph_copper-primary.txt
+ cache_artifact: references_cache/PMID_42359480.txt
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: mire_omics_flux_and_route_limits
+ evidence_index: 0
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Stordalen_Mire_Methylotrophic_Methanogenesis_Community
+ node: mire_omics_flux_and_route_limits
+ evidence_index: 1
+ reference: PMID:38063415
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/mire-primary.txt
+ cache_artifact: references_cache/PMID_38063415.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Streptomyces_A2_A5_A11_M7_Pesticide_Consortium
+ node: c1_gene_presence_and_outcome_mediation
+ evidence_index: 0
+ reference: PMID:41678860
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/pesticide-primary.txt
+ cache_artifact: references_cache/PMID_41678860.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Streptomyces_A2_A5_A11_M7_Pesticide_Consortium
+ node: c1_gene_presence_and_outcome_mediation
+ evidence_index: 1
+ reference: PMID:41678860
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/pesticide-primary.txt
+ cache_artifact: references_cache/PMID_41678860.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Subsurface_Carboxydocella_CO_Aquifer_Community
+ node: aquifer_relative_abundance_and_functional_potential
+ evidence_index: 0
+ reference: PMID:32633030
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch106/aquifer-primary.txt
+ cache_artifact: references_cache/PMID_32633030.md
+ scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Qualify existing observation/mechanism boundaries and participant scope; retain five qualified directions,
+ remove one workflow node and five unsupported/restatement arrows. No new mechanisms or directions.
+limitations:
+- 'Fresh both-root baseline before source reads: 460 records, 923 caches, 56 existing warnings, zero structural
+ defects. Four whole records and all19 original nodes/10 directions reviewed;18 nodes and five qualified existing
+ directions retained, one workflow node and five arrows removed, eight renames. No new topology or Edison submission/spend.'
+- 'Eleven primary sources independently retrieved. All nine abstract-only retrievals were read whole, including
+ the six Staphylococcus-Candida studies, 2018 mire catalog, 2026 pesticide study and aquifer study. Available full-text
+ leads were not fetched for Staphylococcus-Candida: fresh PMCID leads exist for three and the pre-existing copper
+ cache lists PMC13306210 despite missing fresh PMCID metadata. This is an abstract-bounded metadata correction,
+ not an assertion of full-text absence.'
+- Fresh EuropePMC full-body XML retrieved for mire2023 and pesticide2013. Mire abstract1-33, results/discussion238-477
+ and methods528-676 read; pesticide2013 results182-246 read. Other spans were indexed or not read, not whole-paper
+ review. No figure-pixel, supplement, raw-data or full-pipeline certification. Mire CC BY4.0 and pesticide2013
+ CC BY3.0 metadata retained.
+- Existing six Staphylococcus-Candida caches, pesticide2026, both aquifer caches and both lindane abstract caches
+ read whole. Large mire2023, mire2018 and pesticide2013 caches used for bounded context and normalized claim matching,
+ not exhaustive duplicated full-text review. Wiley aquifer and Elsevier pesticide2026 web requests returned Internal
+ Error with no HTTP code reported; no bypass or global full-text-absence assertion. No cache imports, license949/loader1703/DOI-case1091
+ certification.
+- 'Staphylococcus-Candida: retain six separate-study observations; remove cross-study arrows and categorical reciprocal
+ competition/universal mutualism. Preserve the copper authors mutualism interpretation as HYPOTHESIZED/PARTIAL
+ and source-supported scaffold facilitation. Transcript/ontology associations are not demonstrated virulence, genotype
+ change or colonization. No new growth, biofilm, survival, resistance, virulence or colonization enhancement procedures,
+ genetic designs, strain-selection advice or partner mechanisms.'
+- 'Mire: preserve encoded potential, transcripts and metabolite observations with canonical identity-only archaeal/bacterial
+ scope and computational provenance. Remove unestablished syntrophic product-removal feedback and traced cross-feeding.
+ Acetate supports an acetoclastic route, not the removed methylotrophic target; no replacement mechanism/node added.
+ Preserve source-proposed fen niche partitioning and its existing direction as HYPOTHESIZED/PARTIAL; no measured
+ substrate flux or competition reduction. Remove redundant habitat arrows and unrelated catalog support for specific
+ syntrophy.'
+- 'Pesticide: retain the exact four-member non-antagonism, aggregate growth, gene detection, removal and phytotoxicity
+ results. Remove reciprocal-mutualism typing and qualify both existing directions; gene presence is not expression/flux,
+ removal is not mineralization or an isolated toxicity mediator. Do not transfer six-member immobilized-culture
+ results or claim universal consortium superiority. Existing22840534/31430718 caches requested by open764 are present;
+ no duplicate cache issue/import.'
+- 'Aquifer: remove only the genome-resolution workflow node and preserve prior2026-10-02 analysis-edge removal.
+ Retain field perturbation and relative-abundance observation without absolute loss or fitness claims. Gene-based
+ CO-oxidation potential and carbon/electron-flow implications receive computational provenance and HYPOTHESIZED/PARTIAL
+ causal descriptions. No invented methods or measured flux.'
+- Graph issues1829-1832 addressed here and remain open until protected-main merge; non-graph1833 remains open. Fresh
+ all-state title/body dedup matches294/691/763/764. Hidden/ignored local search excludes.git/docs/site/references_cache
+ with relevant caches separately covered. PRs/comments not exhaustively searched. Non-graph role, abundance, placeholder
+ taxonomy, habitat-note and substrate extrapolations remain separately scoped and byte-preserved, not certified.
+- Four guarded writes and append-only histories;456 other records and all923 caches unchanged. Every unrelated raw
+ block preserved. No schema/runtime/audit rule changes. Self-adversarial review is not independent approval or
+ corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication not preasserted.
+records:
+- path: kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml
+ id: CommunityMech:000326
+ original_sha256: 9aa79042fb33eac69fefdf66b0bd3a02057bd8cdb0e861e449ac2204dfb93a6e
+ record_sha256: b56a50fee784e1e8d6c07167f9faeccef0dc6ec979cc7f3b79861cb7034bc68e
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
+ scope: Whole record and every existing node/direction reviewed; no new-mechanism discovery or non-graph certification.
+ summary: Retain aggregate suppression, removing reciprocal-competition typing not established by aggregate endpoints.;
+ Retain study-specific contact-associated fungal suppression without reciprocal-competition typing or a cross-study
+ mechanism arrow.; Retain the authors mutualism proposal as HYPOTHESIZED/PARTIAL, separating proteomic inference
+ from aggregate biomass.; Retain the source-supported scaffold facilitation without importing another study requirement.;
+ Retain context-dependent observations without universal mutualism or a cross-study hyphal-requirement arrow.;
+ Retain transcript and ontology associations; remove demonstrated-virulence/genotype and colonization interpretations.
+ node_decisions:
+ - node: Antagonistic Dual-Species Biofilm Suppression
+ rationale: Retain aggregate suppression, removing reciprocal-competition typing not established by aggregate
+ endpoints.
+ - node: Contact-Dependent Strain-Specific Fungal Suppression
+ rationale: Retain study-specific contact-associated fungal suppression without reciprocal-competition typing
+ or a cross-study mechanism arrow.
+ - node: Copper-Mediated Nutritional Mutualism
+ rationale: Retain the authors mutualism proposal as HYPOTHESIZED/PARTIAL, separating proteomic inference from
+ aggregate biomass.
+ - node: Candida Biofilm Scaffold Supports Staphylococcus Colonization
+ rationale: Retain the source-supported scaffold facilitation without importing another study requirement.
+ - node: Growth-State and Hyphal Context Dependence
+ rationale: Retain context-dependent observations without universal mutualism or a cross-study hyphal-requirement
+ arrow.
+ - node: Study-Specific Candida Transcript Response
+ rationale: Retain transcript and ontology associations; remove demonstrated-virulence/genotype and colonization
+ interpretations.
+ removed_node_decisions: []
+ renamed_nodes:
+ Staphylococcus-Induced Candida Virulence Response: Study-Specific Candida Transcript Response
+ edges_before:
+ - source: Contact-Dependent Strain-Specific Fungal Suppression
+ target: Antagonistic Dual-Species Biofilm Suppression
+ description: Contact-dependent C. albicans suppression by most S. aureus strains provides a strain-level mechanism
+ for antagonistic dual-species biofilm outcomes.
+ - source: Growth-State and Hyphal Context Dependence
+ target: Candida Biofilm Scaffold Supports Staphylococcus Colonization
+ description: Hyphae-competent biofilm growth creates the Candida scaffold context that supports S. aureus adhesion,
+ proliferation, and mature biofilm architecture.
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Contact-Dependent Strain-Specific Fungal Suppression
+ target: Antagonistic Dual-Species Biofilm Suppression
+ description: Contact-dependent C. albicans suppression by most S. aureus strains provides a strain-level mechanism
+ for antagonistic dual-species biofilm outcomes.
+ rationale: Separate-study observations do not establish a cross-study causal mechanism.
+ - source: Growth-State and Hyphal Context Dependence
+ target: Candida Biofilm Scaffold Supports Staphylococcus Colonization
+ description: Hyphae-competent biofilm growth creates the Candida scaffold context that supports S. aureus adhesion,
+ proliferation, and mature biofilm architecture.
+ rationale: Separate-study observations do not establish a cross-study causal mechanism.
+ references:
+ - PMID:33831044
+ - PMID:34888261
+ - PMID:41324029
+ - PMID:42359480
+ - PMID:42413741
+ - PMID:42629020
+ issues:
+ - 1829
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture/2026-10-08T020856Z-codex-69aaae.yaml
+- path: kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml
+ id: CommunityMech:000254
+ original_sha256: c61a85e2234af044ee022537059e465eb1571d50a78a5430cc9fc532aef48285
+ record_sha256: 3f9b3c0e30a8f745ccaa24400d3523ef7306000486ab5e1b5c05a0cf3f877e27
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
+ scope: Whole record and every existing node/direction reviewed; no new-mechanism discovery or non-graph certification.
+ summary: Retain archaeal encoded potential and transcripts with canonical participant scope; remove unsupported
+ syntrophy and unrelated catalog evidence.; Retain bacterial encoded potential and transcripts with canonical
+ participant scope; remove categorical cross-feeding and the acetate-to-methylotrophic route error.; Retain source-proposed
+ fen niche partitioning and its existing functional direction as HYPOTHESIZED/PARTIAL, not measured uptake or
+ reduced competition.; Retain habitat-associated transcript patterns with computational provenance; remove niche
+ typing and activity-restatement arrows.
+ node_decisions:
+ - node: Methanogenic Methylotrophic Potential and Expression
+ rationale: Retain archaeal encoded potential and transcripts with canonical participant scope; remove unsupported
+ syntrophy and unrelated catalog evidence.
+ - node: Bacterial Anaerobic Methylotrophic Potential and Expression
+ rationale: Retain bacterial encoded potential and transcripts with canonical participant scope; remove categorical
+ cross-feeding and the acetate-to-methylotrophic route error.
+ - node: Proposed Methylated-Substrate Niche Partitioning
+ rationale: Retain source-proposed fen niche partitioning and its existing functional direction as HYPOTHESIZED/PARTIAL,
+ not measured uptake or reduced competition.
+ - node: Thaw-Stage Methylotrophic Expression Patterns
+ rationale: Retain habitat-associated transcript patterns with computational provenance; remove niche typing
+ and activity-restatement arrows.
+ removed_node_decisions: []
+ renamed_nodes:
+ Methanogenic Methylotrophy Across Thaw Gradient: Methanogenic Methylotrophic Potential and Expression
+ Bacterial Anaerobic Methylotrophy: Bacterial Anaerobic Methylotrophic Potential and Expression
+ Methylated-Compound Substrate Niche Partitioning: Proposed Methylated-Substrate Niche Partitioning
+ Thaw-Stage Activity Gradient: Thaw-Stage Methylotrophic Expression Patterns
+ edges_before:
+ - source: Bacterial Anaerobic Methylotrophy
+ target: Methanogenic Methylotrophy Across Thaw Gradient
+ description: 'Anaerobic bacterial methylotrophs provide a potential indirect route to methane production by
+ forming methanogenic by-products such as acetate.
+
+ '
+ - &id001
+ source: Methylated-Compound Substrate Niche Partitioning
+ target: Methanogenic Methylotrophy Across Thaw Gradient
+ description: 'Substrate-partitioned methyltransferase expression routes methylated oxygen compounds, sulfides,
+ and amines into direct methylotrophic methanogenesis by different methanogen orders.
+
+ '
+ - source: Thaw-Stage Activity Gradient
+ target: Methanogenic Methylotrophy Across Thaw Gradient
+ description: 'Partially thawed bog and fully thawed fen habitats housed active methanogenic methylotrophy, while
+ the frozen palsa was described as non-methanogenic.
+
+ '
+ - source: Thaw-Stage Activity Gradient
+ target: Bacterial Anaerobic Methylotrophy
+ description: 'Bacterial methylotrophy was active across the thaw gradient, including in palsa where methanogenic
+ methylotrophy was not detected.
+
+ '
+ edges_after:
+ - &id002
+ source: Proposed Methylated-Substrate Niche Partitioning
+ target: Methanogenic Methylotrophic Potential and Expression
+ description: 'HYPOTHESIZED/PARTIAL: differing inferred substrate preferences could support co-occurring methylotrophic
+ pathways among fen methanogens. The expression and metabolite evidence motivates this existing direction but
+ does not isolate niche partitioning as its cause, measure substrate-specific flux or demonstrate reduced competition.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: Existing source-grounded direction retained without extension.
+ removed_edge_decisions:
+ - source: Bacterial Anaerobic Methylotrophy
+ target: Methanogenic Methylotrophy Across Thaw Gradient
+ description: 'Anaerobic bacterial methylotrophs provide a potential indirect route to methane production by
+ forming methanogenic by-products such as acetate.
+
+ '
+ rationale: Acetate points to the wrong methanogenesis route, or the habitat pattern merely restates the target
+ activity; preserve supported observations independently.
+ - source: Thaw-Stage Activity Gradient
+ target: Methanogenic Methylotrophy Across Thaw Gradient
+ description: 'Partially thawed bog and fully thawed fen habitats housed active methanogenic methylotrophy, while
+ the frozen palsa was described as non-methanogenic.
+
+ '
+ rationale: Acetate points to the wrong methanogenesis route, or the habitat pattern merely restates the target
+ activity; preserve supported observations independently.
+ - source: Thaw-Stage Activity Gradient
+ target: Bacterial Anaerobic Methylotrophy
+ description: 'Bacterial methylotrophy was active across the thaw gradient, including in palsa where methanogenic
+ methylotrophy was not detected.
+
+ '
+ rationale: Acetate points to the wrong methanogenesis route, or the habitat pattern merely restates the target
+ activity; preserve supported observations independently.
+ references:
+ - PMID:38063415
+ issues:
+ - 1830
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Stordalen_Mire_Methylotrophic_Methanogenesis_Community/2026-10-08T020857Z-codex-bf13e7.yaml
+- path: kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml
+ id: CommunityMech:000335
+ original_sha256: 29276efda4a5ebd299c0284da81aab5388909fed51cb0c32c276c79c00b2dc4a
+ record_sha256: 4ef09a74970615b914a26247da7f2919234df7487a087c51923c41dea1a9042c
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
+ scope: Whole record and every existing node/direction reviewed; no new-mechanism discovery or non-graph certification.
+ summary: Retain exact-mixture non-antagonism and aggregate biomass, removing reciprocal-mutualism typing and excluding
+ other source formulations.; Retain herbicide-catabolism gene detection as genetic potential, with the existing
+ outcome direction HYPOTHESIZED/PARTIAL.; Retain observed atrazine growth/removal without mineralization or reciprocal-benefit
+ claims; qualify the existing toxicity direction.; Retain positive tested phytotoxicity reversal without claiming
+ its sole causal mediator or universal detoxification.
+ node_decisions:
+ - node: Non-antagonistic community-level growth enhancement
+ rationale: Retain exact-mixture non-antagonism and aggregate biomass, removing reciprocal-mutualism typing and
+ excluding other source formulations.
+ - node: C1 Herbicide-Catabolism Gene Detection
+ rationale: Retain herbicide-catabolism gene detection as genetic potential, with the existing outcome direction
+ HYPOTHESIZED/PARTIAL.
+ - node: C1 Atrazine Growth and Removal
+ rationale: Retain observed atrazine growth/removal without mineralization or reciprocal-benefit claims; qualify
+ the existing toxicity direction.
+ - node: C1 Atrazine Phytotoxicity Reversal
+ rationale: Retain positive tested phytotoxicity reversal without claiming its sole causal mediator or universal
+ detoxification.
+ removed_node_decisions: []
+ renamed_nodes:
+ C1 Distributed Atrazine Catabolism: C1 Herbicide-Catabolism Gene Detection
+ edges_before:
+ - &id003
+ source: C1 Distributed Atrazine Catabolism
+ target: C1 Atrazine Growth and Removal
+ description: 'Distributed herbicide-catabolism genes provide the mechanistic basis for C1 growth on and removal
+ of atrazine as a sole carbon or nitrogen source.
+
+ '
+ - &id005
+ source: C1 Atrazine Growth and Removal
+ target: C1 Atrazine Phytotoxicity Reversal
+ description: 'Atrazine growth and removal by C1 reduces the herbicide toxicity of the treated liquid system.
+
+ '
+ edges_after:
+ - &id004
+ source: C1 Herbicide-Catabolism Gene Detection
+ target: C1 Atrazine Growth and Removal
+ description: 'HYPOTHESIZED/PARTIAL: the detected catabolic genes could underlie the reported C1 atrazine growth/removal
+ phenotype. The accessible abstract reports gene presence and community outcomes but does not isolate gene
+ activity or member-specific contributions as causal mediators.'
+ - &id006
+ source: C1 Atrazine Growth and Removal
+ target: C1 Atrazine Phytotoxicity Reversal
+ description: 'HYPOTHESIZED/PARTIAL: atrazine removal could contribute to the reported decrease in phytotoxicity
+ after C1 treatment. The accessible abstract does not establish parent-compound depletion as the sole cause,
+ resolve transformation-product effects or demonstrate complete mineralization.'
+ retained_edge_decisions:
+ - before: *id003
+ after: *id004
+ rationale: Existing source-grounded direction retained without extension.
+ - before: *id005
+ after: *id006
+ rationale: Existing source-grounded direction retained without extension.
+ removed_edge_decisions: []
+ references:
+ - PMID:23865051
+ - PMID:41678860
+ issues:
+ - 1831
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium/2026-10-08T020858Z-codex-c3faca.yaml
+- path: kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml
+ id: CommunityMech:000251
+ original_sha256: 3178b917450aea35808474c98945cf604ddb2a0835e48fb8a1c8c72c0fb3b47a
+ record_sha256: 0f750d563e028d6b70a47ac876aec68e29bef5b87eae6ec06ba34630e43e6bd9
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml
+ scope: Whole record and every existing node/direction reviewed; no new-mechanism discovery or non-graph certification.
+ summary: Retain field perturbation input with its existing relative-abundance direction HYPOTHESIZED/PARTIAL,
+ not aggregate restructuring as a proven mediator.; Retain observed relative-abundance decline without inferring
+ absolute loss, mortality or fitness.; Retain CODH-associated genomic potential with computational provenance,
+ not a demonstrated physiological switch.; Retain potential carbon/electron-flow implications and their existing
+ direction as HYPOTHESIZED/PARTIAL, not measured flux.
+ node_decisions:
+ - node: scCO2 Injection Reshapes Subsurface Community
+ rationale: Retain field perturbation input with its existing relative-abundance direction HYPOTHESIZED/PARTIAL,
+ not aggregate restructuring as a proven mediator.
+ - node: Post-Injection Carboxydocella Decline
+ rationale: Retain observed relative-abundance decline without inferring absolute loss, mortality or fitness.
+ - node: CODH-Associated CO-Oxidation Potential
+ rationale: Retain CODH-associated genomic potential with computational provenance, not a demonstrated physiological
+ switch.
+ - node: Potential Subsurface Carbon-Electron Flow Through CO
+ rationale: Retain potential carbon/electron-flow implications and their existing direction as HYPOTHESIZED/PARTIAL,
+ not measured flux.
+ removed_node_decisions:
+ - node: Native Carboxydocella Genome Resolution
+ rationale: Genome-resolution workflow is analytical provenance, not an ecological causal node. Preserve the
+ earlier removal of its analysis-provenance arrows.
+ renamed_nodes:
+ CODH-Mediated CO-Oxidation Switch: CODH-Associated CO-Oxidation Potential
+ Subsurface Carbon-Electron Flow Through CO: Potential Subsurface Carbon-Electron Flow Through CO
+ edges_before:
+ - &id007
+ source: scCO2 Injection Reshapes Subsurface Community
+ target: Post-Injection Carboxydocella Decline
+ description: 'Community restructuring after supercritical carbon dioxide injection was associated with a decline
+ in native carboxydotrophic Carboxydocella.
+
+ '
+ - &id009
+ source: CODH-Mediated CO-Oxidation Switch
+ target: Subsurface Carbon-Electron Flow Through CO
+ description: 'A CODH-mediated change in carbon monoxide oxidation can alter subsurface carbon and electron transfer
+ through the CO intermediate.
+
+ '
+ edges_after:
+ - &id008
+ source: scCO2 Injection Reshapes Subsurface Community
+ target: Post-Injection Carboxydocella Decline
+ description: 'HYPOTHESIZED/PARTIAL: the injected supercritical carbon dioxide is the upstream field perturbation
+ proposed to alter conditions underlying the subsequent Carboxydocella relative-abundance decrease. The temporal
+ association does not establish that aggregate community restructuring itself caused the decline or isolate
+ the physiological mediator.'
+ - &id010
+ source: CODH-Associated CO-Oxidation Potential
+ target: Potential Subsurface Carbon-Electron Flow Through CO
+ description: 'HYPOTHESIZED/PARTIAL: a change in encoded CO-oxidation potential could alter carbon/electron flow
+ through carbon monoxide. The source discusses this implication; the accessible abstract does not report a
+ measured flux or isolate CODH variation as the causal mediator.'
+ retained_edge_decisions:
+ - before: *id007
+ after: *id008
+ rationale: Existing source-grounded direction retained without extension.
+ - before: *id009
+ after: *id010
+ rationale: Existing source-grounded direction retained without extension.
+ removed_edge_decisions: []
+ references:
+ - PMID:32633030
+ issues:
+ - 1832
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Subsurface_Carboxydocella_CO_Aquifer_Community/2026-10-08T020859Z-codex-ab9af4.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 60bbc9634..e5d0f8056 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -384,10 +384,10 @@ kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml CommunityM
kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml CommunityMech:000362 e2555ecc152f3bbdbb5c2d557a17fc46da135500092494e0379c73fbb85c117a 2 0 57.5 reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml reviewed
kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml CommunityMech:000267 fa5b1abb2f9493bb52263f1041fe4075028d57daf40abe7cd804edd6c65aa05c 3 1 80.0 reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml reviewed
kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml CommunityMech:000418 ece6ced257acf7538a072ee6fb940f73d96f0f36d83a6e1eae1514356884ab12 3 0 61.7 reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml reviewed
-kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml CommunityMech:000326 9aa79042fb33eac69fefdf66b0bd3a02057bd8cdb0e861e449ac2204dfb93a6e 6 2 100.0 pending
-kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml CommunityMech:000254 c61a85e2234af044ee022537059e465eb1571d50a78a5430cc9fc532aef48285 4 4 100.0 pending
-kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml CommunityMech:000335 29276efda4a5ebd299c0284da81aab5388909fed51cb0c32c276c79c00b2dc4a 4 2 100.0 pending
-kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml CommunityMech:000251 3178b917450aea35808474c98945cf604ddb2a0835e48fb8a1c8c72c0fb3b47a 5 2 100.0 pending
+kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml CommunityMech:000326 b56a50fee784e1e8d6c07167f9faeccef0dc6ec979cc7f3b79861cb7034bc68e 6 0 68.3 reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml reviewed
+kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml CommunityMech:000254 3f9b3c0e30a8f745ccaa24400d3523ef7306000486ab5e1b5c05a0cf3f877e27 4 1 81.2 reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml reviewed
+kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml CommunityMech:000335 4ef09a74970615b914a26247da7f2919234df7487a087c51923c41dea1a9042c 4 2 90.0 reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml reviewed
+kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml CommunityMech:000251 0f750d563e028d6b70a47ac876aec68e29bef5b87eae6ec06ba34630e43e6bd9 4 2 100.0 reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml reviewed
kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml CommunityMech:000312 aa951b219710a3b699cd561d2fed9a7d10a2dfd49e90745957d0ce68093fcd30 4 3 100.0 pending
kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml CommunityMech:000222 bdde368007b748fab8102646934b696e16102c0adffbd28df7fef6aa382c32a0 3 2 100.0 pending
kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml CommunityMech:000127 660c1b3de9165421c53f76fdee1ef9609e6101d50ab1850fbc68c52ea474b563 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index d46932eb4..d33342c98 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": 1387,
- "edges": 558,
+ "nodes": 1386,
+ "edges": 553,
"records_without_nodes": 10,
- "records_without_edges": 181,
+ "records_without_edges": 182,
"review_status_counts": {
"needs_research": 50,
- "pending": 76,
- "reviewed": 334
+ "pending": 72,
+ "reviewed": 338
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch106.json b/reports/causal_graph_review/validation-20261008-batch106.json
new file mode 100644
index 000000000..aae80aed8
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch106.json
@@ -0,0 +1,1096 @@
+{
+ "base_commit": "20d6692b687fa6826bc25f8673543215c18aa310",
+ "scope": [
+ "kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml",
+ "kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml",
+ "kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml",
+ "kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch106.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/focused.log",
+ "log_sha256": "cd3c49fb184dd7c6f413ee36fcc2466614dd66690bc0b1036332cd9fc03e88e5",
+ "output_tail": "........ [100%]\n8 passed in 10.34s\n"
+ },
+ {
+ "check": "Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch106/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-strict.tsv",
+ "kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-strict.log",
+ "log_sha256": "5185dc0c9b0772483d3c5cc6d52e44082a023dab1b654c32044abcfd02dba8a4",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch106/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-batch106/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-references.log",
+ "log_sha256": "a369dc957e7d333c84126e8e20fa22a5236d25616c9fc4cc2563663ade439073",
+ "output_tail": "Validating kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.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/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.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": "Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-snippets.log",
+ "log_sha256": "7cb30458f959a4a7649fd96c05ca0aecb145f69b34e2ebea471b4c38e6956f10",
+ "output_tail": "# 31 evidence snippets scanned across 1 files\n MATCH 31\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": "Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-rank.log",
+ "log_sha256": "0ce5d39408aa6afe20cabb92863f94b498edde0f9a3724de0277533023a3ccdf",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000326\",\n \"name\": \"Staphylococcus-Candida Context-Dependent Biofilm Coculture\",\n \"score\": 68.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 6,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 12,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture/2026-10-08T020856Z-codex-69aaae.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Stordalen_Mire_Methylotrophic_Methanogenesis_Community-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Stordalen_Mire_Methylotrophic_Methanogenesis_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Stordalen_Mire_Methylotrophic_Methanogenesis_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch106/Stordalen_Mire_Methylotrophic_Methanogenesis_Community-strict.tsv",
+ "kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Stordalen_Mire_Methylotrophic_Methanogenesis_Community-strict.log",
+ "log_sha256": "2d05be12e901d94b08b61757fd2060da9db35ace5b647a536cd5e8ed1c98cf12",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch106/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-batch106/Stordalen_Mire_Methylotrophic_Methanogenesis_Community-strict.tsv\n"
+ },
+ {
+ "check": "Stordalen_Mire_Methylotrophic_Methanogenesis_Community-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Stordalen_Mire_Methylotrophic_Methanogenesis_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Stordalen_Mire_Methylotrophic_Methanogenesis_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Stordalen_Mire_Methylotrophic_Methanogenesis_Community-references.log",
+ "log_sha256": "9b2541cf483307e7226ae11751a8f0e7084dfd626046c028b2cc0116b6e0dd19",
+ "output_tail": "Validating kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Stordalen_Mire_Methylotrophic_Methanogenesis_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Stordalen_Mire_Methylotrophic_Methanogenesis_Community-snippets.log",
+ "log_sha256": "1125ff0dde8c88267205b8aa843a32ef58e84b65fee929f651c20facd8785df0",
+ "output_tail": "# 26 evidence snippets scanned across 1 files\n MATCH 26\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": "Stordalen_Mire_Methylotrophic_Methanogenesis_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Stordalen_Mire_Methylotrophic_Methanogenesis_Community-rank.log",
+ "log_sha256": "8162ef1206b59f038ee7d41168d206ce5c7ad26c28ab4d0887720ff8021a67ac",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000254\",\n \"name\": \"Stordalen Mire Methylotrophic Methanogenesis Community\",\n \"score\": 81.2,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Stordalen_Mire_Methylotrophic_Methanogenesis_Community-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Stordalen_Mire_Methylotrophic_Methanogenesis_Community/2026-10-08T020857Z-codex-bf13e7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Stordalen_Mire_Methylotrophic_Methanogenesis_Community-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch106/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-strict.tsv",
+ "kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-strict.log",
+ "log_sha256": "1bca2290e2cb622ec8a4e5b049fb683cb1263fd734f32df5c445091a7262ae30",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch106/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-batch106/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-references.log",
+ "log_sha256": "e3b71272f5b8ddf0db0ff90caa3d6943a18d70a29f135aff07a21bc771533e64",
+ "output_tail": "Validating kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_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/Streptomyces_A2_A5_A11_M7_Pesticide_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": "Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-snippets.log",
+ "log_sha256": "2ffa6e242265b4c1c2eb555bd8bd14abb6cc63ed4d5a8a818da9b515db44daff",
+ "output_tail": "# 24 evidence snippets scanned across 1 files\n MATCH 24\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-rank.log",
+ "log_sha256": "94a3bf6908214ffe282bb7faab188b2d527ea61b63600f06ea71c55c9232d84c",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000335\",\n \"name\": \"Streptomyces A2-A5-A11-M7 Pesticide-Bioremediation Consortium\",\n \"score\": 90.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Streptomyces_A2_A5_A11_M7_Pesticide_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/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium/2026-10-08T020858Z-codex-c3faca.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Subsurface_Carboxydocella_CO_Aquifer_Community-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Subsurface_Carboxydocella_CO_Aquifer_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Subsurface_Carboxydocella_CO_Aquifer_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch106/Subsurface_Carboxydocella_CO_Aquifer_Community-strict.tsv",
+ "kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Subsurface_Carboxydocella_CO_Aquifer_Community-strict.log",
+ "log_sha256": "9982ad626115d83ad3b73ff17c081fc4fab7bdacc312904010c08d71a921069c",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch106/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-batch106/Subsurface_Carboxydocella_CO_Aquifer_Community-strict.tsv\n"
+ },
+ {
+ "check": "Subsurface_Carboxydocella_CO_Aquifer_Community-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Subsurface_Carboxydocella_CO_Aquifer_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Subsurface_Carboxydocella_CO_Aquifer_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Subsurface_Carboxydocella_CO_Aquifer_Community-references.log",
+ "log_sha256": "4d3d818d2461a5c82f2e1735259eab36d4a408ebc7768d852038b92e220dba75",
+ "output_tail": "Validating kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Subsurface_Carboxydocella_CO_Aquifer_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Subsurface_Carboxydocella_CO_Aquifer_Community-snippets.log",
+ "log_sha256": "32e79f5bf36e5c97f219c301b9924d6a9da1ff1bf07e2b076f93f0d0ee74a358",
+ "output_tail": "# 9 evidence snippets scanned across 1 files\n MATCH 9\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": "Subsurface_Carboxydocella_CO_Aquifer_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Subsurface_Carboxydocella_CO_Aquifer_Community-rank.log",
+ "log_sha256": "098104aa36f7b2e4331aecdcb2d642539dd9b9266438d5cd4d11ef4c445013e2",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000251\",\n \"name\": \"Subsurface Carboxydocella CO-Oxidation Aquifer Community\",\n \"score\": 100.0,\n \"taxonomy\": 1,\n \"connected_taxa\": 1,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [],\n \"path\": \"kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Subsurface_Carboxydocella_CO_Aquifer_Community-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Subsurface_Carboxydocella_CO_Aquifer_Community/2026-10-08T020859Z-codex-ab9af4.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/Subsurface_Carboxydocella_CO_Aquifer_Community-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "inventory",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "reports/causal_graph_review/build_inventory.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/inventory.log",
+ "log_sha256": "5354c00e9feca483bf6798b3bb8de6124a7f3917e6fea9f6981e5b98d8f53248",
+ "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\": 1386,\n \"edges\": 553,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 182,\n \"review_status_counts\": {\n \"needs_research\": 50,\n \"pending\": 72,\n \"reviewed\": 338\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-batch106/verification/network.log",
+ "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+ "output_tail": " \"total_genomes\": 17191,\n \"is_reclassified\": false,\n \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n },\n \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"mexZ\"\n },\n \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n \"evidence\": [\n {\n \"reference\": \"PMID:42153623\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' 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": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/just-network-json.log",
+ "log_sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/rank-all.log",
+ "log_sha256": "004958f841cc787feb3888ad2d6ef78df5129af7486a591c05cb6dbb6ee9c94c",
+ "output_tail": "henol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n402\t100.0\tkb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml\tCommunityMech:000290\tPhosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture\t2\t2\t0\t3\t2\t4\t\t0\t0\n403\t100.0\tkb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml\tCommunityMech:000289\tPseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n404\t100.0\tkb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml\tCommunityMech:000092\tRhodopseudomonas-E. coli Cross-Feeding Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n405\t100.0\tkb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml\tCommunityMech:000109\tRice Acid Soil Bioinoculant SynCom\t1\t1\t0\t4\t4\t4\t\t0\t0\n406\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t4\t2\t4\t\t0\t0\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"
+ },
+ {
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 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/private/tmp/communitymech-causal-batch106/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 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Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 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/private/tmp/communitymech-causal-batch106/docs/index.html\n"
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Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 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TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch106/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch106/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch106/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch106/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-batch105')),('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-batch106/verification/connectivity-survey.log",
+ "log_sha256": "38a12f49cbc88c7b8677195d203bbd2c525ef38242aa0ab91633314f37a45aa7",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1544, \"credited_solely_by_the_rule\": 1270}, \"current\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1544, \"credited_solely_by_the_rule\": 1270}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_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_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_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-batch106/verification/regressions.log",
+ "log_sha256": "861c2203b4572e0c64cb38b2e2e5e018c98368d590324ccb9fa2aa4b68d53740",
+ "output_tail": "........................................................................ [ 7%]\n........................................................................ [ 15%]\n........................................................................ [ 22%]\n........................................................................ [ 30%]\n........................................................................ [ 37%]\n........................................................................ [ 45%]\n........................................................................ [ 52%]\n........................................................................ [ 60%]\n........................................................................ [ 67%]\n........................................................................ [ 75%]\n........................................................................ [ 82%]\n........................................................................ [ 90%]\n........................................................................ [ 97%]\n....................... [100%]\n959 passed in 793.39s (0:13:13)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0,
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/just-lint.log",
+ "log_sha256": "b66912cc03515c14a71cadf5d56f8b6962a4d4f5e1f2ebe5d28f83ff091139e9",
+ "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n359 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n"
+ },
+ {
+ "check": "mypy-explicit-runtime",
+ "command": [
+ "/private/tmp/communitymech-batch100/lint-env/bin/mypy",
+ "--no-incremental",
+ "--python-executable",
+ "/private/tmp/communitymech-batch100/lint-env/bin/python",
+ "src/"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/mypy-explicit-runtime.log",
+ "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875",
+ "output_tail": "Success: no issues found in 49 source files\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/audit-snippets-all.log",
+ "log_sha256": "c4bebaf6770334cd35310ea1759542995655b3ce1fcd2d10fef1165b9956f4d0",
+ "output_tail": "# 8960 evidence snippets scanned across 460 files\n MATCH 8824\n RENDERING 20\n ASSEMBLED 1\n WEAK 0\n MISMATCH 39\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch106/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Fresh both-root baseline before source reads: 460 records, 923 caches, 56 existing warnings, zero structural defects. Four whole records and all19 original nodes/10 directions reviewed;18 nodes and five qualified existing directions retained, one workflow node and five arrows removed, eight renames. No new topology or Edison submission/spend.",
+ "Eleven primary sources independently retrieved. All nine abstract-only retrievals were read whole, including the six Staphylococcus-Candida studies, 2018 mire catalog, 2026 pesticide study and aquifer study. Available full-text leads were not fetched for Staphylococcus-Candida: fresh PMCID leads exist for three and the pre-existing copper cache lists PMC13306210 despite missing fresh PMCID metadata. This is an abstract-bounded metadata correction, not an assertion of full-text absence.",
+ "Fresh EuropePMC full-body XML retrieved for mire2023 and pesticide2013. Mire abstract1-33, results/discussion238-477 and methods528-676 read; pesticide2013 results182-246 read. Other spans were indexed or not read, not whole-paper review. No figure-pixel, supplement, raw-data or full-pipeline certification. Mire CC BY4.0 and pesticide2013 CC BY3.0 metadata retained.",
+ "Existing six Staphylococcus-Candida caches, pesticide2026, both aquifer caches and both lindane abstract caches read whole. Large mire2023, mire2018 and pesticide2013 caches used for bounded context and normalized claim matching, not exhaustive duplicated full-text review. Wiley aquifer and Elsevier pesticide2026 web requests returned Internal Error with no HTTP code reported; no bypass or global full-text-absence assertion. No cache imports, license949/loader1703/DOI-case1091 certification.",
+ "Staphylococcus-Candida: retain six separate-study observations; remove cross-study arrows and categorical reciprocal competition/universal mutualism. Preserve the copper authors mutualism interpretation as HYPOTHESIZED/PARTIAL and source-supported scaffold facilitation. Transcript/ontology associations are not demonstrated virulence, genotype change or colonization. No new growth, biofilm, survival, resistance, virulence or colonization enhancement procedures, genetic designs, strain-selection advice or partner mechanisms.",
+ "Mire: preserve encoded potential, transcripts and metabolite observations with canonical identity-only archaeal/bacterial scope and computational provenance. Remove unestablished syntrophic product-removal feedback and traced cross-feeding. Acetate supports an acetoclastic route, not the removed methylotrophic target; no replacement mechanism/node added. Preserve source-proposed fen niche partitioning and its existing direction as HYPOTHESIZED/PARTIAL; no measured substrate flux or competition reduction. Remove redundant habitat arrows and unrelated catalog support for specific syntrophy.",
+ "Pesticide: retain the exact four-member non-antagonism, aggregate growth, gene detection, removal and phytotoxicity results. Remove reciprocal-mutualism typing and qualify both existing directions; gene presence is not expression/flux, removal is not mineralization or an isolated toxicity mediator. Do not transfer six-member immobilized-culture results or claim universal consortium superiority. Existing22840534/31430718 caches requested by open764 are present; no duplicate cache issue/import.",
+ "Aquifer: remove only the genome-resolution workflow node and preserve prior2026-10-02 analysis-edge removal. Retain field perturbation and relative-abundance observation without absolute loss or fitness claims. Gene-based CO-oxidation potential and carbon/electron-flow implications receive computational provenance and HYPOTHESIZED/PARTIAL causal descriptions. No invented methods or measured flux.",
+ "Graph issues1829-1832 addressed here and remain open until protected-main merge; non-graph1833 remains open. Fresh all-state title/body dedup matches294/691/763/764. Hidden/ignored local search excludes.git/docs/site/references_cache with relevant caches separately covered. PRs/comments not exhaustively searched. Non-graph role, abundance, placeholder taxonomy, habitat-note and substrate extrapolations remain separately scoped and byte-preserved, not certified.",
+ "Four guarded writes and append-only histories;456 other records and all923 caches unchanged. Every unrelated raw block preserved. No schema/runtime/audit rule changes. Self-adversarial review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication not preasserted."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml": {
+ "MATCH": 31,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml": {
+ "MATCH": 26,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml": {
+ "MATCH": 24,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml": {
+ "MATCH": 9,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 63,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [],
+ "repair_scope": "Qualify existing observation/mechanism boundaries and participant scope; retain five qualified directions, remove one workflow node and five unsupported/restatement arrows. No new mechanisms or directions."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch106/aquifer-metadata.json": "b1e4de41d816a090b77f9a2ca105b576b50eac63d370d36b1c486a2886547ad7",
+ "/private/tmp/communitymech-batch106/aquifer-primary.txt": "204b98e38f62e044ddf34cb884576998ee008424c92b85f77172bb23d52be88f",
+ "/private/tmp/communitymech-batch106/baseline.json": "64492fd221761056719dff3b6beecd8945d2d14600caaf9d60ecbd173cc7d331",
+ "/private/tmp/communitymech-batch106/dedup-local-current.txt": "1399ae89b6a64f403353e6fa84ce230524c8614229de31ed93d22ec19eb0cc52",
+ "/private/tmp/communitymech-batch106/issue-dedup-current.json": "9efea81e5ca9f4e0e80e6c6113e687d07db1cc050e5be4ead759b93498826e48",
+ "/private/tmp/communitymech-batch106/mire-metadata.json": "fcc216c196bd49dd3cf84bd9c073ce8cba637be5f111c1664aa20b1a73b0dc96",
+ "/private/tmp/communitymech-batch106/mire-primary.txt": "b1dec101dafc02dd1487614a0ad47a44405b881f00549598428acdbd51d06d27",
+ "/private/tmp/communitymech-batch106/mire-primary.xml": "66955fd4d62846fc1506c264ead507e7517656051e8673a840fc9e43c286c4aa",
+ "/private/tmp/communitymech-batch106/mire_catalog-metadata.json": "776df37f829b35905e2ae1476b3dbdef5c9f186aa3717f562ec056b64f91a581",
+ "/private/tmp/communitymech-batch106/mire_catalog-primary.txt": "a4f2d9c07fd09a8e2028e0c81df1351cbff2534d36287e97d335e34378069de9",
+ "/private/tmp/communitymech-batch106/pesticide-metadata.json": "2d6cbd20b17100bfe7acbcc5a53c68abf86105b7eefd66ab75d1cc88411f609d",
+ "/private/tmp/communitymech-batch106/pesticide-primary.txt": "470b762cd60cf273dd9cf0e26aacb3fd595f1d5813744900be8a208e82089693",
+ "/private/tmp/communitymech-batch106/pesticide_2013-metadata.json": "7b53440cb84eec4ff6a2271daa7f0c142e00dec4f94c6f50317c3bf03ecead64",
+ "/private/tmp/communitymech-batch106/pesticide_2013-primary.txt": "ea8455cbe6d9abfd92e384a97ccaed46df18e2da8c64f52d847bcc9e7dd93716",
+ "/private/tmp/communitymech-batch106/pesticide_2013-primary.xml": "f0fc6037eb356cb4ef5fc38c97b48462d110741ff2dacfa81433f7b880fcbe66",
+ "/private/tmp/communitymech-batch106/primary-manifest.json": "c3267231491957e9cc73ff03a2c7ff90cc84ac01d787bc075d54d9ddf0949d14",
+ "/private/tmp/communitymech-batch106/staph_antagonism-metadata.json": "b5213ddb96b1ac893ec0e16bbbdf1ed142ff408654d9ba71eec169456136558a",
+ "/private/tmp/communitymech-batch106/staph_antagonism-primary.txt": "ab8b5a878459d775ee0017a963d82e5da8a3cd0909e72228ca9bcfc9ee5ddb0e",
+ "/private/tmp/communitymech-batch106/staph_context-metadata.json": "21f5fd0102eae97b6b080bc6f46df36792139b57b7e6d62c754cae7297267694",
+ "/private/tmp/communitymech-batch106/staph_context-primary.txt": "6ff06f5bc10d3c823d533519b1b423f2d652f9808cc5a293cac656fef4e5088a",
+ "/private/tmp/communitymech-batch106/staph_copper-metadata.json": "a4b6f1ed90c3e6dfe5d54ff1738d6f38929cc7348dc43b2104bb8b4de2660948",
+ "/private/tmp/communitymech-batch106/staph_copper-primary.txt": "9179a1dc45c8e1e0299399b551d82c100b63fbdefc50c35f812719c7f3567f19",
+ "/private/tmp/communitymech-batch106/staph_scaffold-metadata.json": "ac827088cb44ab0d62e021f0b2d50605548626eb046ed5aa63b7ff8a596fc634",
+ "/private/tmp/communitymech-batch106/staph_scaffold-primary.txt": "a1680570bae29f12f7be2e87d324b904bb1fc9d6ecbbdd7e79c97592530fad71",
+ "/private/tmp/communitymech-batch106/staph_strains-metadata.json": "325d880f6dac07b7bc9fad948d1a99df1f9465ad6af210187e44e2927c906b67",
+ "/private/tmp/communitymech-batch106/staph_strains-primary.txt": "a382e518b14dc08353628d08345a783e51e4e8cd388fa265238414717d8e96c9",
+ "/private/tmp/communitymech-batch106/staph_transcript-metadata.json": "1c49f6bdfd62416fb1094e34c9c4313113ef7d658c5580ba51b1ffc4887e8ac7",
+ "/private/tmp/communitymech-batch106/staph_transcript-primary.txt": "4351cb6288a362b7c92528a584eea87bb137fb2cdaa324477fe43e4ea6084267",
+ "references_cache/PMID_23865051.md": "b6f2d840482ad523fff23c79452a547fbfc54f3638a6f937b1948351b5a86505",
+ "references_cache/PMID_32633030.md": "99909ac1a677b513c9caad23462b6eb03d61612d4abf1be65171c023a06cc86c",
+ "references_cache/PMID_33831044.txt": "9883828c4225a2a4249a01163fb84eaa0dbe263630ed1aba05aa2e8d7a64b375",
+ "references_cache/PMID_34888261.txt": "36613735b96dbc704cae754bf4da56b8c6d55258fc897b889b654a088b1a271e",
+ "references_cache/PMID_38063415.md": "597b8ba99a589ed0ce36f84eece15513ad3752f6dc73b2a23f14bb2fd3203ac8",
+ "references_cache/PMID_41324029.txt": "0d421c030c68a206de344912b7dc58c42f4fac96496720b88dd20ef81eaa58a4",
+ "references_cache/PMID_41678860.md": "e3f673e77ae22dff910a26fcababaa9db6f80279ce9c2252438017663dbab77f",
+ "references_cache/PMID_42359480.txt": "c6c60a230f8dcb6f62e8d5f1b57e7796e2c156922e48cf15c2b2ff85ff98dd72",
+ "references_cache/PMID_42413741.txt": "9e677b5066a30ba1bef805f2ed01c5020ef7e4cd3d2d85df088b52f327a0f752",
+ "references_cache/PMID_42629020.txt": "6630c1c1bf989211e851c339c4ff31db1ff91a23df7ffaf1f8bf701154d0595d"
+ },
+ "immutable_prior_history_and_decision_files": 817,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 29,
+ "new_discussion_quotations": 7,
+ "fresh_primary_literal_matches": 36,
+ "all_cached_literal_matches": 36,
+ "retained_nodes": 18,
+ "removed_nodes": 1,
+ "retained_arrows": 5,
+ "removed_arrows": 5,
+ "new_nodes_or_directions": 0,
+ "scope": "All reviewed quotations match fresh primary text and unchanged existing caches literally after normalization; entailment separately reviewed. Staphylococcus-Candida, mire2018, pesticide2026 and aquifer abstracts; mire2023 and pesticide2013 have bounded main-text coverage. No cache text or audit exception."
+ },
+ "network_delta": {
+ "existing_findings_preserved": 56,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "One analysis-workflow node and five cross-study/wrong-route/restatement arrows removed;18 observations and five qualified existing directions retained. All56existing warnings unchanged and zero structural defects. No audit rules changed."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1372,
+ "arrows": 545
+ },
+ "render_scope": "Deterministic rendering and exact HTML-description parser, not browser screenshots; postcommit docs-current separately required.",
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 403,
+ "mixed": 128,
+ "community_level_only": 275,
+ "taxa": 1544,
+ "credited_solely_by_the_rule": 1270
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 403,
+ "mixed": 128,
+ "community_level_only": 275,
+ "taxa": 1544,
+ "credited_solely_by_the_rule": 1270
+ }
+ },
+ "delta": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "interpretation": "Mire archaeal/bacterial nodes gain identity-only canonical scope. Its gradient observation still encompasses the community, so the global census is unchanged. No census threshold or runtime rule changes."
+ },
+ "lint_limitation": "Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked.",
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary Python3.13 lint environment reuses validation runtime and locked mypy1.19.1/stubs/scikit-learn1.8.0/pacmap0.9.1 for static checks; not a complete embedding runtime. Project dependencies unchanged."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 8960,
+ "categories": {
+ "MATCH": 8824,
+ "RENDERING": 20,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 39,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Both-root informational audit exit0 is not clean-corpus certification; literal matches are not entailment.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1386,
+ "edges": 553,
+ "records_without_nodes": 10,
+ "records_without_edges": 182,
+ "review_status_counts": {
+ "needs_research": 50,
+ "pending": 72,
+ "reviewed": 338
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml": "af866c82bb491b74c48f353aeb02c43bda4dd426af2f03dea2a24613dcf6e065",
+ "tests/test_causal_review_batch106.py": "14c625feb3e733b49012ba53b53c8efedd3ad639cc28f68cf3ad3dc81cc8117a",
+ "tests/test_participating_taxa.py": "4b0f435e5401b563a03420068c3a9893e5731546950db84dce2505f4fd99812b",
+ "tests/test_community_level_connectivity_credit.py": "383a0f5904085a5cda800b5102923fc99301831f5769d8d4821e000773d2ea4c",
+ "reports/causal_graph_review/cache-provenance-20261008-batch106.json": "d8a73c0adb6e7239ee5719d2767c24e1dfcdd10314ef888572f14e8a4138846e",
+ "kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml": "b56a50fee784e1e8d6c07167f9faeccef0dc6ec979cc7f3b79861cb7034bc68e",
+ "kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml": "3f9b3c0e30a8f745ccaa24400d3523ef7306000486ab5e1b5c05a0cf3f877e27",
+ "kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml": "4ef09a74970615b914a26247da7f2919234df7487a087c51923c41dea1a9042c",
+ "kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml": "0f750d563e028d6b70a47ac876aec68e29bef5b87eae6ec06ba34630e43e6bd9"
+ },
+ "pre_research_baseline": {
+ "base_commit": "20d6692b687fa6826bc25f8673543215c18aa310",
+ "base_tree": "eea2b5739e61f7587840dfa918f79ec5474bdb23",
+ "research_worktree": "/private/tmp/communitymech-causal-batch105",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch106/baseline-rank.log",
+ "sha256": "21cb9bbd7625ba23cdc808ff9c37390a0ba4ff425463db162871a5f39f389837"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch106/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch106/baseline-network.log",
+ "sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097"
+ },
+ {
+ "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-batch106/baseline-downstream.log",
+ "sha256": "a75158f7a827884f295556db4c76ee924764ef4a5970d04b1a8849b4d5bcff1c"
+ }
+ ],
+ "baseline_sha256": "64492fd221761056719dff3b6beecd8945d2d14600caaf9d60ecbd173cc7d331"
+ },
+ "reference_validator_caveat": "Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.",
+ "status": "verified_existing_graph_repairs_with_source_access_limits",
+ "total_recorded_gate_outputs": 41
+}
diff --git a/tests/test_causal_review_batch106.py b/tests/test_causal_review_batch106.py
new file mode 100644
index 000000000..fb3466979
--- /dev/null
+++ b/tests/test_causal_review_batch106.py
@@ -0,0 +1,151 @@
+"""Guard source boundaries, omics interpretation and retained causal hypotheses."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_species_pair_observations_do_not_form_cross_study_arrows():
+ _, _, docs = records()
+ nodes = docs[0]["ecological_interactions"]
+ assert len(nodes) == 6 and all(not n.get("downstream") for n in nodes)
+ assert [n.get("interaction_type") for n in nodes] == [
+ None,
+ None,
+ "MUTUALISM",
+ "COLONIZATION_FACILITATION",
+ None,
+ None,
+ ]
+ assert "HYPOTHESIZED/PARTIAL:" in nodes[2]["description"]
+ assert nodes[2]["evidence"][0]["supports"] == "PARTIAL"
+ assert nodes[2]["evidence"][0]["evidence_source"] == "COMPUTATIONAL"
+ assert nodes[2]["evidence"][1]["evidence_source"] == "IN_VITRO"
+ assert len(nodes[3]["evidence"]) == 3
+ assert "without importing a hyphal requirement" in nodes[3]["description"]
+
+
+def test_transcript_associations_are_not_virulence_or_colonization():
+ _, _, docs = records()
+ transcript = docs[0]["ecological_interactions"][-1]
+ assert transcript["name"] == "Study-Specific Candida Transcript Response"
+ assert "interaction_type" not in transcript
+ assert [p["term"]["id"] for p in transcript["biological_processes"]] == ["GO:0010467"]
+ assert len(transcript["evidence"]) == 1
+ assert transcript["evidence"][0]["evidence_source"] == "COMPUTATIONAL"
+ assert "not demonstrated changes in genotype" in transcript["description"]
+ assert "computational_provenance" in transcript["evidence"][0]
+ assert all("computational_provenance" not in e for e in docs[0]["discussions"][-1]["evidence"])
+
+
+def test_mire_scopes_omics_and_retains_only_the_fen_niche_hypothesis():
+ _, _, docs = records()
+ doc = docs[1]
+ archaea, bacteria, niche, gradient = doc["ecological_interactions"]
+ for node, index in [(archaea, 1), (bacteria, 2), (niche, 1)]:
+ assert node["participating_taxa"] == [
+ {k: doc["taxonomy"][index]["taxon_term"][k] for k in ["preferred_term", "term"]}
+ ]
+ assert "source_taxon" not in node
+ assert all("interaction_type" not in n for n in [archaea, bacteria, gradient])
+ assert niche["interaction_type"] == "NICHE_PARTITIONING"
+ assert "fen" in niche["description"] and niche["evidence"][1]["supports"] == "PARTIAL"
+ assert niche["downstream"][0]["target"] == archaea["name"]
+ assert niche["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+ assert all(not n.get("downstream") for n in [archaea, bacteria, gradient])
+ evidence = [e for n in doc["ecological_interactions"] for e in n["evidence"]]
+ assert len(evidence) == 8
+ assert all(e["reference"] == "PMID:38063415" for e in evidence)
+ assert all(
+ e["evidence_source"] == "COMPUTATIONAL" and e["computational_provenance"] for e in evidence
+ )
+ assert "wrong recipient route" in bacteria["description"]
+
+
+def test_pesticide_performance_and_gene_presence_do_not_assert_mutualism():
+ _, _, docs = records()
+ growth, genes, removal, toxicity = docs[2]["ecological_interactions"]
+ assert all("interaction_type" not in n for n in [growth, genes, removal, toxicity])
+ assert "six-member immobilized" in growth["description"]
+ assert genes["name"] == "C1 Herbicide-Catabolism Gene Detection"
+ assert "not measured expression" in genes["description"]
+ assert genes["evidence"][0]["supports"] == "SUPPORT"
+ assert "complete mineralization" in removal["description"]
+ assert toxicity["evidence"][0]["supports"] == "SUPPORT"
+
+
+def test_pesticide_existing_directions_remain_qualified_not_deleted():
+ _, _, docs = records()
+ growth, genes, removal, toxicity = docs[2]["ecological_interactions"]
+ assert genes["downstream"][0]["target"] == removal["name"]
+ assert removal["downstream"][0]["target"] == toxicity["name"]
+ assert all(
+ n["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+ for n in [genes, removal]
+ )
+ assert not growth.get("downstream") and not toxicity.get("downstream")
+
+
+def test_aquifer_workflow_is_not_an_ecological_node_and_potential_is_not_flux():
+ _, rows, docs = records()
+ perturbation, decline, potential, flow = docs[3]["ecological_interactions"]
+ assert [n["node"] for n in rows[3]["removed_node_decisions"]] == [
+ "Native Carboxydocella Genome Resolution"
+ ]
+ assert perturbation["downstream"][0]["target"] == decline["name"]
+ assert potential["downstream"][0]["target"] == flow["name"]
+ assert all(
+ n["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+ for n in [perturbation, potential]
+ )
+ assert "does not establish absolute cell loss" in decline["description"]
+ for node in [potential, flow]:
+ assert node["evidence"][0]["evidence_source"] == "COMPUTATIONAL"
+ assert node["evidence"][0]["computational_provenance"]["prediction_type"] == "OTHER"
+ assert flow["evidence"][0]["supports"] == "PARTIAL"
+ assert (
+ "Removed two Subsurface Carboxydocella analysis edges"
+ in docs[3]["curation_history"][0]["changes"]
+ )
+
+
+def test_all_original_nodes_and_directions_have_dispositions():
+ ledger, rows, docs = records()
+ assert sum(len(r["node_decisions"]) for r in rows) == 18
+ assert sum(len(r["removed_node_decisions"]) for r in rows) == 1
+ assert sum(len(r["renamed_nodes"]) for r in rows) == 8
+ assert sum(len(r["retained_edge_decisions"]) for r in rows) == 5
+ assert sum(len(r["removed_edge_decisions"]) for r in rows) == 5
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert row["status"] == "reviewed"
+ assert row["curation_events_added"] == len(row["history_files"]) == 1
+ assert (ROOT / row["history_files"][0]).is_file()
+ assert doc["curation_history"][-1]["llm_assisted"]
+ assert ledger["primary_graph_snippet_count"] == len(ledger["snippet_checks"]) == 29
+ assert len(ledger["discussion_snippet_checks"]) == 7
+ assert all(
+ c["cache_matched"] and c["independent_primary_match"]
+ for c in ledger["snippet_checks"] + ledger["discussion_snippet_checks"]
+ )
+
+
+def test_followups_and_provider_scope_are_not_silently_resolved():
+ ledger, _, _ = records()
+ assert ledger["issues"] == [1829, 1830, 1831, 1832]
+ assert ledger["unresolved_non_graph_issues"] == [1833]
+ assert ledger["unresolved_research_issues"] == []
+ assert not ledger["independent_approval"]
+ assert ledger["cache_changes"] == []
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert ledger["issue_deduplication"]["matching_issues"] == [294, 691, 763, 764]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index e8bc07d16..d8ccda173 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -412,6 +412,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Soymilk_Mixed_Starter_Metabolic_Division_SynCom.yaml",
"Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml",
"Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml",
+ "Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml",
"Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml",
"SynComBac10_Chicken_Intestinal_SynCom.yaml",
"SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml",