Later transfer generations were analyzed by 3-day versus 7-day interval, categorizing ASVs enriched at 3 days as fast growers and those enriched at 7 days as slow growers; 1/10 R2A, asparagine, and glucuronic acid best retained both growth-rate classes.
-
For a fixed carbon source and original inoculum, ASVs more abundant after 7-day transfers than 3-day transfers were called slow growers, and the converse were called fast growers. The comparison used generations 6 and 9. These are operational relative-abundance classes, not measured isolate growth rates; transfer duration also changes other ecological conditions. The reported capacity of 1/10 R2A, asparagine and glucuronic acid to enrich both classes is retained. Network-hub genera are not substituted for the set of ASVs in this differential-abundance analysis.
"certain keystone species, including members of the Rhizobiaceae family and the genera Paenibacillus, Sphingomonas, Mucilaginibacter, and Terriglobus, were consistent across multiple generations
@@ -1240,20 +1194,12 @@
Evidence
-
Five 1/10 R2A RCC glycerol stocks from 3-day and 7-day transfers were thawed, serially propagated, and resequenced, producing stable dominant genera and a revived-stock network in which Burkholderia remained a shared hub for both transfer intervals.
-
+
Five selected 1/10 R2A RCC stocks were revived and serially propagated, with broadly consistent dominant genera and relative abundances in those tests. This does not establish universal revival of all initial enrichments, exact strain-level identity, or retention of every rare taxon. Burkholderia and Mesorhizobium were shared statistical hubs in the revived-stock networks, not demonstrated causes of revival. The original broad 1/10 R2A enrichments were less stable than most other carbon arms; that result is distinct from stability of these five selected stocks.
-
Participating Taxa:
-
- Burkholderia
-
-
-
@@ -1296,7 +1242,7 @@
Evidence
PMID:38846575
- - SUPPORT (IN_VITRO)
+ - SUPPORT (COMPUTATIONAL)
"Genus Burkholderia and Mesorhizobium were shared keystone taxa among 3-day and 7-day intervals
@@ -1348,6 +1294,45 @@
Associated Datasets
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which inferred RCC hubs have experimentally necessary ecological functions beyond association centrality?
+
+
The study manipulates carbon conditions and transfer intervals and directly tests selected-stock revival, but hub identity is assigned from correlation and eigenvector centrality. Taxon-removal/rescue, direct growth measurements and strain-resolved functional tests are needed before asserting niche partitioning, causal stabilization or PGP activity. The source represents multiple enrichments and selected stocks, not a single fixed ten-member community.
+
+
Attaches to: ecological_interactions#Root Exudate-Mimicking Enrichment Assembly, ecological_interactions#Carbon-Source ASV Sorting, ecological_interactions#Transfer-interval ASV abundance classification, ecological_interactions#Transfer-interval association-network hubs, ecological_interactions#Recurring association-network hubs, ecological_interactions#1/10 R2A Glycerol Stock Revival
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
The hub node (keystone taxa) is identified if the node’s eigenvector centrality value is above the 90% quantile.
+
+
+
+
+
@@ -1661,15 +1646,11 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("biological process involved in interspecies interaction between organisms");
-
-
var evidenceCount = 2;
nodes.push({
@@ -1689,7 +1670,7 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1732,7 +1713,7 @@
Evidence
(function() {
var intId = "interaction:2";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1745,7 +1726,7 @@
Evidence
nodes.push({
id: intId,
- label: "Transfer-Interval Growth-Rate Sorting",
+ label: "Transfer-interval ASV abundance classification",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1756,43 +1737,20 @@
Evidence
- var participantKeys = [
-
- "Methylobacterium",
-
- "Stenotrophomonas",
-
- "Pseudomonas",
-
- "Terriglobus",
-
- "Arthrobacter"
-
- ];
- 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("biological process involved in interspecies interaction between organisms");
-
-
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
- label: "Growth-Rate Hub Network Divergence",
+ label: "Transfer-interval association-network hubs",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1826,20 +1784,16 @@
Evidence
(function() {
var intId = "interaction:4";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("biological process involved in interspecies interaction between organisms");
-
-
var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Generational Keystone Persistence",
+ label: "Recurring association-network hubs",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1871,7 +1825,7 @@
Evidence
(function() {
var intId = "interaction:5";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1895,17 +1849,6 @@
Evidence
- var participantKeys = [
-
- "Burkholderia"
-
- ];
- participantKeys.forEach(function(key) {
- if (taxonNodeIds[key]) {
- links.push({ source: taxonNodeIds[key], target: intId });
- }
- });
-
})();
diff --git a/history/records/THOR_Rhizosphere_Model_Community/2026-10-08T133242Z-codex-305b58.yaml b/history/records/THOR_Rhizosphere_Model_Community/2026-10-08T133242Z-codex-305b58.yaml
new file mode 100644
index 000000000..374d7d8f5
--- /dev/null
+++ b/history/records/THOR_Rhizosphere_Model_Community/2026-10-08T133242Z-codex-305b58.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/THOR_Rhizosphere_Model_Community.yaml
+ slug: THOR_Rhizosphere_Model_Community
+session:
+ id: 2026-10-08T133242Z-codex-305b58
+ timestamp: '2026-10-08T13:32:42Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1922
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain locus-dependent UW101 inhibition without asserting bilateral fitness harm.;
+ Retain experimental transcriptional dependence with correct denominators and direct/indirect
+ limits.; Retain UW101 protection with all three participants, while bounding the CI04
+ chemical mechanism.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
diff --git a/history/records/TYQ1_Nematode_Biocontrol_SynCom/2026-10-08T133242Z-codex-3eb620.yaml b/history/records/TYQ1_Nematode_Biocontrol_SynCom/2026-10-08T133242Z-codex-3eb620.yaml
new file mode 100644
index 000000000..943f62b29
--- /dev/null
+++ b/history/records/TYQ1_Nematode_Biocontrol_SynCom/2026-10-08T133242Z-codex-3eb620.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml
+ slug: TYQ1_Nematode_Biocontrol_SynCom
+session:
+ id: 2026-10-08T133242Z-codex-3eb620
+ timestamp: '2026-10-08T13:32:42Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1923
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Separate TYQ1 inoculation from nematode-driven enrichment and avoid assigning mutualism
+ from abundance.; Retain all seven positive biofilm pairings with the SX attraction exception
+ and in-vitro provenance.; Retain measured spent-medium cross-feeding with AS, medium,
+ direction and network-weight limits.; Retain biological omission and host-outcome evidence
+ without overclaiming the specific mediator.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
diff --git a/history/records/Teosinte_Maize_Biofertilizer_SynCom7/2026-10-08T133243Z-codex-d993e7.yaml b/history/records/Teosinte_Maize_Biofertilizer_SynCom7/2026-10-08T133243Z-codex-d993e7.yaml
new file mode 100644
index 000000000..ad21e79f0
--- /dev/null
+++ b/history/records/Teosinte_Maize_Biofertilizer_SynCom7/2026-10-08T133243Z-codex-d993e7.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml
+ slug: Teosinte_Maize_Biofertilizer_SynCom7
+session:
+ id: 2026-10-08T133243Z-codex-d993e7
+ timestamp: '2026-10-08T13:32:43Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1924
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain the field-treatment input with correct evidence source and unresolved timing
+ boundary.; Retain reported agronomic outcomes without typing host benefit as microbial
+ mutualism or measured nitrogen fixation.; Keep soil relative-abundance responses separate
+ from inoculant establishment and absolute growth.; Represent Bacillus centrality as computational
+ association, not validated ecological function or necessity.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
diff --git a/history/records/mCAFEs_Brachypodium_RCC/2026-10-08T133243Z-codex-458ed6.yaml b/history/records/mCAFEs_Brachypodium_RCC/2026-10-08T133243Z-codex-458ed6.yaml
new file mode 100644
index 000000000..a70929c0f
--- /dev/null
+++ b/history/records/mCAFEs_Brachypodium_RCC/2026-10-08T133243Z-codex-458ed6.yaml
@@ -0,0 +1,30 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/mCAFEs_Brachypodium_RCC.yaml
+ slug: mCAFEs_Brachypodium_RCC
+session:
+ id: 2026-10-08T133243Z-codex-458ed6
+ timestamp: '2026-10-08T13:32:43Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1925
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain the abiotic enrichment design and its two selection arrows without asserting
+ niche partitioning.; Preserve carbon-associated ASV sorting with representative participants
+ and no inferred substrate flux.; Define fast/slow as operational abundance classes rather
+ than growth-rate measurements or hub membership.; Keep transfer-specific hubs computational
+ and distinguish centrality from ecological necessity.; Keep recurring hubs as statistical
+ observations without assigning validated PGP or stability function.; Retain reproducible
+ revival only for the five selected stocks and separate it from initial enrichment stability.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
diff --git a/kb/communities/THOR_Rhizosphere_Model_Community.yaml b/kb/communities/THOR_Rhizosphere_Model_Community.yaml
index a83f6cdfa..00eddaa21 100644
--- a/kb/communities/THOR_Rhizosphere_Model_Community.yaml
+++ b/kb/communities/THOR_Rhizosphere_Model_Community.yaml
@@ -131,12 +131,12 @@ taxonomy:
snippet: co-isolate from field-grown soybean roots
explanation: Supports the natural coisolation context for the THOR members.
ecological_interactions:
-- name: Koreenceine-Mediated Inhibition
- description: Pseudomonas koreensis produces koreenceine, an alkaloid antibiotic that inhibits Flavobacterium
- johnsoniae and strongly structures transcriptional responses within THOR. Removing koreenceine or
- changing the starting abundance of P. koreensis increases F. johnsoniae populations, indicating that
- the antibiotic is a major regulatory and competitive mechanism in this model community.
- interaction_type: COMPETITION
+- name: Koreenceine production and UW101 growth inhibition
+ description: P. koreensis CI12 produces koreenceine and inhibits F. johnsoniae UW101 in the 2022 THOR study. Deleting
+ the koreenceine locus or reducing the initial P. koreensis inoculum increases UW101 populations. P. koreensis
+ and B. cereus growth are not impaired by coculture under the tested conditions, so this one-sided inhibition
+ does not establish mutual negative fitness effects. This UW101 assay must not be conflated with the founding
+ CI04 root-exudate experiment.
scope: PAIRWISE
source_taxon:
preferred_term: Pseudomonas koreensis CI12
@@ -153,8 +153,8 @@ ecological_interactions:
term:
id: CHEBI:22315
label: alkaloid
- notes: Koreenceine is represented at the chemical-class level because a specific CHEBI term was not
- identified during curation.
+ notes: Koreenceine is represented at the chemical-class level because a specific CHEBI term was not identified
+ during curation.
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
@@ -162,26 +162,35 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Koreenceine-Driven Transcriptional Regulation
- description: >
- Pseudomonas koreensis koreenceine production drives most Flavobacterium
- johnsoniae and part of the Bacillus cereus transcriptional response to
- pairwise encounter with P. koreensis.
+ description: 'The wild-type versus koreenceine-locus-deletion comparison supports koreenceine-dependent gene
+ regulation in UW101 and B. cereus. PARTIAL for the direct molecular route: antibiotic exposure and indirect
+ physiological effects can both contribute. This arrow starts from koreenceine production, not an assumption
+ that reduced UW101 growth causes all transcriptional changes or that B. cereus growth is inhibited.'
evidence:
- - reference: PMID:30837345
+ - reference: PMID:35435700
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: both deletion of the koreenceine locus and reduction of P. koreensis inoculum size increase F. johnsoniae
+ populations
+ explanation: Two perturbations support population inhibition in the UW101 study; they are not equivalent transcriptional
+ perturbations.
+ - reference: PMID:35435700
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: P. koreensis produces a novel family of alkaloid antibiotics that inhibit growth of F. johnsoniae
- explanation: Supports koreenceine-mediated inhibition by P. koreensis.
+ snippet: the growth of P. koreensis and B. cereus was not affected by coculture
+ explanation: Bounds the growth phenotype and prevents coding the interaction as demonstrated bilateral competition.
- reference: PMID:35435700
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: mediated either directly or indirectly by its production of the antibiotic koreenceine
- explanation: Supports koreenceine as a major driver of community transcriptional response.
+ snippet: Bacillus cereus UW85 (B), Flavobacterium johnsoniae UW101 (F), Pseudomonas koreensis CI12 (P)
+ explanation: The Methods explicitly identify the three strains in this study.
- name: Koreenceine-Driven Transcriptional Regulation
- description: Comparative metatranscriptomics showed that the P. koreensis koreenceine biosynthetic
- locus accounts for much of the pairwise transcriptional response in THOR, including most
- differentially regulated F. johnsoniae genes and a smaller B. cereus response.
- interaction_type: COMPETITION
+ description: At the assayed early time point, the P. koreensis koreenceine locus accounts for 85% of the greater-than-twofold
+ pairwise response in UW101 and 22% in B. cereus. These are proportions of differentially regulated genes, not
+ of each whole genome or of all three-member responses. Locus deletion supports dependence, while direct sensing
+ and indirect effects of altered growth remain unresolved. B. cereus changes expression without a measured growth
+ defect. Reducing P. koreensis initial abundance, unlike deleting the locus alone, increases its own response
+ to UW101.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: koreenceine
@@ -198,27 +207,26 @@ ecological_interactions:
- reference: PMID:35435700
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: In pairwise interactions, the koreenceine biosynthetic cluster is responsible for 85 and
- 22% of differentially regulated genes in F. johnsoniae and B. cereus, respectively.
- explanation: Quantifies koreenceine-dependent gene-expression changes in the two strains responding
- to P. koreensis in pairwise cocultures.
+ snippet: In pairwise interactions, the koreenceine biosynthetic cluster is responsible for 85 and 22% of differentially
+ regulated genes in F. johnsoniae and B. cereus, respectively.
+ explanation: Quantifies koreenceine-dependent gene-expression changes in the two strains responding to P. koreensis
+ in pairwise cocultures.
confidence_score: 0.9
-- name: Bacillus Modulation of Pseudomonas Antibiotic Production
- description: Bacillus cereus modulates the inhibitory interaction between P. koreensis and F. johnsoniae
- by suppressing production of the P. koreensis alkaloid antibiotic family. This creates a higher-order
- interaction where the effect of P. koreensis on F. johnsoniae changes in the presence of B. cereus.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Bacillus cereus UW85
- term:
- id: NCBITaxon:1396
- label: Bacillus cereus
- target_taxon:
- preferred_term: Pseudomonas koreensis CI12
- term:
- id: NCBITaxon:198620
- label: Pseudomonas koreensis
+ - reference: PMID:35435700
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: likely a combination of direct effects from koreenceine and indirect effects due to slower growth rate
+ of F. johnsoniae in the presence of an antibiotic
+ explanation: The authors explicitly retain direct and indirect explanations for the locus-dependent expression
+ response.
+- name: Bacillus protection in the UW101 THOR community
+ description: 'Adding B. cereus UW85 to P. koreensis CI12 and F. johnsoniae UW101 raises UW101 abundance relative
+ to the inhibited pair in the 2022 study. This is a three-member protective effect, not facilitation of P. koreensis
+ colonization. PARTIAL: the proposed chemical explanation draws on the earlier CI04 variant, where B. cereus
+ reduced accumulated koreenceines A and C and its spo0H mutant lost protection. Those CI04 measurements neither
+ quantify A/C changes in UW101 culture nor isolate reduced biosynthesis from other routes of reduced metabolite
+ accumulation.'
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: koreenceine
term:
@@ -231,34 +239,36 @@ ecological_interactions:
id: GO:0048519
label: negative regulation of biological process
downstream:
- - target: Koreenceine-Mediated Inhibition
- description: Bacillus suppression of Pseudomonas koreenceine production changes the
- antibiotic-mediated inhibition that P. koreensis exerts on F. johnsoniae.
+ - target: Koreenceine production and UW101 growth inhibition
+ description: 'B. cereus addition reduces the population inhibition of UW101 in the three-member assay. PARTIAL
+ for mediation by altered koreenceine accumulation: the detailed metabolite and spo0H comparisons were performed
+ with CI04, not UW101, and do not uniquely demonstrate a biosynthesis-suppression mechanism in the UW101 community.'
evidence:
- - reference: PMID:30837345
+ - reference: PMID:35435700
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: production is inhibited by B. cereus
- explanation: Supports B. cereus modulation of P. koreensis antibiotic production.
-- name: Emergent Three-Member Biofilm Formation
- description: The complete THOR community produces a stronger biofilm phenotype than its individual
- members, demonstrating an emergent community property that is not captured by monoculture behavior.
- This makes THOR useful for studying how pairwise and higher-order interactions shape aggregate
- community outputs.
- interaction_type: COLONIZATION_FACILITATION
- scope: COMMUNITY_LEVEL
- metabolites: []
- biological_processes:
- - preferred_term: biofilm formation
- term:
- id: GO:0042710
- label: biofilm formation
- evidence:
+ snippet: P. koreensis reduced growth of F. johnsoniae when they were grown as a pair, but F. johnsoniae abundance
+ was higher when B. cereus was also present
+ explanation: Directly supports protection in the UW101 experiment, not a uniquely resolved chemical mechanism.
- reference: PMID:30837345
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: production of more robust biofilms by the three members together than individually
- explanation: Supports biofilm formation as an emergent three-member community phenotype.
+ snippet: The addition of B. cereus to cocultures of P. koreensis and F. johnsoniae severely reduced the accumulation
+ of koreenceine A and C, with a minor effect on the level of koreenceine B
+ explanation: Mechanistic context from the founding CI04 variant only; not direct measurement of UW101 cultures.
+ participating_taxa:
+ - preferred_term: Bacillus cereus UW85
+ term:
+ id: NCBITaxon:1396
+ label: Bacillus cereus
+ - preferred_term: Pseudomonas koreensis CI12
+ term:
+ id: NCBITaxon:198620
+ label: Pseudomonas koreensis
+ - preferred_term: Flavobacterium johnsoniae UW101
+ term:
+ id: NCBITaxon:986
+ label: Flavobacterium johnsoniae
cultivation_setup:
- cultivation_mode: BATCH
operating_temperature: 28.0
@@ -393,3 +403,33 @@ growth_media:
in liquid culture in 1/2-strength tryptic soy broth (TSB) at 28°C with vigorous shaking
explanation: Reports the cultivation medium (1/2-strength TSB, 1/10 TSA), temperature (28°C),
and shaking used to grow THOR members.
+discussions:
+- discussion_id: thor_causal_graph_scope_batch119
+ prompt: Which CI04-variant biofilm and metabolite mechanisms transfer experimentally to the UW101 THOR community?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Koreenceine production and UW101 growth inhibition
+ - ecological_interactions#Koreenceine-Driven Transcriptional Regulation
+ - ecological_interactions#Bacillus protection in the UW101 THOR community
+ rationale: The founding study used CI04; the 2022 Methods name UW101. In CI04 assays, both partners enhanced P.
+ koreensis biofilm and the triple culture sustained it longer, but this does not establish the corresponding
+ UW101 phenotype. Likewise, CI04 metabolite accumulation and spo0H tests do not resolve the UW101 protection
+ mechanism. Strain-matched biofilm and chemical perturbations are needed before restoring that node or asserting
+ a specific route. The UW101 locus-deletion, population and expression results remain experimental evidence.
+ evidence:
+ - reference: PMID:35435700
+ snippet: Bacillus cereus UW85 (B), Flavobacterium johnsoniae UW101 (F), Pseudomonas koreensis CI12 (P)
+ - reference: PMID:30837345
+ snippet: F. johnsoniae CI04 and B. cereus UW85 each increased the maximum biofilm formed by P. koreensis CI12
+ at 18 h
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T13:32:40Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain locus-dependent UW101 inhibition without asserting bilateral fitness harm.; Retain experimental
+ transcriptional dependence with correct denominators and direct/indirect limits.; Retain UW101 protection with
+ all three participants, while bounding the CI04 chemical mechanism. Issue#1922; reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
+ llm_assisted: true
diff --git a/kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml b/kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml
index df939df29..12902cef6 100644
--- a/kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml
+++ b/kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml
@@ -252,12 +252,10 @@ taxonomy:
explanation: Documents MA as recruited biomarker contributing to biofilm and metabolic network
ecological_interactions:
- name: Keystone-Mediated Community Recruitment
- description: 'TYQ1 enrichment during root-knot nematode infection causes restructuring of the rhizobacterial
- community, leading to enrichment of 7 biomarker species. RKN infection restructured the rhizosphere
- bacterial community in RKN-susceptible cucumber plants regardless of soil type.
-
- '
- interaction_type: MUTUALISM
+ description: TYQ1 inoculation changes the cucumber rhizobacterial community relative to uninoculated controls
+ and enriches biomarker OTUs from which seven partner strains were selected. This intervention is distinct from
+ the initial nematode-induced enrichment of TYQ1. Relative-abundance enrichment alone does not establish mutual
+ fitness benefit, absolute growth of every partner, or a compound-specific recruitment mechanism.
scope: COMMUNITY_LEVEL
source_taxon:
preferred_term: Rhizobium pusense TYQ1
@@ -270,28 +268,27 @@ ecological_interactions:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
downstream:
- - target: Synergistic Biofilm Formation
- description: TYQ1-mediated recruitment enriches the biomarker species that,
- in collaboration with TYQ1, increase the community's biofilm-forming
- ability.
- - target: Metabolic Cross-Feeding Network
- description: TYQ1-mediated recruitment enriches the biomarker species that
- establish a tightly interconnected metabolic interaction network centered
- on TYQ1.
+ - target: TYQ1-partner biofilm enhancement
+ description: 'PARTIAL: TYQ1 inoculation enriches the pool of partners whose reconstructed pairings enhance biofilm
+ in vitro. This supports a recruitment-to-biofilm hypothesis across the linked assays, not direct measurement
+ of biofilm mediation in the root community.'
+ - target: Condition-dependent TYQ1 spent-medium cross-feeding
+ description: 'PARTIAL: TYQ1-driven partner enrichment provides members with experimentally demonstrated spent-medium
+ utilization. The reconstructed laboratory network does not establish that the same directional fluxes occur
+ in situ after recruitment.'
evidence:
- reference: PMID:41660888
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: root-knot nematode (RKN) infection restructured the rhizosphere bacterial community in RKN-susceptible
- cucumber plants, regardless of the soil type
- explanation: Documents stress-induced community restructuring mediated by TYQ1
-- name: Synergistic Biofilm Formation
- description: 'All 7 recruited biomarker species show mutual attraction to TYQ1 and enhance biofilm-forming
- ability of the community. Biofilm formation is a key mechanism for community cohesion and nematode
- suppression.
-
- '
- interaction_type: MUTUALISM
+ snippet: This strain not only directly inhibited RKNs but also caused the restructuring of the rhizobacterial
+ community, thereby leading to the enrichment of multiple biomarker species
+ explanation: Supports the TYQ1 inoculation effect, rather than substituting the separate nematode-infection
+ comparison.
+- name: TYQ1-partner biofilm enhancement
+ description: 'All seven TYQ1-partner pairings increased the measured biofilm phenotype in vitro. Colony attraction
+ is a separate assay: SX showed no obvious attraction or repulsion, while the other six partners induced colony
+ enlargement with TYQ1. These observations do not establish bilateral growth benefit for all pairs or prove that
+ biofilm enhancement mediates nematode suppression in roots.'
scope: COMMUNITY_LEVEL
source_taxon:
preferred_term: Rhizobium pusense TYQ1
@@ -305,21 +302,28 @@ ecological_interactions:
label: biofilm formation
downstream:
- target: Synergistic Nematode Suppression
- description: The enhanced biofilm-forming ability of the recruited
- eight-member consortium strengthens rhizosphere colonization of TYQ1 and
- contributes to stable root-knot nematode inhibition.
+ description: 'PARTIAL: increased biofilm may support the observed transient increase in TYQ1 root colonization
+ and contribute to suppression. The study does not selectively disrupt biofilm while preserving other TYQ1
+ and partner functions, so mediation remains unresolved.'
evidence:
- reference: PMID:41660888
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming ability
- of the community and established a tightly interconnected metabolic interaction network
- explanation: Documents synergistic biofilm enhancement across the SynCom
-- name: Metabolic Cross-Feeding Network
- description: 'TYQ1 serves as the central metabolic hub in a tightly interconnected metabolic interaction
- network with the 7 biomarker species, enabling metabolic cross-feeding that supports community function.
-
- '
+ evidence_source: IN_VITRO
+ snippet: all strains exhibited a synergistic effect with TYQ1 in biofilm formation
+ explanation: Supports the seven pairwise biofilm results, not a species-resolved mutualism claim.
+ - reference: PMID:41660888
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: With the exception of SX, which did not display obvious attraction or repulsion toward TYQ1
+ explanation: Records the explicit exception to the attraction claim.
+- name: Condition-dependent TYQ1 spent-medium cross-feeding
+ description: Metabolite-feeding assays support a cross-feeding network, with important medium and direction limits.
+ TYQ1 grows on filtrates of all seven partners in M9; six partners grow on TYQ1-derived metabolites, with AS
+ the reported exception. In TSB, adding TYQ1 supernatant generally increases partner growth rates without changing
+ carrying capacity, whereas partner supernatants do not enhance TYQ1 growth. Directed network weights summarize
+ fitted carrying capacities, not measured metabolite fluxes. Gephi node removal is an in-silico centrality analysis,
+ distinct from biological strain omission. No particular exchanged molecule or obligatory seven-way mutualism
+ is established.
interaction_type: CROSS_FEEDING
scope: COMMUNITY_LEVEL
source_taxon:
@@ -334,22 +338,40 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Synergistic Nematode Suppression
- description: TYQ1-centered metabolic exchanges help organize the recruited
- beneficial strains into the high-efficacy network required for stable
- root-knot nematode suppression.
+ description: 'PARTIAL: assayed exchange capacity may support the community that improves nematode suppression.
+ Biological TYQ1 omission and diversity gradients support its community contribution, but neither isolate exchange
+ from direct nematicidal activity, biofilm effects or host responses. In-silico node removal is not that biological
+ test.'
evidence:
- reference: PMID:41660888
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming ability
- of the community and established a tightly interconnected metabolic interaction network
- explanation: Documents TYQ1 as central metabolic hub in cross-feeding network
+ evidence_source: IN_VITRO
+ snippet: TYQ1 could utilize the metabolites secreted by all seven enriched strains for growth
+ explanation: Supports partner-to-TYQ1 utilization in the metabolite-feeding assay.
+ - reference: PMID:41660888
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Except for AS, which exhibited a relatively slow background growth in M9 basic medium, the other six
+ strains could also grow using the metabolites of TYQ1
+ explanation: Bounds the reverse direction to six partners rather than seven.
+ - reference: PMID:41660888
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: the supernatant of the enriched strains did not influence TYQ1growth
+ explanation: Preserves the rich-medium negative result; it does not negate the distinct M9 filtrate result.
+ - reference: PMID:41660888
+ supports: SUPPORT
+ evidence_source: COMPUTATIONAL
+ snippet: directed edge weights defined as the carrying capacity (K) derived from logistic growth curve fitting
+ explanation: Network weights summarize the growth assay; they are not directly measured exchange fluxes.
- name: Synergistic Nematode Suppression
- description: 'The complete 8-member TYQ1-centered SynCom exhibits more efficient and stable root-knot
- nematode inhibition than individual members alone, demonstrating emergent synergistic biocontrol activity.
-
- '
- interaction_type: MUTUALISM
+ description: 'The eight-member consortium enhances nematode suppression and cucumber performance compared with
+ TYQ1 alone in the tested pot assays. Actual leave-one-strain-out and diversity-gradient communities support
+ a major contribution of TYQ1: omitting it abolishes efficient suppression and can promote egg-mass formation.
+ The source reports validation in 12 soil types, not universal field performance. Root defense-expression and
+ metabolite changes accompany protection, but neither strain omission nor these profiles isolate biofilm, specific
+ cross-fed metabolites, or host defense as the sole mediator. Plant benefit is not evidence of mutual fitness
+ benefit among all microbes.'
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: defense response
@@ -360,8 +382,20 @@ ecological_interactions:
- reference: PMID:41660888
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: the TYQ1-centered synthetic community exhibited more efficient and stable inhibition of RKNs
- explanation: Documents synergistic nematode suppression by the complete SynCom
+ snippet: the TYQ1-centered SynCom is significantly more effective than the single inoculation of TYQ1
+ explanation: Supports the tested consortium-versus-TYQ1 outcome.
+ - reference: PMID:41660888
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: The -TYQ1 not only lost its inhibitory function but even had the opposite effect, facilitating the
+ formation of egg masses on the roots.
+ explanation: Actual biological omission supports TYQ1 contribution, not isolation of an exchange pathway.
+ - reference: PMID:41660888
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: 535 commonly induced DEGs enriched in defense and abscisic acid response pathways
+ explanation: Supports the retained defense-response association without claiming a pathway-specific loss-of-function
+ experiment.
associated_datasets:
- title: 16S Amplicon Sequencing (Rhizosphere)
dataset_type: AMPLICON_16S
@@ -464,3 +498,33 @@ growth_media:
snippet: plated on TSA and R2A media. The plates were then incubated at 28°C for 3–5 days
explanation: Reports the TSA/R2A media, 28°C temperature, and 3-5 day incubation used to
culture the community's constituent strains.
+discussions:
+- discussion_id: tyq1_causal_graph_scope_batch119
+ prompt: How much of TYQ1-dependent nematode suppression is specifically mediated by biofilm or metabolite exchange?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Keystone-Mediated Community Recruitment
+ - ecological_interactions#TYQ1-partner biofilm enhancement
+ - ecological_interactions#Condition-dependent TYQ1 spent-medium cross-feeding
+ - ecological_interactions#Synergistic Nematode Suppression
+ rationale: Pairwise biofilm and filtrate assays support real functions, and biological strain omission supports
+ the contribution of TYQ1. Removing an organism also removes its direct nematicidal and host-modulating effects;
+ it is not a selective biofilm or exchange perturbation. The reported colonization increase is transient within
+ the first week. Medium-matched and mechanism-specific loss/rescue experiments are needed to resolve the two
+ downstream mediation arrows without erasing the positive consortium outcome.
+ evidence:
+ - reference: PMID:41660888
+ snippet: The -TYQ1 not only lost its inhibitory function but even had the opposite effect, facilitating the
+ formation of egg masses on the roots.
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T13:32:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Separate TYQ1 inoculation from nematode-driven enrichment and avoid assigning mutualism from abundance.;
+ Retain all seven positive biofilm pairings with the SX attraction exception and in-vitro provenance.; Retain
+ measured spent-medium cross-feeding with AS, medium, direction and network-weight limits.; Retain biological
+ omission and host-outcome evidence without overclaiming the specific mediator. Issue#1923; reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
+ llm_assisted: true
diff --git a/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml b/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml
index d4270c82d..bbb5d3fca 100644
--- a/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml
+++ b/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml
@@ -109,123 +109,48 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: PGP-Trait SynCom7 Formulation
- description: >
- Seven teosinte-seed bacterial isolates with plant-growth-promoting,
- nutrient-cycling, and pathogen-suppression phenotypes were selected to form
- the maize biofertilizer SynCom.
- scope: COMMUNITY_LEVEL
- interaction_type: COLONIZATION_FACILITATION
- metabolites:
- - preferred_term: phosphate ion
- term:
- id: CHEBI:35780
- label: phosphate ion
- - preferred_term: indole-3-acetic acid
- term:
- id: CHEBI:16411
- label: indole-3-acetic acid
- biological_processes:
- - preferred_term: nitrogen fixation
- term:
- id: GO:0009399
- label: nitrogen fixation
- evidence:
- - *id001
- - reference: PMID:40270813
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: screening bacterial isolates for nitrogen fixation, phosphate solubilization, and production
- of phytohormones such as indole-3-acetic acid (IAA)
- explanation: Names nitrogen fixation, phosphate solubilization, and IAA
- production as screened traits used to select the teosinte-derived
- SynCom.
-- name: Equal-Volume Field Inoculum
- description: >
- Independently grown R2A cultures were centrifuged, resuspended to a common
- cell density in saline, mixed in equal volumes, and checked for strain
- viability before the final SynCom was applied to maize field plots.
- scope: COMMUNITY_LEVEL
- interaction_type: COLONIZATION_FACILITATION
- biological_processes:
- - preferred_term: biological process involved in interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
- evidence:
- - reference: PMID:40270813
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- The SynCom was prepared for field application by mixing equal volumes of
- each bacterial suspension
- explanation: >
- Supports the final equal-volume mixing step used to formulate the
- seven-strain SynCom inoculum.
- - reference: PMID:40270813
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- The viability of each strain in the final mixture was confirmed through
- colony-forming unit (CFU) counts on selective media
- explanation: >
- Supports viability checking after SynCom formulation.
- name: Four-Stage Maize Biofertilization
- description: >
- Manual and drone-assisted delivery applied the SynCom to maize plants at
- four crop stages, using a 50 mL per-plant dose that matched the conventional
- fertilization comparison arms.
+ description: The field experiment compared no application, conventional fertilizer and seven-strain biofertilizer,
+ each active treatment delivered manually or by drone. The reported protocol used 50 mL per plant and four application
+ times (0, 25, 55 and 85 days after sowing). Delivery is a manipulated input, not microbial colonization facilitation.
+ The source separately describes about 120 days for yield harvest; those timing descriptions are not silently
+ reconciled here.
scope: COMMUNITY_LEVEL
- interaction_type: COLONIZATION_FACILITATION
- biological_processes:
- - preferred_term: growth
- term:
- id: GO:0040007
- label: growth
downstream:
- target: Biofertilizer-Linked Soil and Yield Response
- description: >
- Repeated teosinte SynCom delivery drove the measured soil, maize
- physiology, yield, and disease-protection responses.
- - target: Beneficial-Taxon Soil Microbiome Shift
- description: >
- Repeated teosinte SynCom delivery restructured bacterial and fungal
- communities over the field season.
+ description: The repeated biofertilizer treatment is the manipulated input compared with control and conventional-fertilizer
+ arms in the reported field design. The resulting agronomic differences support a treatment-level effect, not
+ proof that a particular strain, nitrogen-fixation route or within-consortium mutualism mediated it.
+ - target: Treatment-associated soil microbiome shifts
+ description: The biofertilizer application arms produced distinct soil-community profiles across the sampled
+ season. This treatment-to-profile link does not establish absolute taxon growth, tracking of the introduced
+ strains, or causation by the individual edges of the co-occurrence network.
evidence:
- reference: PMID:40270813
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- The drone was calibrated to deliver 50 mL of treatment solution per plant
- explanation: >
- Supports the per-plant dose used in drone-assisted biofertilizer delivery.
+ evidence_source: IN_VIVO
+ snippet: 'The drone was calibrated to deliver 50 mL of treatment solution per plant
+
+ '
+ explanation: "Supports the per-plant dose used in drone-assisted biofertilizer delivery.\n Field-treatment protocol,\
+ \ not an in-vitro ecological interaction."
- reference: PMID:40270813
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- Applications were carried out at four key growth stages: pre-treatment at
- 0 days after sowing (DAS), mid-season at 25 DAS, early reproductive stage
- at 55 DAS, and harvest at 85 DAS
- explanation: >
- Documents the four maize growth stages used for treatment applications.
+ evidence_source: IN_VIVO
+ snippet: 'Applications were carried out at four key growth stages: pre-treatment at 0 days after sowing (DAS),
+ mid-season at 25 DAS, early reproductive stage at 55 DAS, and harvest at 85 DAS
+
+ '
+ explanation: "Documents the four maize growth stages used for treatment applications.\n Field-treatment protocol,\
+ \ not an in-vitro ecological interaction."
- name: Biofertilizer-Linked Soil and Yield Response
- description: >
- Biofertilization, especially by drone delivery, was associated with higher
- soil microbial biomass, aggregate stability, nutrient uptake, chlorophyll,
- maize yield, and disease protection than the conventional and untreated
- comparison arms.
+ description: The study reports higher soil microbial biomass, aggregate stability, plant nutrient uptake, chlorophyll,
+ growth and yield, with lower disease incidence, under biofertilization, especially drone delivery, than its
+ comparison treatments. These are treatment-level outcomes of the reported field experiment, not measurements
+ of nitrogen-fixation flux, phosphate transfer, mutual benefit among seven strains, or a uniquely demonstrated
+ microbial mechanism. The field statistics were not independently reproduced.
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
- metabolites:
- - preferred_term: phosphate ion
- term:
- id: CHEBI:35780
- label: phosphate ion
biological_processes:
- - preferred_term: nitrogen fixation
- term:
- id: GO:0009399
- label: nitrogen fixation
- preferred_term: growth
term:
id: GO:0040007
@@ -234,30 +159,29 @@ ecological_interactions:
- reference: PMID:40270813
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- Biofertilization treatments, mainly when applied via drone technology,
- demonstrated the most pronounced positive impacts on soil microbial
- diversity, nutrient availability, crop yield, and disease resistance
- explanation: >
- Supports the positive agronomic and soil responses to the teosinte-derived
- biofertilizer treatments.
+ snippet: 'Biofertilization treatments, mainly when applied via drone technology, demonstrated the most pronounced
+ positive impacts on soil microbial diversity, nutrient availability, crop yield, and disease resistance
+
+ '
+ explanation: 'Supports the positive agronomic and soil responses to the teosinte-derived biofertilizer treatments.
+
+ '
- reference: PMID:40270813
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- Biofertilization also enhanced plant nutrient uptake and physiological
- performance
- explanation: >
- Supports improved maize nutrient uptake and host physiology after
- SynCom-based biofertilization.
-- name: Beneficial-Taxon Soil Microbiome Shift
- description: >
- Biofertilization most strongly restructured the soil community, decreasing
- Enterobacteriaceae dominance while enriching beneficial Bacillus, Pantoea,
- Serratia, Rhizobium, Pseudomonas, and Bradyrhizobium populations over
- consecutive sampling points.
+ snippet: 'Biofertilization also enhanced plant nutrient uptake and physiological performance
+
+ '
+ explanation: 'Supports improved maize nutrient uptake and host physiology after SynCom-based biofertilization.
+
+ '
+- name: Treatment-associated soil microbiome shifts
+ description: Soil bacterial and fungal relative-abundance profiles shifted across fertilization treatments and
+ sampling times, including reduced Enterobacteriaceae dominance and increased representation of source-described
+ beneficial genera. The soil community includes indigenous taxa beyond the seven inoculant strains. Relative
+ abundance does not prove absolute population growth, inoculant strain establishment, or uniformly beneficial
+ function of every organism assigned to those genera.
scope: COMMUNITY_LEVEL
- interaction_type: COLONIZATION_FACILITATION
biological_processes:
- preferred_term: biological process involved in interspecies interaction between organisms
term:
@@ -267,56 +191,54 @@ ecological_interactions:
- reference: PMID:40270813
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- Biofertilization treatments produced the most pronounced shifts, reducing
- Enterobacteriaceae below 50% while significantly increasing beneficial
- taxa like Bacillus, Pantoea, and Serratia
- explanation: >
- Supports beneficial-taxon enrichment and Enterobacteriaceae reduction
- after SynCom biofertilization.
+ snippet: 'Biofertilization treatments produced the most pronounced shifts, reducing Enterobacteriaceae below
+ 50% while significantly increasing beneficial taxa like Bacillus, Pantoea, and Serratia
+
+ '
+ explanation: 'Supports beneficial-taxon enrichment and Enterobacteriaceae reduction after SynCom biofertilization.
+
+ '
- reference: PMID:40270813
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >
- Bacterial communities exhibited complementary patterns, with plant
- growth-promoting rhizobacteria showing significant enrichment in
- biofertilization treatments
- explanation: >
- Supports enrichment of plant-growth-promoting rhizobacteria in the
- biofertilized soil community.
-- name: Bacillus-Centered Nutrient-Cycling Network
- description: >
- Co-occurrence analysis resolved increasingly complex biofertilizer-associated
- microbial networks, including Bacillus as a central node and positive
- correlations linking plant-growth-promoting, nitrogen-fixing,
- organic-matter-degrading, and biocontrol guilds.
+ snippet: 'Bacterial communities exhibited complementary patterns, with plant growth-promoting rhizobacteria
+ showing significant enrichment in biofertilization treatments
+
+ '
+ explanation: 'Supports enrichment of plant-growth-promoting rhizobacteria in the biofertilized soil community.
+
+ '
+- name: Statistical Bacillus-centered soil association network
+ description: Computational co-occurrence analysis of soil abundance profiles identifies Bacillus as a central
+ taxonomic node and correlated responses among putative functional guilds. Correlation and centrality do not
+ establish mutualism, directed nutrient exchange, nitrogen-fixation activity, pathogen suppression by a particular
+ edge, or experimental keystone necessity. These are soil-community associations, not a resolved interaction
+ network among the seven inoculant strains.
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
- biological_processes:
- - preferred_term: biological process involved in interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
evidence:
- reference: PMID:40270813
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >
- Network analysis demonstrated that microbial interaction complexity
- increased across treatments, with Bacillus emerging as a keystone species
- explanation: >
- Supports Bacillus centrality and increased microbial network complexity
- in treatment-associated soils.
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: 'Network analysis demonstrated that microbial interaction complexity increased across treatments, with
+ Bacillus emerging as a keystone species
+
+ '
+ explanation: Supports a source-interpreted co-occurrence pattern; ecological mechanism and necessity are not
+ experimentally established.
+ - reference: PMID:40270813
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: 'Drone-assisted biofertilization fostered particularly intricate microbial networks, enhancing synergistic
+ relationships involved in nutrient cycling and biocontrol
+
+ '
+ explanation: Supports a source-interpreted co-occurrence pattern; ecological mechanism and necessity are not
+ experimentally established.
- reference: PMID:40270813
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >
- Drone-assisted biofertilization fostered particularly intricate microbial
- networks, enhancing synergistic relationships involved in nutrient cycling
- and biocontrol
- explanation: >
- Supports correlated nutrient-cycling and biocontrol guild responses in
- the drone-assisted biofertilization network.
+ evidence_source: COMPUTATIONAL
+ snippet: based on correlated changes in abundance throughout the crop cycle
+ explanation: Identifies the observational basis of the network, rather than a perturbation test of its edges.
environmental_factors:
- name: defined synthetic community design
value: Seven bacterial strains from teosinte-associated microbes were formulated as a SynCom.
@@ -361,7 +283,35 @@ curation_history:
- timestamp: '2026-10-02T06:04:09Z'
curator: codex
action: REPAIR_CAUSAL_GRAPH
- changes: Removed three Teosinte SynCom formulation and network-analysis edges,
- and rewrote the retained four-stage biofertilization edges to state
- measured soil, yield, and microbiome responses directly.
+ changes: Removed three Teosinte SynCom formulation and network-analysis edges, and rewrote the retained four-stage
+ biofertilization edges to state measured soil, yield, and microbiome responses directly.
+ llm_assisted: true
+- timestamp: '2026-10-08T13:32:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain the field-treatment input with correct evidence source and unresolved timing boundary.; Retain
+ reported agronomic outcomes without typing host benefit as microbial mutualism or measured nitrogen fixation.;
+ Keep soil relative-abundance responses separate from inoculant establishment and absolute growth.; Represent
+ Bacillus centrality as computational association, not validated ecological function or necessity. Issue#1924;
+ reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
llm_assisted: true
+discussions:
+- discussion_id: teosinte_causal_graph_scope_batch119
+ prompt: Which inoculant strains and ecological mechanisms mediate the reported field effects?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Four-Stage Maize Biofertilization
+ - ecological_interactions#Biofertilizer-Linked Soil and Yield Response
+ - ecological_interactions#Treatment-associated soil microbiome shifts
+ - ecological_interactions#Statistical Bacillus-centered soil association network
+ rationale: The seven-strain formulation and field-treatment contrasts are described, but soil amplicon profiles
+ and correlation networks do not identify strain-resolved establishment or necessary exchange pathways. The record
+ taxonomy is an incomplete broad representation of the seven isolates. Source timing and sample/replicate descriptions
+ also differ; raw-data and design reconciliation are needed for quantitative reanalysis. No extra causal arrow
+ from the statistical network to yield is introduced.
+ evidence:
+ - reference: PMID:40270813
+ snippet: based on correlated changes in abundance throughout the crop cycle
+ posed_by: codex
+ posed_date: '2026-10-08'
diff --git a/kb/communities/mCAFEs_Brachypodium_RCC.yaml b/kb/communities/mCAFEs_Brachypodium_RCC.yaml
index 68784508b..432e3c732 100644
--- a/kb/communities/mCAFEs_Brachypodium_RCC.yaml
+++ b/kb/communities/mCAFEs_Brachypodium_RCC.yaml
@@ -308,54 +308,49 @@ taxonomy:
explanation: Identified as a genus enriched by the dominant Brachypodium root-exudate substrate asparagine.
ecological_interactions:
- name: Root Exudate-Mimicking Enrichment Assembly
- description: >
- Co-localized microbes from Brachypodium roots grown in Angelo Coast Range
- Reserve soil were introduced into a multiplexed high-throughput enrichment
- design, coupling root-exudate-like carbon substrates to 3-day and 7-day
- transfers to produce fast- and slow-growing reduced-complexity consortia.
+ description: A multiplexed enrichment experiment varied root-associated inocula, carbon conditions and 3-day versus
+ 7-day transfer intervals to generate a collection of Brachypodium-derived RCC. It is not one fixed consortium
+ of the ten listed representative taxa. The abiotic selection treatments are experimental inputs, not direct
+ evidence that species partition niches or reduce competition.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- biological_processes:
- - preferred_term: biological process involved in interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
downstream:
- target: Carbon-Source ASV Sorting
- description: >
- The 768 enrichments crossed rhizosphere inocula with root-exudate carbon
- substrates, allowing carbon chemistry to sort enriched ASVs.
- - target: Transfer-Interval Growth-Rate Sorting
- description: >
- The same enrichment design used serial 3-day and 7-day transfers to
- separate ASVs favored by fast and slow subculture intervals.
+ description: Changing the supplied carbon condition alters the ASV composition of enrichment cultures, with
+ inoculum source accounted for in comparisons. This experimentally imposed selection does not demonstrate reciprocal
+ niche partitioning or consumption of distinct substrates by each named organism.
+ - target: Transfer-interval ASV abundance classification
+ description: Changing serial-transfer interval alters which ASVs are relatively enriched at later generations.
+ The resulting 3-day/7-day abundance classification is a response to the transfer regime, not a direct per-ASV
+ growth-rate measurement.
evidence:
- reference: PMID:38846575
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- We enriched co-localized microbes from Brachypodium roots grown in field
- soil with carbon substrates mimicking Brachypodium root exudates
- explanation: >
- Supports using Brachypodium rhizosphere inocula and root-exudate-like
- substrates to seed the RCC enrichment design.
+ snippet: 'We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates
+ mimicking Brachypodium root exudates
+
+ '
+ explanation: 'Supports using Brachypodium rhizosphere inocula and root-exudate-like substrates to seed the RCC
+ enrichment design.
+
+ '
- reference: PMID:38846575
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- Thereafter, plates were transferred 10 times at two different intervals,
- 3 days and 7 days for targeting fast and slow growing microbes.
- explanation: >
- Supports the two serial-transfer regimes used to enrich fast- and
- slow-growing reduced-complexity consortia.
+ snippet: 'Thereafter, plates were transferred 10 times at two different intervals, 3 days and 7 days for targeting
+ fast and slow growing microbes.
+
+ '
+ explanation: 'Supports the two serial-transfer regimes used to enrich fast- and slow-growing reduced-complexity
+ consortia.
+
+ '
- name: Carbon-Source ASV Sorting
- description: >
- Carbon substrate choice imposed a measurable selection on the enrichment
- communities: 1/10 R2A gave the broadest ASV enrichment and repeatedly
- selected Terriglobus and Arthrobacter, while asparagine selected
- Bradyrhizobium and a related rhizobial clade.
+ description: Carbon amendments selected different ASVs in inoculum-stratified comparisons. Complex 1/10 R2A supported
+ broad enrichment including Terriglobus and Arthrobacter; asparagine enriched Bradyrhizobium and a related rhizobial
+ clade. The listed participants are representative named taxa, not all enriched ASVs. These relative-abundance
+ changes do not isolate substrate consumption, microbial cooperation or reduced competition as their mechanism.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
participating_taxa:
- preferred_term: Terriglobus
term:
@@ -378,48 +373,27 @@ ecological_interactions:
- reference: PMID:38846575
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- 1/10 R2A had the highest potential to enrich ASVs compared to other
- carbon sources
- explanation: >
- Supports 1/10 R2A as the high-diversity complex-carbon condition used for
- deeper network analysis.
+ snippet: '1/10 R2A had the highest potential to enrich ASVs compared to other carbon sources
+
+ '
+ explanation: 'Supports 1/10 R2A as the high-diversity complex-carbon condition used for deeper network analysis.
+
+ '
- reference: PMID:38846575
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- significantly enriched ASVs from genera Bradyrhizobium and
- Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium
+ snippet: 'significantly enriched ASVs from genera Bradyrhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium
+
+ '
explanation: Supports Bradyrhizobium enrichment in asparagine-amended RCC.
-- name: Transfer-Interval Growth-Rate Sorting
- description: >
- Later transfer generations were analyzed by 3-day versus 7-day interval,
- categorizing ASVs enriched at 3 days as fast growers and those enriched at
- 7 days as slow growers; 1/10 R2A, asparagine, and glucuronic acid best
- retained both growth-rate classes.
+- name: Transfer-interval ASV abundance classification
+ description: For a fixed carbon source and original inoculum, ASVs more abundant after 7-day transfers than 3-day
+ transfers were called slow growers, and the converse were called fast growers. The comparison used generations
+ 6 and 9. These are operational relative-abundance classes, not measured isolate growth rates; transfer duration
+ also changes other ecological conditions. The reported capacity of 1/10 R2A, asparagine and glucuronic acid
+ to enrich both classes is retained. Network-hub genera are not substituted for the set of ASVs in this differential-abundance
+ analysis.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- participating_taxa:
- - preferred_term: Methylobacterium
- term:
- id: NCBITaxon:407
- label: Methylobacterium
- - preferred_term: Stenotrophomonas
- term:
- id: NCBITaxon:40323
- label: Stenotrophomonas
- - preferred_term: Pseudomonas
- term:
- id: NCBITaxon:286
- label: Pseudomonas
- - preferred_term: Terriglobus
- term:
- id: NCBITaxon:392733
- label: Terriglobus
- - preferred_term: Arthrobacter
- term:
- id: NCBITaxon:1667
- label: Arthrobacter sp.
biological_processes:
- preferred_term: growth
term:
@@ -429,29 +403,30 @@ ecological_interactions:
- reference: PMID:38846575
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- microbes significantly more abundant in 7-day interval samples compared
- to 3-day interval samples were categorized as
- explanation: >
- Supports the 7-day versus 3-day comparison used to classify slow- and
- fast-growing ASVs.
+ snippet: 'microbes significantly more abundant in 7-day interval samples compared to 3-day interval samples
+ were categorized as
+
+ '
+ explanation: 'Supports the 7-day versus 3-day comparison used to classify slow- and fast-growing ASVs.
+
+ '
- reference: PMID:38846575
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- 1/10 R2A medium, along with asparagine and glucuronic acid, demonstrated
- the greatest capability to enrich both slow and fast-growing microbes
- explanation: >
- Supports the substrate set that best retained both transfer-interval
- growth classes.
-- name: Growth-Rate Hub Network Divergence
- description: >
- NetCoMi analysis of 1/10 R2A core ASVs produced distinct 3-day and 7-day
- association networks: Methylobacterium-Methylorubrum, Stenotrophomonas,
- and Pseudomonas were hubs after 3-day transfers, whereas Terriglobus and
- Arthrobacter were hubs after 7-day transfers.
+ snippet: '1/10 R2A medium, along with asparagine and glucuronic acid, demonstrated the greatest capability to
+ enrich both slow and fast-growing microbes
+
+ '
+ explanation: 'Supports the substrate set that best retained both transfer-interval growth classes.
+
+ '
+- name: Transfer-interval association-network hubs
+ description: NetCoMi Pearson-correlation analysis of core ASVs in the 1/10 R2A enrichments identified different
+ high-eigenvector-centrality hubs in 3-day and 7-day networks. The named taxa are representative reported hubs,
+ including the Methylobacterium-Methylorubrum source clade, not an exhaustive community roster. Association centrality
+ does not establish ecological niche partitioning, directly measured growth rate, keystone necessity or plant-growth
+ promotion by those ASVs.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
participating_taxa:
- preferred_term: Methylobacterium
term:
@@ -473,36 +448,37 @@ ecological_interactions:
term:
id: NCBITaxon:1667
label: Arthrobacter sp.
- biological_processes:
- - preferred_term: biological process involved in interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
evidence:
- reference: PMID:38846575
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- ASVs belong to genus Methylobacterium-Methylorubrum, Stenotrophomonas,
- Pseudomonas are hubs for 3-day interval transfers
- explanation: >
- Supports the Methylobacterium-Methylorubrum, Stenotrophomonas, and
- Pseudomonas hubs in the 3-day 1/10 R2A network.
+ evidence_source: COMPUTATIONAL
+ snippet: 'ASVs belong to genus Methylobacterium-Methylorubrum, Stenotrophomonas, Pseudomonas are hubs for 3-day
+ interval transfers
+
+ '
+ explanation: Reports association-network hubs; centrality is not experimental evidence of an ecological mechanism
+ or necessity.
- reference: PMID:38846575
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- ASVs from family Rhizobiaceae, genus Lactobacillus, Terriglobus, and
- Arthrobacter are hubs for 7-day interval transfers
- explanation: Supports the Terriglobus and Arthrobacter hubs in the 7-day 1/10 R2A network.
-- name: Generational Keystone Persistence
- description: >
- Network comparisons across adjacent generations retained recurring hubs,
- including Paenibacillus, Sphingomonas, Mucilaginibacter, and Terriglobus,
- indicating that several low-abundance taxa stayed central after repeated
- passaging.
+ evidence_source: COMPUTATIONAL
+ snippet: 'ASVs from family Rhizobiaceae, genus Lactobacillus, Terriglobus, and Arthrobacter are hubs for 7-day
+ interval transfers
+
+ '
+ explanation: Reports association-network hubs; centrality is not experimental evidence of an ecological mechanism
+ or necessity.
+ - reference: PMID:38846575
+ supports: SUPPORT
+ evidence_source: COMPUTATIONAL
+ snippet: The hub node (keystone taxa) is identified if the node’s eigenvector centrality value is above the
+ 90% quantile.
+ explanation: Defines the statistical hub criterion rather than a biological loss-of-function criterion.
+- name: Recurring association-network hubs
+ description: Adjacent-generation network comparisons identified recurring hub taxa, including Paenibacillus, Sphingomonas,
+ Mucilaginibacter and Terriglobus. This is persistence of a statistical hub designation across sampled transfers,
+ not a taxon-removal test of community stability or direct measurement of niche partitioning. Inferred importance
+ and PGP traits known for related genera are not validated functions of every enriched ASV.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
participating_taxa:
- preferred_term: Paenibacillus
term:
@@ -520,35 +496,24 @@ ecological_interactions:
term:
id: NCBITaxon:392733
label: Terriglobus
- biological_processes:
- - preferred_term: biological process involved in interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
evidence:
- reference: PMID:38846575
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- certain keystone species, including members of the Rhizobiaceae family
- and the genera Paenibacillus, Sphingomonas, Mucilaginibacter, and
- Terriglobus, were consistent across multiple generations
- explanation: >
- Supports persistence of Paenibacillus, Sphingomonas, Mucilaginibacter,
- and Terriglobus as recurring hubs over sequential transfers.
+ evidence_source: COMPUTATIONAL
+ snippet: 'certain keystone species, including members of the Rhizobiaceae family and the genera Paenibacillus,
+ Sphingomonas, Mucilaginibacter, and Terriglobus, were consistent across multiple generations
+
+ '
+ explanation: Reports association-network hubs; centrality is not experimental evidence of an ecological mechanism
+ or necessity.
- name: 1/10 R2A Glycerol Stock Revival
- description: >
- Five 1/10 R2A RCC glycerol stocks from 3-day and 7-day transfers were
- thawed, serially propagated, and resequenced, producing stable dominant
- genera and a revived-stock network in which Burkholderia remained a shared
- hub for both transfer intervals.
+ description: Five selected 1/10 R2A RCC stocks were revived and serially propagated, with broadly consistent dominant
+ genera and relative abundances in those tests. This does not establish universal revival of all initial enrichments,
+ exact strain-level identity, or retention of every rare taxon. Burkholderia and Mesorhizobium were shared statistical
+ hubs in the revived-stock networks, not demonstrated causes of revival. The original broad 1/10 R2A enrichments
+ were less stable than most other carbon arms; that result is distinct from stability of these five selected
+ stocks.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- participating_taxa:
- - preferred_term: Burkholderia
- term:
- id: NCBITaxon:32008
- label: Burkholderia
biological_processes:
- preferred_term: growth
term:
@@ -558,19 +523,21 @@ ecological_interactions:
- reference: PMID:38846575
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- dominant genera from the glycerol stocks (>0.5% in at least one sample)
- and their relative abundances remained consistent between transfers
- explanation: >
- Supports stability of the genera recovered during serial propagation from
- frozen 1/10 R2A glycerol stocks.
+ snippet: 'dominant genera from the glycerol stocks (>0.5% in at least one sample) and their relative abundances
+ remained consistent between transfers
+
+ '
+ explanation: 'Supports stability of the genera recovered during serial propagation from frozen 1/10 R2A glycerol
+ stocks.
+
+ '
- reference: PMID:38846575
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- Genus Burkholderia and Mesorhizobium were shared keystone taxa among
- 3-day and 7-day intervals
- explanation: Supports Burkholderia as a shared hub in revived-stock network analysis.
+ evidence_source: COMPUTATIONAL
+ snippet: 'Genus Burkholderia and Mesorhizobium were shared keystone taxa among 3-day and 7-day intervals
+
+ '
+ explanation: Shared hubs of revived-stock association networks, not experimentally necessary revival partners.
environmental_factors:
- name: Carbon Substrate
value: glucose, glucuronic acid, glutamine, asparagine, 1/10 R2A
@@ -648,8 +615,40 @@ curation_history:
- timestamp: '2026-10-02T06:04:09Z'
curator: codex
action: REPAIR_CAUSAL_GRAPH
- changes: Removed five mCAFEs network-analysis or revival workflow edges from
- carbon-source, transfer-interval, hub-network, and generational-keystone
- nodes, while retaining enrichment edges where carbon source and transfer
+ changes: Removed five mCAFEs network-analysis or revival workflow edges from carbon-source, transfer-interval,
+ hub-network, and generational-keystone nodes, while retaining enrichment edges where carbon source and transfer
interval were the selection pressures.
llm_assisted: true
+- timestamp: '2026-10-08T13:32:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain the abiotic enrichment design and its two selection arrows without asserting niche partitioning.;
+ Preserve carbon-associated ASV sorting with representative participants and no inferred substrate flux.; Define
+ fast/slow as operational abundance classes rather than growth-rate measurements or hub membership.; Keep transfer-specific
+ hubs computational and distinguish centrality from ecological necessity.; Keep recurring hubs as statistical
+ observations without assigning validated PGP or stability function.; Retain reproducible revival only for the
+ five selected stocks and separate it from initial enrichment stability. Issue#1925; reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
+ llm_assisted: true
+discussions:
+- discussion_id: mcafes_causal_graph_scope_batch119
+ prompt: Which inferred RCC hubs have experimentally necessary ecological functions beyond association centrality?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Root Exudate-Mimicking Enrichment Assembly
+ - ecological_interactions#Carbon-Source ASV Sorting
+ - ecological_interactions#Transfer-interval ASV abundance classification
+ - ecological_interactions#Transfer-interval association-network hubs
+ - ecological_interactions#Recurring association-network hubs
+ - ecological_interactions#1/10 R2A Glycerol Stock Revival
+ rationale: The study manipulates carbon conditions and transfer intervals and directly tests selected-stock revival,
+ but hub identity is assigned from correlation and eigenvector centrality. Taxon-removal/rescue, direct growth
+ measurements and strain-resolved functional tests are needed before asserting niche partitioning, causal stabilization
+ or PGP activity. The source represents multiple enrichments and selected stocks, not a single fixed ten-member
+ community.
+ evidence:
+ - reference: PMID:38846575
+ snippet: The hub node (keystone taxa) is identified if the node’s eigenvector centrality value is above the
+ 90% quantile.
+ posed_by: codex
+ posed_date: '2026-10-08'
diff --git a/references_cache/PMID_35435700.md b/references_cache/PMID_35435700.md
index 5e9beb477..9378e6107 100644
--- a/references_cache/PMID_35435700.md
+++ b/references_cache/PMID_35435700.md
@@ -85,4 +85,18 @@ PMCID: PMC9239112
PMID: 35435700 [Indexed for MEDLINE]
Conflict of interest statement: The authors declare a conflict of interest. J.H.
-holds equity in Wacasa, Inc.
\ No newline at end of file
+holds equity in Wacasa, Inc.
+
+## Source-Checked Excerpts (2026-10-08, Causal Review Batch119)
+
+Selected quotations from the primary article (PMID:35435700): https://pmc.ncbi.nlm.nih.gov/articles/PMC9239112/
+License: Creative Commons Attribution 4.0 (CC BY 4.0), as stated in the article XML.
+Retrieved through Europe PMC; only these bounded excerpts are appended. The existing cache prefix and metadata are preserved.
+
+> the growth of P. koreensis and B. cereus was not affected by coculture
+
+> Bacillus cereus UW85 (B), Flavobacterium johnsoniae UW101 (F), Pseudomonas koreensis CI12 (P)
+
+> likely a combination of direct effects from koreenceine and indirect effects due to slower growth rate of F. johnsoniae in the presence of an antibiotic
+
+> P. koreensis reduced growth of F. johnsoniae when they were grown as a pair, but F. johnsoniae abundance was higher when B. cereus was also present
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 0cff7f593..55fbde5f5 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,40 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch119: Strain Identity And Inferred Networks
+
+[Decisions](decisions/20261008-four-records-batch119.yaml),
+[provenance](cache-provenance-20261008-batch119.json),
+[validation](validation-20261008-batch119.json), and
+[self-adversarial review](adversarial-review-20261008-batch119.yaml) cover
+THOR, TYQ1, teosinte biofertilization and mCAFEs RCC. Seventeen of twenty
+nodes and all ten existing arrows remain, with nine renames and no new topology.
+
+THOR separates the founding CI04 biofilm result from the UW101 population
+and transcription experiments. TYQ1 retains seven positive biofilm pairings,
+medium-specific spent-medium utilization and biological omission evidence,
+without treating them as selective tests of the mechanism of protection.
+Teosinte retains reported field-treatment effects but removes two preparation
+nodes. Its soil association network does not establish microbial mutualism.
+mCAFEs retains experimental enrichment selection and revival of five selected
+stocks; abundance classes and network hubs are not direct growth measurements
+or demonstrations of ecological necessity.
+
+Five complete primary main-body XML texts, including methods, tables and
+captions, were reviewed. Original figure pixels, supplements, raw data and
+analysis code were not audited. All 43 graph/discussion quotations match
+the primary texts and caches. Four missing, licensed excerpts were appended
+to one THOR cache without modifying its prefix; 922 caches are unchanged.
+Four guarded writes and append-only histories preserve unrelated raw fields
+and 456 other records. One participant-list user is added. Moving THOR protection
+to a three-member scope raises sole community-level credit by one, to 1281 taxa;
+record-scope counts, connectivity logic and thresholds are unchanged.
+
+Repairs #1922-#1925 await protected-main merge. Non-graph strain, composition,
+design and metadata follow-ups #1926-#1929 remain open. No Edison extension
+or spend was required. This is self-review, not independent approval or
+completion of the overall review.
+
## Batch118: Treatment Identity And Modeled Mechanisms
[Decisions](decisions/20261008-four-records-batch118.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch119.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch119.yaml
new file mode 100644
index 000000000..a6b3681e9
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch119.yaml
@@ -0,0 +1,455 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 97c48512fb91a69598093e9d097e84341ffdfae0
+scope:
+- kb/communities/THOR_Rhizosphere_Model_Community.yaml
+- kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml
+- kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml
+- kb/communities/mCAFEs_Brachypodium_RCC.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch119.json
+findings:
+- issue: 1922
+ severity: P2
+ finding: Separate THOR strain variants and antibiotic effects in causal graph
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1923
+ severity: P2
+ finding: Bound TYQ1 biofilm and cross-feeding mediation to the actual assays
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1924
+ severity: P2
+ finding: Separate teosinte formulation workflow and soil associations from ecological mechanisms
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1925
+ severity: P2
+ finding: Separate mCAFEs enrichment selection from inferred growth and network mechanisms
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1926
+ severity: P2
+ finding: Reconcile THOR non-graph strain origin and cultivation across the two studies
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1927
+ severity: P2
+ finding: Review TYQ1 non-graph strain evidence and AF functional-role assignment
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1928
+ severity: P2
+ finding: Resolve the seven teosinte inoculant strains and source-design ambiguities
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1929
+ severity: P2
+ finding: Reconcile mCAFEs collection metadata with condition-specific ASVs
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+adversarial_checks:
+- All20original nodes/10arrows accounted for:17nodes/10arrows retained,three nodes removed,nine renames,no new topology.
+ Targets and discussion anchors resolve; no shortcut edge invented.
+- THOR2022Methods explicitly identify UW101,not founding CI04. Keep UW101 inhibition,locus-dependent expression
+ and three-member protection. One-sided inhibition is not bilateral competition. Expression percentages describe
+ greater-than-twofold pairwise DEGs,not whole genomes. CI04 biofilm stays positive contextual evidence,not a UW101
+ node; chemical mediation remains PARTIAL.
+- TYQ1 retains all seven positive biofilm pairings with the SX attraction exception. Cross-feeding is medium- and
+ direction-specific,with the AS reverse-use exception and rich-medium negative result. Carrying-capacity weights
+ are not flux. Real strain omission remains positive experimental evidence,distinct from Gephi node removal; specific
+ biofilm/exchange mediation remains PARTIAL.
+- Teosinte formulation/preparation nodes removed while non-graph protocol remains. Reported field-treatment effects
+ and both treatment arrows retained; no field-statistics reproduction claimed. Soil relative abundance does not
+ track inoculant strains. Bacillus centrality is computational correlation,not microbial mutualism,measured nitrogen
+ fixation or necessary function.
+- mCAFEs is multiple enrichment communities. Carbon and transfer-interval interventions retain two selection arrows.
+ Fast/slow is an operational abundance comparison,not measured isolate growth rates. Hub membership is not growth-class
+ membership. Statistical hubs are not experimental keystones or validated PGP functions. Positive revival is bounded
+ to five selected stocks,not all initial enrichments.
+- Thirty-eight graph and five discussion quotes match five fresh primary texts and caches. Five complete main-body
+ XML texts read,including methods,tables and captions; no original pixels,supplements,raw data or analysis-code
+ audit. Matching is not entailment certification. One CC-BY4.0 cache receives four missing selected excerpts append-only,not
+ a full-body import.
+- Four guarded writes and append-only histories preserve456otherrecords,922caches,unrelated raw blocks and previous
+ histories/decisions. Canonical taxon identities/ranks unchanged; source-identity limitations remain separate issues1926-1929.
+ Shared evidence aliases detached before edits.
+- Fifteen focused tests and twelve control/mutation/restored-control probes pass. Mutations reject bilateral competition,unbounded
+ molecular mediation,CI04-to-UW101 transfer,erasure of positive biofilm/cross-feeding/omission evidence,unmeasured
+ nitrogen fixation,experimental hub necessity,loss of observed selection and universal stock revival. No canonical
+ writes during probes.
+- All four records pass schema,strict,terms,full-record references,snippets,rank and history.1116selected tests
+ including palette pass; not full Linux CI certification. Network57unchanged warnings,zero structural defects.456pages/1361nodes/523arrows
+ exactly match descriptions with deterministic rendering,not screenshot QA.
+- Participant-list users rise298to299 for THOR protection. Record-scope census remains414community-level,136mixed,278community-only,1568taxa;
+ sole credit rises1280to1281 because Bacillus leaves the incorrect pairwise node and is named in three-member protection.
+ Initial verifier expectation corrected after inspecting this delta; no graph or threshold changed to pass. Scope
+ credit is not actual participant coverage. Connectivity logic and all thresholds unchanged.
+- Issues1922-1925 addressed pending protected-main merge;1926-1929 remain open. No Edison extension or credits.
+ Prior Ruegeria1883 still needs configured authentication and was not retried unchanged. Self-adversarial review
+ is not independent approval; root1836 and real exact-head protected checks remain required.
+- Corpus384reviewed,22pending,54needs_research across460records. Overall goal,protected merge and branch deletion
+ incomplete. Postcommit docs-current and exact-head publication are separate gates,not preasserted here.
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Turn one-sided inhibition into bilateral competition
+ test: test_thor_inhibition_is_locus_dependent_not_bilateral_competition
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 21
+ assertion: assert "UW101" in node["name"] and "interaction_type" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/interaction_type
+ before: null
+ after: COMPETITION
+ - mutation: Promote indirect expression route to demonstrated mechanism
+ test: test_thor_expression_retains_the_correct_denominator_and_indirect_limit
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 33
+ assertion: assert expression["evidence"][1]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/1/evidence/1/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Promote CI04 metabolite result to UW101 proof
+ test: test_thor_protection_has_three_participants_and_variant_bounded_chemistry
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 49
+ assertion: assert protection["evidence"][1]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/2/evidence/1/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Erase positive CI04 biofilm contextual evidence
+ test: test_thor_ci04_biofilm_is_context_not_a_uw101_node
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 64
+ assertion: assert "increased the maximum biofilm" in discussion["evidence"][1]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/discussions/0/evidence/1/snippet
+ before: F. johnsoniae CI04 and B. cereus UW85 each increased the maximum biofilm formed by P. koreensis
+ CI12 at 18 h
+ after: No biofilm enhancement was observed.
+ - mutation: Type seven biofilm pairings as demonstrated mutualism
+ test: test_tyq1_seven_positive_biofilms_do_not_erase_the_sx_attraction_exception
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 70
+ assertion: assert "interaction_type" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/1/interaction_type
+ before: null
+ after: MUTUALISM
+ - mutation: Erase experimentally measured cross-feeding
+ test: test_tyq1_cross_feeding_keeps_medium_direction_and_as_limits
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 79
+ assertion: assert node["interaction_type"] == "CROSS_FEEDING"
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/2/interaction_type
+ before: CROSS_FEEDING
+ after: COMPETITION
+ - mutation: Erase biological omission evidence
+ test: test_tyq1_biological_omission_is_positive_but_not_specific_mediation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 92
+ assertion: assert "lost its inhibitory function" in nodes[3]["evidence"][1]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/3/evidence/1/snippet
+ before: The -TYQ1 not only lost its inhibitory function but even had the opposite effect, facilitating the
+ formation of egg masses on the roots.
+ after: Only computational node removal was performed.
+ - mutation: Add nitrogen fixation to field outcome as measured process
+ test: test_teosinte_field_effects_remain_without_claiming_nitrogen_flux
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 117
+ assertion: assert {p["term"]["id"] for p in outcome["biological_processes"]} == {"GO:0040007"}
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/1/biological_processes
+ before:
+ - preferred_term: growth
+ term:
+ id: GO:0040007
+ label: growth
+ after:
+ - preferred_term: growth
+ term:
+ id: GO:0040007
+ label: growth
+ - preferred_term: nitrogen fixation
+ term:
+ id: GO:0009399
+ label: nitrogen fixation
+ - mutation: Make soil network experimentally necessary
+ test: test_teosinte_soil_association_network_is_not_mutualism_or_necessity
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 127
+ assertion: assert all(e["evidence_source"] == "COMPUTATIONAL" for e in network["evidence"])
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/3/evidence/0/evidence_source
+ before: COMPUTATIONAL
+ after: IN_VIVO
+ - path: records/2/ecological_interactions/3/evidence/0/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Remove observed carbon selection arrow
+ test: test_mcafes_selection_keeps_both_experimental_directions
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 137
+ assertion: assert [e["target"] for e in nodes[0]["downstream"]] == [nodes[1]["name"], nodes[2]["name"]]
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/0/downstream
+ before:
+ - target: Carbon-Source ASV Sorting
+ description: Changing the supplied carbon condition alters the ASV composition of enrichment cultures,
+ with inoculum source accounted for in comparisons. This experimentally imposed selection does not demonstrate
+ reciprocal niche partitioning or consumption of distinct substrates by each named organism.
+ - target: Transfer-interval ASV abundance classification
+ description: Changing serial-transfer interval alters which ASVs are relatively enriched at later generations.
+ The resulting 3-day/7-day abundance classification is a response to the transfer regime, not a direct
+ per-ASV growth-rate measurement.
+ after:
+ - target: Transfer-interval ASV abundance classification
+ description: Changing serial-transfer interval alters which ASVs are relatively enriched at later generations.
+ The resulting 3-day/7-day abundance classification is a response to the transfer regime, not a direct
+ per-ASV growth-rate measurement.
+ - mutation: Treat hubs as experimentally validated functions
+ test: test_mcafes_hubs_are_computational_not_necessary_ecological_functions
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 154
+ assertion: assert all(e["evidence_source"] == "COMPUTATIONAL" for e in node["evidence"])
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/3/evidence/0/evidence_source
+ before: COMPUTATIONAL
+ after: IN_VITRO
+ - mutation: Generalize selected stock revival to all enrichments
+ test: test_mcafes_revival_is_positive_for_five_selected_stocks_only
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 164
+ assertion: assert "Five selected" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/5/description
+ before: Five selected 1/10 R2A RCC stocks were revived and serially propagated, with broadly consistent
+ dominant genera and relative abundances in those tests. This does not establish universal revival of all
+ initial enrichments, exact strain-level identity, or retention of every rare taxon. Burkholderia and Mesorhizobium
+ were shared statistical hubs in the revived-stock networks, not demonstrated causes of revival. The original
+ broad 1/10 R2A enrichments were less stable than most other carbon arms; that result is distinct from
+ stability of these five selected stocks.
+ after: All initial enrichments reliably revive with identical strains.
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/THOR_Rhizosphere_Model_Community.yaml: 1d75a279b70b1ece18d4453f8576a849996e712bfb2f4a0ea9542db2f22f0dca
+ kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml: a5c33db18b80a233099b80289b173c8c57e1420ced3a4f282ef99bb9100d0f11
+ kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml: d2b51e34f56530cb2992a40d195eae0f2395925e9d4f39b135d77a8822309320
+ kb/communities/mCAFEs_Brachypodium_RCC.yaml: 273500dc8bec3a1e35cea5c32a9ac77be1c36ed5f5d01cd5f7861dfe65e40ecb
+ tests/test_causal_review_batch119.py: f917f104f5b09dd7a98dcd9cf967a44962b410e6722443ec880e29c1d55cdc14
+ probe_script_sha256: fbc84b7f0fc2ef9204e3904a1fc979a7a6a321b28df216e584594c64cca10c82
+ scope: In-memory control/mutation/restored-control; no canonical writes and not additional pytest tests.
+ artifact: /private/tmp/communitymech-batch119/adversarial-regression-proof.json
+ sha256: cd359f8889bf6a33044eb920ecddf5b75c1d61344fa5c8fb1580667fb62ac60b
+verification:
+ combined_regressions: 1116 passed in 319.85s (0:05:19)
+ new_regression_tests: 15
+ total_recorded_gate_outputs: 41
+ primary_graph_snippet_proof:
+ graph_quotations: 38
+ discussion_quotations: 5
+ fresh_primary_literal_matches: 43
+ all_cached_literal_matches: 43
+ retained_nodes: 17
+ removed_nodes: 3
+ renamed_nodes: 9
+ retained_arrows: 10
+ removed_arrows: 0
+ new_nodes_or_directions: 0
+ references: Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment.
+ Total checks in the reference CLI counts issues, not examined snippets.
+ snippet_counts_by_record:
+ kb/communities/THOR_Rhizosphere_Model_Community.yaml:
+ MATCH: 22
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml:
+ MATCH: 27
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml:
+ MATCH: 18
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/mCAFEs_Brachypodium_RCC.yaml:
+ MATCH: 30
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9046
+ categories:
+ MATCH: 8901
+ RENDERING: 28
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 76
+ caveat: Informational audit exit0 is not clean-corpus or entailment certification.
+ network:
+ existing_findings_preserved: 57
+ added_findings: {}
+ removed_findings: {}
+ structural_defects: 0
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml: f8bdcb0de3409627788a931ea8c49717dfd9aeba50fb061fde838f6d7b67b955
+ tests/test_causal_review_batch119.py: f917f104f5b09dd7a98dcd9cf967a44962b410e6722443ec880e29c1d55cdc14
+ tests/test_participating_taxa.py: f438815b4a028c0f38a077df53c95f685f98b3c2b523593896a124b544269db1
+ tests/test_community_level_connectivity_credit.py: 996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a
+ tests/test_causal_review_batch109.py: ff8e9e26771545e1ace22b3c1d42076789c99cc4bc83e588b6a4b9ad698d3d73
+ tests/test_datamodel.py: f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25
+ reports/causal_graph_review/cache-provenance-20261008-batch119.json: c01b47ab2bb142eb1db61e7faaf5572da929325e7fae67b6a4a36477582b2a61
+ kb/communities/THOR_Rhizosphere_Model_Community.yaml: 1d75a279b70b1ece18d4453f8576a849996e712bfb2f4a0ea9542db2f22f0dca
+ kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml: a5c33db18b80a233099b80289b173c8c57e1420ced3a4f282ef99bb9100d0f11
+ kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml: d2b51e34f56530cb2992a40d195eae0f2395925e9d4f39b135d77a8822309320
+ kb/communities/mCAFEs_Brachypodium_RCC.yaml: 273500dc8bec3a1e35cea5c32a9ac77be1c36ed5f5d01cd5f7861dfe65e40ecb
+ history_sha256:
+ history/records/THOR_Rhizosphere_Model_Community/2026-10-08T133242Z-codex-305b58.yaml: 2480f0818833def1bb635a521d667c088bf839e57bfcad1d39bb23fe02d02251
+ history/records/TYQ1_Nematode_Biocontrol_SynCom/2026-10-08T133242Z-codex-3eb620.yaml: 20e31ff610de2b9debc0b70dc8ee07cc7b080d0dbcda146cc8a667d7f8c61909
+ history/records/Teosinte_Maize_Biofertilizer_SynCom7/2026-10-08T133243Z-codex-d993e7.yaml: 20fe9cfb9998648207189fbbfd22179d0cb0fde878b2a1b687ba3118c9cdbc9f
+ history/records/mCAFEs_Brachypodium_RCC/2026-10-08T133243Z-codex-458ed6.yaml: 90c1165340e252e704af5065e62ae0260c27e74dc3bb66fcbb30e3acc0c4bacb
+ unchanged_records: 456
+ unchanged_caches: 922
+ immutable_prior_history_and_decision_files: 884
+ cache_changes:
+ - path: references_cache/PMID_35435700.md
+ before_sha256: 93e63a122d58bca129dd8bf1b30d76d8ff6ef8dfbd55c62022a646c4329b4015
+ after_sha256: 4c801186b23c80af1db7a38872e597f00d709a7406768fcece1dd640c1bbf7eb
+ original_bytes: 4401
+ added_bytes: 868
+ quotations:
+ - the growth of P. koreensis and B. cereus was not affected by coculture
+ - Bacillus cereus UW85 (B), Flavobacterium johnsoniae UW101 (F), Pseudomonas koreensis CI12 (P)
+ - likely a combination of direct effects from koreenceine and indirect effects due to slower growth rate of
+ F. johnsoniae in the presence of an antibiotic
+ - P. koreensis reduced growth of F. johnsoniae when they were grown as a pair, but F. johnsoniae abundance was
+ higher when B. cereus was also present
+ primary_artifact: /private/tmp/communitymech-batch119/thor_transcript-primary.txt
+ primary_sha256: b9a9f6c077c7d82c95f3f3fe393c68986aa2765d614c95361f3b1e036b7e4362
+ source_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC9239112/
+ license: CC BY 4.0
+ license_url: https://creativecommons.org/licenses/by/4.0/
+ scope: Append-only selected literal excerpts; not full-paper import or entailment certification.
+ edison:
+ required_for_this_repair: false
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior approved invocation;
+ no unchanged-state retry.'
+ post_commit_docs_current: Separate publication gate,not preasserted.
+participant_census:
+ current:
+ records: 460
+ with_community_level: 414
+ mixed: 136
+ community_level_only: 278
+ taxa: 1568
+ credited_solely_by_the_rule: 1281
+ delta_from_batch118:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 1
+ explanation: One explicit participant-list user added for THOR three-member protection;299total. Bacillus cereus
+ UW85 leaves the incorrectly assigned pairwise protection node and is explicitly named in the three-member node.
+ Sole-credit rises1280to1281; record-scope counts remain unchanged. Sole-credit does not certify actual participant
+ coverage. Connectivity logic and thresholds are unchanged.
+corpus:
+ records: 460
+ nodes: 1375
+ edges: 531
+ review_status_counts:
+ needs_research: 54
+ pending: 22
+ reviewed: 384
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary established Python3.13 lint environment; project dependencies unchanged.
+limitations:
+- Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects.
+ All20existing nodes/10arrows reviewed across four whole records. Retain17nodes/10arrows,remove three nodes,rename
+ nine,no new topology.
+- Five fresh EuropePMC abstracts and Crossref identities checked; all five complete main-body XML texts read including
+ methods/results/discussion,table text and captions. No original figure pixels,separate supplementary files,raw
+ data or analysis code audited. Literal matching is not entailment proof.
+- THOR founding study uses CI04,whereas2022Methods explicitly name UW101. Keep UW101 inhibition,expression and protection;
+ CI04 biofilm remains contextual discussion,not a UW101 node. CI04 accumulation and spo0H results only partially
+ support UW101 chemical mediation. Non-graph strain/cultivation reconciliation remains1926.
+- TYQ1 positive pairwise biofilm,medium-specific filtrate assays and actual biological omission retained. SX attraction
+ and AS reverse-use exceptions preserved. Fitted network weights and in-silico node removal are not measured flux
+ or biological omission. Root mechanism mediation remains PARTIAL; metadata/AF-role follow-up1927.
+- Teosinte field-treatment effects retained as reported,not independently reproduced statistics. Two formulation-workflow
+ nodes removed while preparation remains in non-graph fields. Relative abundance and correlation centrality do
+ not establish mutualism,nitrogen flux or necessary inoculant strains. Seven-strain roster and source-design ambiguities
+ remain1928.
+- mCAFEs is a collection of enrichments,not a fixed ten-member consortium. Keep carbon/transfer selection arrows,operational
+ abundance classes,computational hubs and revival of five selected stocks. No niche-partitioning or keystone-necessity
+ claim. Metadata/carbon-arm reconciliation remains1929.
+- Fresh all-state1160issue titles/bodies searched initially; pre-creation receipt records fresh count. Matching1288/615/497/258/25/14/12
+ bodies read and distinct. Hidden/ignored-inclusive local search found130paths excluding.git,docs,site,references_cache,.env;
+ not a historical PR-comment audit.
+- Four guarded writes preserve456otherrecords,922unchanged caches,unrelated raw YAML blocks,all prior histories/decisions.
+ One CC-BY4.0 cache gains four source-checked selected excerpts append-only; no whole-body import. Four append-only
+ record histories and curation events. Taxon identities unchanged; shared evidence aliases detached.
+- 'Existing-graph repair with no new nodes/directions: no Edison run,provider submission or credit spend. Prior
+ authorized Ruegeria1883 authentication blocker not retried without state change; no credential inspected. Self-adversarial
+ review is not independent approval. Overall review,protected merge and branch deletion remain incomplete.'
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch119.json b/reports/causal_graph_review/cache-provenance-20261008-batch119.json
new file mode 100644
index 000000000..1099d6be9
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch119.json
@@ -0,0 +1,367 @@
+{
+ "changes": [
+ {
+ "path": "references_cache/PMID_35435700.md",
+ "before_sha256": "93e63a122d58bca129dd8bf1b30d76d8ff6ef8dfbd55c62022a646c4329b4015",
+ "after_sha256": "4c801186b23c80af1db7a38872e597f00d709a7406768fcece1dd640c1bbf7eb",
+ "original_bytes": 4401,
+ "added_bytes": 868,
+ "quotations": [
+ "the growth of P. koreensis and B. cereus was not affected by coculture",
+ "Bacillus cereus UW85 (B), Flavobacterium johnsoniae UW101 (F), Pseudomonas koreensis CI12 (P)",
+ "likely a combination of direct effects from koreenceine and indirect effects due to slower growth rate of F. johnsoniae in the presence of an antibiotic",
+ "P. koreensis reduced growth of F. johnsoniae when they were grown as a pair, but F. johnsoniae abundance was higher when B. cereus was also present"
+ ],
+ "primary_artifact": "/private/tmp/communitymech-batch119/thor_transcript-primary.txt",
+ "primary_sha256": "b9a9f6c077c7d82c95f3f3fe393c68986aa2765d614c95361f3b1e036b7e4362",
+ "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9239112/",
+ "license": "CC BY 4.0",
+ "license_url": "https://creativecommons.org/licenses/by/4.0/",
+ "scope": "Append-only selected literal excerpts; not full-paper import or entailment certification."
+ }
+ ],
+ "unchanged_cache_files": 922,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch119/baseline.json": "934b2a66a6b4e2cf32378820bd0efe6b83a7142153311829380e666d53aad95e",
+ "/private/tmp/communitymech-batch119/issue-dedup-current.json": "91f16ad7a8d31aeff13fc90fec776d75c34d41e504da9a02099a49d5047a5165",
+ "/private/tmp/communitymech-batch119/local-matches.txt": "1627b5ca8314f11f2a8a0a3ca75375267ed14b8e8ce221bc94d804897eeb502a",
+ "/private/tmp/communitymech-batch119/mcafes-abstract.txt": "6f85720d27f17a0ced0fd9e52a8894dec9766183c9893864b74df941d8d2a1f7",
+ "/private/tmp/communitymech-batch119/mcafes-crossref.json": "0330f6d22e37bdf969b9c91ecbecc189c49a617c7a82f16070297cf2d3ca8895",
+ "/private/tmp/communitymech-batch119/mcafes-metadata.json": "ab966255aecd2c7e11e2a4c3b522f45a87f8f7576364d23176b2326693d4b947",
+ "/private/tmp/communitymech-batch119/mcafes-primary.txt": "100f2538d83ba8340a4597d94bc350f347f23b8a8022a8b440745c02441de746",
+ "/private/tmp/communitymech-batch119/mcafes-primary.xml": "0251515379b4dc8a1a35f8714b48ee5d689f848ffd2a6690f0d7d13b3385f691",
+ "/private/tmp/communitymech-batch119/primary-manifest.json": "383d8c776bb085916976b3fbbb8cec84f081c6c6846abda0dac4b681fe3b513e",
+ "/private/tmp/communitymech-batch119/target-baseline.json": "6b57cc3e1330f058d16bb21d3491d609eafad0002035dac8d2b0eb0a0ab5846c",
+ "/private/tmp/communitymech-batch119/teosinte-abstract.txt": "1786cb570a19790190afbb711b3a59d7d67e638b3bdb31503ce95fa6ab665978",
+ "/private/tmp/communitymech-batch119/teosinte-crossref.json": "afe27f2fdb9ca088e53c13253f103d4a37c2b6483b6b1a217b5b218cdac72d89",
+ "/private/tmp/communitymech-batch119/teosinte-metadata.json": "92e515c4f9d6920b311ca8bb4d4a03421ff688d560bc3714179cb009cadd56dc",
+ "/private/tmp/communitymech-batch119/teosinte-primary.txt": "9429a36c9a2f5aba42cca117de33b6e84d038b0d140fe2b360ccc49529f21a63",
+ "/private/tmp/communitymech-batch119/teosinte-primary.xml": "16952d1a74ea4f4c32b18738c1ae81002b5afb8a963570af976ca19f9c21494e",
+ "/private/tmp/communitymech-batch119/thor-abstract.txt": "aba0a9eb50423bb6b946b6967d8af78458d08c08554c5b17aee0338321020188",
+ "/private/tmp/communitymech-batch119/thor-crossref.json": "f40bc596050e40dd6d86c7fda159a1a734aaae3110c8f25f723228ec7202aedd",
+ "/private/tmp/communitymech-batch119/thor-metadata.json": "1bd54c130797ed4e39c3cfffa7811a8249141d10d58ae25f6114b665bf758513",
+ "/private/tmp/communitymech-batch119/thor-primary.txt": "19977f829c30cd8e501768b69217b49b9adfdcb07c388b70824b340da22c5e24",
+ "/private/tmp/communitymech-batch119/thor-primary.xml": "c663e5119014062be939d6f25a3f31434f5bfbbc7e5c7acbfd062592bc8711ef",
+ "/private/tmp/communitymech-batch119/thor_transcript-abstract.txt": "53539b846730e3982b83ea8a50b09e9c3e5a58ac6b230afea51cbef8d6c4553a",
+ "/private/tmp/communitymech-batch119/thor_transcript-crossref.json": "162f8f635424cc0debbd549d79a47e11f0f80f0b1e84ffc9ac92ad3f1ce91ed4",
+ "/private/tmp/communitymech-batch119/thor_transcript-metadata.json": "f65ac38bab962e8778365530766cbc8f6ca5c29d77500c637e7fc784156acbf0",
+ "/private/tmp/communitymech-batch119/thor_transcript-primary.txt": "b9a9f6c077c7d82c95f3f3fe393c68986aa2765d614c95361f3b1e036b7e4362",
+ "/private/tmp/communitymech-batch119/thor_transcript-primary.xml": "1bad9ec1b49b84443f7e8124afdd6088e7c453d914ce8558e532db3d42cd151b",
+ "/private/tmp/communitymech-batch119/tyq1-abstract.txt": "12dbff0f276f4b4ac7171ad8211ed026e242e26666640cc21f32fe815bb15876",
+ "/private/tmp/communitymech-batch119/tyq1-crossref.json": "d7c14368903ca8af9dcfb12ade9faaed2e23c7719d530509d2f4aae89e9ebea2",
+ "/private/tmp/communitymech-batch119/tyq1-metadata.json": "d8677749fe15356890bf0925f4cddd846b2353cbb6989abf59ff0257a906fc0f",
+ "/private/tmp/communitymech-batch119/tyq1-primary.txt": "eb456f3033f2233ac13f686b54d3c9b34c221b290d0ecae000fcd9d9f1acd160",
+ "/private/tmp/communitymech-batch119/tyq1-primary.xml": "2b7f977d7da5531e3f1a4fa4a1c2b5a81aeb2f5b5baccc0ac43da4ba675be828",
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+ "references_cache/PMID_38846575.md": "4f1536ee5dab23901310db1fb06bfaccedc8d89ba2ae92cb92399a7a60ef8603",
+ "references_cache/PMID_40270813.txt": "4d5eb9bba8bc7d0e92212075395581a151e5580d95c59f71ec0dec87874cdba0",
+ "references_cache/PMID_41660888.md": "1500925aca34ba63cb4d76d3d4d8fdcdc0f038555eaeb4528600119e390e164c"
+ },
+ "source_access": {
+ "retrieval_manifest": {
+ "thor": {
+ "pmid": "30837345",
+ "doi": "10.1128/mbio.02846-18",
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+ "THOR founding study uses CI04,whereas2022Methods explicitly name UW101. Keep UW101 inhibition,expression and protection; CI04 biofilm remains contextual discussion,not a UW101 node. CI04 accumulation and spo0H results only partially support UW101 chemical mediation. Non-graph strain/cultivation reconciliation remains1926.",
+ "TYQ1 positive pairwise biofilm,medium-specific filtrate assays and actual biological omission retained. SX attraction and AS reverse-use exceptions preserved. Fitted network weights and in-silico node removal are not measured flux or biological omission. Root mechanism mediation remains PARTIAL; metadata/AF-role follow-up1927.",
+ "Teosinte field-treatment effects retained as reported,not independently reproduced statistics. Two formulation-workflow nodes removed while preparation remains in non-graph fields. Relative abundance and correlation centrality do not establish mutualism,nitrogen flux or necessary inoculant strains. Seven-strain roster and source-design ambiguities remain1928.",
+ "mCAFEs is a collection of enrichments,not a fixed ten-member consortium. Keep carbon/transfer selection arrows,operational abundance classes,computational hubs and revival of five selected stocks. No niche-partitioning or keystone-necessity claim. Metadata/carbon-arm reconciliation remains1929.",
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+ "TYQ1 positive pairwise biofilm,medium-specific filtrate assays and actual biological omission retained. SX attraction and AS reverse-use exceptions preserved. Fitted network weights and in-silico node removal are not measured flux or biological omission. Root mechanism mediation remains PARTIAL; metadata/AF-role follow-up1927.",
+ "Teosinte field-treatment effects retained as reported,not independently reproduced statistics. Two formulation-workflow nodes removed while preparation remains in non-graph fields. Relative abundance and correlation centrality do not establish mutualism,nitrogen flux or necessary inoculant strains. Seven-strain roster and source-design ambiguities remain1928.",
+ "mCAFEs is a collection of enrichments,not a fixed ten-member consortium. Keep carbon/transfer selection arrows,operational abundance classes,computational hubs and revival of five selected stocks. No niche-partitioning or keystone-necessity claim. Metadata/carbon-arm reconciliation remains1929.",
+ "Fresh all-state1160issue titles/bodies searched initially; pre-creation receipt records fresh count. Matching1288/615/497/258/25/14/12 bodies read and distinct. Hidden/ignored-inclusive local search found130paths excluding.git,docs,site,references_cache,.env; not a historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,922unchanged caches,unrelated raw YAML blocks,all prior histories/decisions. One CC-BY4.0 cache gains four source-checked selected excerpts append-only; no whole-body import. Four append-only record histories and curation events. Taxon identities unchanged; shared evidence aliases detached.",
+ "Existing-graph repair with no new nodes/directions: no Edison run,provider submission or credit spend. Prior authorized Ruegeria1883 authentication blocker not retried without state change; no credential inspected. Self-adversarial review is not independent approval. Overall review,protected merge and branch deletion remain incomplete."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
new file mode 100644
index 000000000..082c34528
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
@@ -0,0 +1,1115 @@
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+pre_source_baseline_sha256: 934b2a66a6b4e2cf32378820bd0efe6b83a7142153311829380e666d53aad95e
+issues:
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+- 1923
+- 1924
+- 1925
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+- 1927
+- 1928
+- 1929
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+ content-version: vor
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+ URL: https://creativecommons.org/licenses/by/4.0/
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+ doi: 10.3389/fmicb.2025.1534327
+ pmcid: PMC12015678
+ title: Teosinte-derived SynCom and precision biofertilization modulate the maize microbiome, enhancing growth,
+ yield, and soil functionality in a Mexican field.
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+ status: retrieved
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+ status: retrieved_not_yet_read
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+ and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance
+ with accepted academic practice. No use, distribution or reproduction is permitted which does not comply
+ with these terms.
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+ doi: 10.3389/fmicb.2024.1401794
+ pmcid: PMC11153752
+ title: Developing stable, simplified, functional consortia from <i>Brachypodium</i> rhizosphere
+ for microbial application in sustainable agriculture.
+ metadata: /private/tmp/communitymech-batch119/mcafes-metadata.json
+ metadata_sha256: ab966255aecd2c7e11e2a4c3b522f45a87f8f7576364d23176b2326693d4b947
+ retrievals:
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+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11153752/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch119/mcafes-abstract.txt
+ abstract_sha256: 6f85720d27f17a0ced0fd9e52a8894dec9766183c9893864b74df941d8d2a1f7
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+ license:
+ - https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of
+ the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums
+ is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original
+ publication in this journal is cited, in accordance with accepted academic practice. No use, distribution
+ or reproduction is permitted which does not comply with these terms.
+ crossref: /private/tmp/communitymech-batch119/mcafes-crossref.json
+ crossref_sha256: 0330f6d22e37bdf969b9c91ecbecc189c49a617c7a82f16070297cf2d3ca8895
+ crossref_license:
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+ timestamp: 1716422400000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0/
+ thor_transcript:
+ pmid: '35435700'
+ doi: 10.1128/mbio.02486-21
+ pmcid: PMC9239112
+ title: 'THOR''s Hammer: the Antibiotic Koreenceine Drives Gene Expression in a Model Microbial Community.'
+ metadata: /private/tmp/communitymech-batch119/thor_transcript-metadata.json
+ metadata_sha256: f65ac38bab962e8778365530766cbc8f6ca5c29d77500c637e7fc784156acbf0
+ retrievals:
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+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9239112/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch119/thor_transcript-abstract.txt
+ abstract_sha256: 53539b846730e3982b83ea8a50b09e9c3e5a58ac6b230afea51cbef8d6c4553a
+ xml: /private/tmp/communitymech-batch119/thor_transcript-primary.xml
+ xml_sha256: 1bad9ec1b49b84443f7e8124afdd6088e7c453d914ce8558e532db3d42cd151b
+ primary_text: /private/tmp/communitymech-batch119/thor_transcript-primary.txt
+ primary_text_sha256: b9a9f6c077c7d82c95f3f3fe393c68986aa2765d614c95361f3b1e036b7e4362
+ license:
+ - 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.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ - https://creativecommons.org/licenses/by/4.0/This content is distributed under the terms of the Creative
+ Commons Attribution 4.0 International license.
+ crossref: /private/tmp/communitymech-batch119/thor_transcript-crossref.json
+ crossref_sha256: 162f8f635424cc0debbd549d79a47e11f0f80f0b1e84ffc9ac92ad3f1ce91ed4
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2022
+ - 6
+ - 28
+ date-time: '2022-06-28T00:00:00Z'
+ timestamp: 1656374400000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0/
+ - start:
+ date-parts:
+ - - 2022
+ - 6
+ - 28
+ date-time: '2022-06-28T00:00:00Z'
+ timestamp: 1656374400000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://journals.asm.org/non-commercial-tdm-license
+ actual_read_scope:
+ - Five fresh EuropePMC abstracts and Crossref identities checked; all five complete main-body XML texts read including
+ methods/results/discussion,table text and captions. No original figure pixels,separate supplementary files,raw
+ data or analysis code audited. Literal matching is not entailment proof.
+ - THOR founding study uses CI04,whereas2022Methods explicitly name UW101. Keep UW101 inhibition,expression and
+ protection; CI04 biofilm remains contextual discussion,not a UW101 node. CI04 accumulation and spo0H results
+ only partially support UW101 chemical mediation. Non-graph strain/cultivation reconciliation remains1926.
+ - TYQ1 positive pairwise biofilm,medium-specific filtrate assays and actual biological omission retained. SX attraction
+ and AS reverse-use exceptions preserved. Fitted network weights and in-silico node removal are not measured
+ flux or biological omission. Root mechanism mediation remains PARTIAL; metadata/AF-role follow-up1927.
+ - Teosinte field-treatment effects retained as reported,not independently reproduced statistics. Two formulation-workflow
+ nodes removed while preparation remains in non-graph fields. Relative abundance and correlation centrality do
+ not establish mutualism,nitrogen flux or necessary inoculant strains. Seven-strain roster and source-design
+ ambiguities remain1928.
+ - mCAFEs is a collection of enrichments,not a fixed ten-member consortium. Keep carbon/transfer selection arrows,operational
+ abundance classes,computational hubs and revival of five selected stocks. No niche-partitioning or keystone-necessity
+ claim. Metadata/carbon-arm reconciliation remains1929.
+ - Fresh all-state1160issue titles/bodies searched initially; pre-creation receipt records fresh count. Matching1288/615/497/258/25/14/12
+ bodies read and distinct. Hidden/ignored-inclusive local search found130paths excluding.git,docs,site,references_cache,.env;
+ not a historical PR-comment audit.
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+ matched_artifact: /private/tmp/communitymech-batch119/thor_transcript-primary.txt
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+ matched_artifact: /private/tmp/communitymech-batch119/thor_transcript-primary.txt
+ cache_artifact: references_cache/PMID_35435700.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: THOR_Rhizosphere_Model_Community
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+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/thor_transcript-primary.txt
+ cache_artifact: references_cache/PMID_35435700.md
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+ scope: Normalized contiguous literal match, not entailment proof.
+- record: TYQ1_Nematode_Biocontrol_SynCom
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+ reference: PMID:40270813
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/teosinte-primary.txt
+ cache_artifact: references_cache/PMID_40270813.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Teosinte_Maize_Biofertilizer_SynCom7
+ node: Biofertilizer-Linked Soil and Yield Response
+ evidence_index: 1
+ reference: PMID:40270813
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/teosinte-primary.txt
+ cache_artifact: references_cache/PMID_40270813.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Teosinte_Maize_Biofertilizer_SynCom7
+ node: Treatment-associated soil microbiome shifts
+ evidence_index: 0
+ reference: PMID:40270813
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/teosinte-primary.txt
+ cache_artifact: references_cache/PMID_40270813.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Teosinte_Maize_Biofertilizer_SynCom7
+ node: Treatment-associated soil microbiome shifts
+ evidence_index: 1
+ reference: PMID:40270813
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/teosinte-primary.txt
+ cache_artifact: references_cache/PMID_40270813.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Teosinte_Maize_Biofertilizer_SynCom7
+ node: Statistical Bacillus-centered soil association network
+ evidence_index: 0
+ reference: PMID:40270813
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/teosinte-primary.txt
+ cache_artifact: references_cache/PMID_40270813.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Teosinte_Maize_Biofertilizer_SynCom7
+ node: Statistical Bacillus-centered soil association network
+ evidence_index: 1
+ reference: PMID:40270813
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/teosinte-primary.txt
+ cache_artifact: references_cache/PMID_40270813.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Teosinte_Maize_Biofertilizer_SynCom7
+ node: Statistical Bacillus-centered soil association network
+ evidence_index: 2
+ reference: PMID:40270813
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/teosinte-primary.txt
+ cache_artifact: references_cache/PMID_40270813.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Root Exudate-Mimicking Enrichment Assembly
+ evidence_index: 0
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Root Exudate-Mimicking Enrichment Assembly
+ evidence_index: 1
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Carbon-Source ASV Sorting
+ evidence_index: 0
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Carbon-Source ASV Sorting
+ evidence_index: 1
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Transfer-interval ASV abundance classification
+ evidence_index: 0
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Transfer-interval ASV abundance classification
+ evidence_index: 1
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Transfer-interval association-network hubs
+ evidence_index: 0
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Transfer-interval association-network hubs
+ evidence_index: 1
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Transfer-interval association-network hubs
+ evidence_index: 2
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: Recurring association-network hubs
+ evidence_index: 0
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: 1/10 R2A Glycerol Stock Revival
+ evidence_index: 0
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: 1/10 R2A Glycerol Stock Revival
+ evidence_index: 1
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+discussion_snippet_checks:
+- record: THOR_Rhizosphere_Model_Community
+ node: thor_causal_graph_scope_batch119
+ evidence_index: 0
+ reference: PMID:35435700
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/thor_transcript-primary.txt
+ cache_artifact: references_cache/PMID_35435700.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: THOR_Rhizosphere_Model_Community
+ node: thor_causal_graph_scope_batch119
+ evidence_index: 1
+ reference: PMID:30837345
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/thor-primary.txt
+ cache_artifact: references_cache/PMID_30837345.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: TYQ1_Nematode_Biocontrol_SynCom
+ node: tyq1_causal_graph_scope_batch119
+ evidence_index: 0
+ reference: PMID:41660888
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/tyq1-primary.txt
+ cache_artifact: references_cache/PMID_41660888.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Teosinte_Maize_Biofertilizer_SynCom7
+ node: teosinte_causal_graph_scope_batch119
+ evidence_index: 0
+ reference: PMID:40270813
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/teosinte-primary.txt
+ cache_artifact: references_cache/PMID_40270813.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: mCAFEs_Brachypodium_RCC
+ node: mcafes_causal_graph_scope_batch119
+ evidence_index: 0
+ reference: PMID:38846575
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch119/mcafes-primary.txt
+ cache_artifact: references_cache/PMID_38846575.md
+ scope: Normalized contiguous literal match, not entailment proof.
+cache_changes:
+- path: references_cache/PMID_35435700.md
+ before_sha256: 93e63a122d58bca129dd8bf1b30d76d8ff6ef8dfbd55c62022a646c4329b4015
+ after_sha256: 4c801186b23c80af1db7a38872e597f00d709a7406768fcece1dd640c1bbf7eb
+ original_bytes: 4401
+ added_bytes: 868
+ quotations:
+ - the growth of P. koreensis and B. cereus was not affected by coculture
+ - Bacillus cereus UW85 (B), Flavobacterium johnsoniae UW101 (F), Pseudomonas koreensis CI12 (P)
+ - likely a combination of direct effects from koreenceine and indirect effects due to slower growth rate of F.
+ johnsoniae in the presence of an antibiotic
+ - P. koreensis reduced growth of F. johnsoniae when they were grown as a pair, but F. johnsoniae abundance was
+ higher when B. cereus was also present
+ primary_artifact: /private/tmp/communitymech-batch119/thor_transcript-primary.txt
+ primary_sha256: b9a9f6c077c7d82c95f3f3fe393c68986aa2765d614c95361f3b1e036b7e4362
+ source_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC9239112/
+ license: CC BY 4.0
+ license_url: https://creativecommons.org/licenses/by/4.0/
+ scope: Append-only selected literal excerpts; not full-paper import or entailment certification.
+edison:
+ required_for_this_repair: false
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior approved invocation; no
+ unchanged-state retry.'
+limitations:
+- Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects.
+ All20existing nodes/10arrows reviewed across four whole records. Retain17nodes/10arrows,remove three nodes,rename
+ nine,no new topology.
+- Five fresh EuropePMC abstracts and Crossref identities checked; all five complete main-body XML texts read including
+ methods/results/discussion,table text and captions. No original figure pixels,separate supplementary files,raw
+ data or analysis code audited. Literal matching is not entailment proof.
+- THOR founding study uses CI04,whereas2022Methods explicitly name UW101. Keep UW101 inhibition,expression and protection;
+ CI04 biofilm remains contextual discussion,not a UW101 node. CI04 accumulation and spo0H results only partially
+ support UW101 chemical mediation. Non-graph strain/cultivation reconciliation remains1926.
+- TYQ1 positive pairwise biofilm,medium-specific filtrate assays and actual biological omission retained. SX attraction
+ and AS reverse-use exceptions preserved. Fitted network weights and in-silico node removal are not measured flux
+ or biological omission. Root mechanism mediation remains PARTIAL; metadata/AF-role follow-up1927.
+- Teosinte field-treatment effects retained as reported,not independently reproduced statistics. Two formulation-workflow
+ nodes removed while preparation remains in non-graph fields. Relative abundance and correlation centrality do
+ not establish mutualism,nitrogen flux or necessary inoculant strains. Seven-strain roster and source-design ambiguities
+ remain1928.
+- mCAFEs is a collection of enrichments,not a fixed ten-member consortium. Keep carbon/transfer selection arrows,operational
+ abundance classes,computational hubs and revival of five selected stocks. No niche-partitioning or keystone-necessity
+ claim. Metadata/carbon-arm reconciliation remains1929.
+- Fresh all-state1160issue titles/bodies searched initially; pre-creation receipt records fresh count. Matching1288/615/497/258/25/14/12
+ bodies read and distinct. Hidden/ignored-inclusive local search found130paths excluding.git,docs,site,references_cache,.env;
+ not a historical PR-comment audit.
+- Four guarded writes preserve456otherrecords,922unchanged caches,unrelated raw YAML blocks,all prior histories/decisions.
+ One CC-BY4.0 cache gains four source-checked selected excerpts append-only; no whole-body import. Four append-only
+ record histories and curation events. Taxon identities unchanged; shared evidence aliases detached.
+- 'Existing-graph repair with no new nodes/directions: no Edison run,provider submission or credit spend. Prior
+ authorized Ruegeria1883 authentication blocker not retried without state change; no credential inspected. Self-adversarial
+ review is not independent approval. Overall review,protected merge and branch deletion remain incomplete.'
+records:
+- path: kb/communities/THOR_Rhizosphere_Model_Community.yaml
+ id: CommunityMech:000079
+ original_sha256: ec95272c2b0ded1ac096cd9e9a53509ae052e7316d4c88b9ef51ceefb58b9f71
+ record_sha256: 1d75a279b70b1ece18d4453f8576a849996e712bfb2f4a0ea9542db2f22f0dca
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain locus-dependent UW101 inhibition without asserting bilateral fitness harm.; Retain experimental
+ transcriptional dependence with correct denominators and direct/indirect limits.; Retain UW101 protection with
+ all three participants, while bounding the CI04 chemical mechanism.
+ node_decisions:
+ - node: Koreenceine production and UW101 growth inhibition
+ rationale: Retain locus-dependent UW101 inhibition without asserting bilateral fitness harm.
+ - node: Koreenceine-Driven Transcriptional Regulation
+ rationale: Retain experimental transcriptional dependence with correct denominators and direct/indirect limits.
+ - node: Bacillus protection in the UW101 THOR community
+ rationale: Retain UW101 protection with all three participants, while bounding the CI04 chemical mechanism.
+ removed_node_decisions:
+ - node: Emergent Three-Member Biofilm Formation
+ rationale: The direct biofilm-persistence experiment used CI04, whereas this record names UW101. Preserve the
+ positive CI04 result as contextual discussion, not an asserted UW101 node.
+ renamed_nodes:
+ Koreenceine-Mediated Inhibition: Koreenceine production and UW101 growth inhibition
+ Bacillus Modulation of Pseudomonas Antibiotic Production: Bacillus protection in the UW101 THOR community
+ edges_before:
+ - &id001
+ source: Koreenceine-Mediated Inhibition
+ target: Koreenceine-Driven Transcriptional Regulation
+ description: 'Pseudomonas koreensis koreenceine production drives most Flavobacterium johnsoniae and part of
+ the Bacillus cereus transcriptional response to pairwise encounter with P. koreensis.
+
+ '
+ - &id003
+ source: Bacillus Modulation of Pseudomonas Antibiotic Production
+ target: Koreenceine-Mediated Inhibition
+ description: Bacillus suppression of Pseudomonas koreenceine production changes the antibiotic-mediated inhibition
+ that P. koreensis exerts on F. johnsoniae.
+ edges_after:
+ - &id002
+ source: Koreenceine production and UW101 growth inhibition
+ target: Koreenceine-Driven Transcriptional Regulation
+ description: 'The wild-type versus koreenceine-locus-deletion comparison supports koreenceine-dependent gene
+ regulation in UW101 and B. cereus. PARTIAL for the direct molecular route: antibiotic exposure and indirect
+ physiological effects can both contribute. This arrow starts from koreenceine production, not an assumption
+ that reduced UW101 growth causes all transcriptional changes or that B. cereus growth is inhibited.'
+ - &id004
+ source: Bacillus protection in the UW101 THOR community
+ target: Koreenceine production and UW101 growth inhibition
+ description: 'B. cereus addition reduces the population inhibition of UW101 in the three-member assay. PARTIAL
+ for mediation by altered koreenceine accumulation: the detailed metabolite and spo0H comparisons were performed
+ with CI04, not UW101, and do not uniquely demonstrate a biosynthesis-suppression mechanism in the UW101 community.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: 'The wild-type versus koreenceine-locus-deletion comparison supports koreenceine-dependent gene regulation
+ in UW101 and B. cereus. PARTIAL for the direct molecular route: antibiotic exposure and indirect physiological
+ effects can both contribute. This arrow starts from koreenceine production, not an assumption that reduced
+ UW101 growth causes all transcriptional changes or that B. cereus growth is inhibited.'
+ - before: *id003
+ after: *id004
+ rationale: 'B. cereus addition reduces the population inhibition of UW101 in the three-member assay. PARTIAL
+ for mediation by altered koreenceine accumulation: the detailed metabolite and spo0H comparisons were performed
+ with CI04, not UW101, and do not uniquely demonstrate a biosynthesis-suppression mechanism in the UW101 community.'
+ removed_edge_decisions: []
+ references:
+ - PMID:30837345
+ - PMID:35435700
+ issues:
+ - 1922
+ - 1926
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/THOR_Rhizosphere_Model_Community/2026-10-08T133242Z-codex-305b58.yaml
+- path: kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml
+ id: CommunityMech:000072
+ original_sha256: 01cbb6970852dad836fce77b480e680a086b088a5ad488aeedfd4788e96f64dc
+ record_sha256: a5c33db18b80a233099b80289b173c8c57e1420ced3a4f282ef99bb9100d0f11
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Separate TYQ1 inoculation from nematode-driven enrichment and avoid assigning mutualism from abundance.;
+ Retain all seven positive biofilm pairings with the SX attraction exception and in-vitro provenance.; Retain
+ measured spent-medium cross-feeding with AS, medium, direction and network-weight limits.; Retain biological
+ omission and host-outcome evidence without overclaiming the specific mediator.
+ node_decisions:
+ - node: Keystone-Mediated Community Recruitment
+ rationale: Separate TYQ1 inoculation from nematode-driven enrichment and avoid assigning mutualism from abundance.
+ - node: TYQ1-partner biofilm enhancement
+ rationale: Retain all seven positive biofilm pairings with the SX attraction exception and in-vitro provenance.
+ - node: Condition-dependent TYQ1 spent-medium cross-feeding
+ rationale: Retain measured spent-medium cross-feeding with AS, medium, direction and network-weight limits.
+ - node: Synergistic Nematode Suppression
+ rationale: Retain biological omission and host-outcome evidence without overclaiming the specific mediator.
+ removed_node_decisions: []
+ renamed_nodes:
+ Synergistic Biofilm Formation: TYQ1-partner biofilm enhancement
+ Metabolic Cross-Feeding Network: Condition-dependent TYQ1 spent-medium cross-feeding
+ edges_before:
+ - &id005
+ source: Keystone-Mediated Community Recruitment
+ target: Synergistic Biofilm Formation
+ description: TYQ1-mediated recruitment enriches the biomarker species that, in collaboration with TYQ1, increase
+ the community's biofilm-forming ability.
+ - &id007
+ source: Keystone-Mediated Community Recruitment
+ target: Metabolic Cross-Feeding Network
+ description: TYQ1-mediated recruitment enriches the biomarker species that establish a tightly interconnected
+ metabolic interaction network centered on TYQ1.
+ - &id009
+ source: Synergistic Biofilm Formation
+ target: Synergistic Nematode Suppression
+ description: The enhanced biofilm-forming ability of the recruited eight-member consortium strengthens rhizosphere
+ colonization of TYQ1 and contributes to stable root-knot nematode inhibition.
+ - &id011
+ source: Metabolic Cross-Feeding Network
+ target: Synergistic Nematode Suppression
+ description: TYQ1-centered metabolic exchanges help organize the recruited beneficial strains into the high-efficacy
+ network required for stable root-knot nematode suppression.
+ edges_after:
+ - &id006
+ source: Keystone-Mediated Community Recruitment
+ target: TYQ1-partner biofilm enhancement
+ description: 'PARTIAL: TYQ1 inoculation enriches the pool of partners whose reconstructed pairings enhance biofilm
+ in vitro. This supports a recruitment-to-biofilm hypothesis across the linked assays, not direct measurement
+ of biofilm mediation in the root community.'
+ - &id008
+ source: Keystone-Mediated Community Recruitment
+ target: Condition-dependent TYQ1 spent-medium cross-feeding
+ description: 'PARTIAL: TYQ1-driven partner enrichment provides members with experimentally demonstrated spent-medium
+ utilization. The reconstructed laboratory network does not establish that the same directional fluxes occur
+ in situ after recruitment.'
+ - &id010
+ source: TYQ1-partner biofilm enhancement
+ target: Synergistic Nematode Suppression
+ description: 'PARTIAL: increased biofilm may support the observed transient increase in TYQ1 root colonization
+ and contribute to suppression. The study does not selectively disrupt biofilm while preserving other TYQ1
+ and partner functions, so mediation remains unresolved.'
+ - &id012
+ source: Condition-dependent TYQ1 spent-medium cross-feeding
+ target: Synergistic Nematode Suppression
+ description: 'PARTIAL: assayed exchange capacity may support the community that improves nematode suppression.
+ Biological TYQ1 omission and diversity gradients support its community contribution, but neither isolate exchange
+ from direct nematicidal activity, biofilm effects or host responses. In-silico node removal is not that biological
+ test.'
+ retained_edge_decisions:
+ - before: *id005
+ after: *id006
+ rationale: 'PARTIAL: TYQ1 inoculation enriches the pool of partners whose reconstructed pairings enhance biofilm
+ in vitro. This supports a recruitment-to-biofilm hypothesis across the linked assays, not direct measurement
+ of biofilm mediation in the root community.'
+ - before: *id007
+ after: *id008
+ rationale: 'PARTIAL: TYQ1-driven partner enrichment provides members with experimentally demonstrated spent-medium
+ utilization. The reconstructed laboratory network does not establish that the same directional fluxes occur
+ in situ after recruitment.'
+ - before: *id009
+ after: *id010
+ rationale: 'PARTIAL: increased biofilm may support the observed transient increase in TYQ1 root colonization
+ and contribute to suppression. The study does not selectively disrupt biofilm while preserving other TYQ1
+ and partner functions, so mediation remains unresolved.'
+ - before: *id011
+ after: *id012
+ rationale: 'PARTIAL: assayed exchange capacity may support the community that improves nematode suppression.
+ Biological TYQ1 omission and diversity gradients support its community contribution, but neither isolate exchange
+ from direct nematicidal activity, biofilm effects or host responses. In-silico node removal is not that biological
+ test.'
+ removed_edge_decisions: []
+ references:
+ - PMID:41660888
+ issues:
+ - 1923
+ - 1927
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/TYQ1_Nematode_Biocontrol_SynCom/2026-10-08T133242Z-codex-3eb620.yaml
+- path: kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml
+ id: CommunityMech:000100
+ original_sha256: 1c99ca183a340680a90fcfa14327288bb8dac56f57733c219bc19902dbb5abac
+ record_sha256: d2b51e34f56530cb2992a40d195eae0f2395925e9d4f39b135d77a8822309320
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain the field-treatment input with correct evidence source and unresolved timing boundary.; Retain
+ reported agronomic outcomes without typing host benefit as microbial mutualism or measured nitrogen fixation.;
+ Keep soil relative-abundance responses separate from inoculant establishment and absolute growth.; Represent
+ Bacillus centrality as computational association, not validated ecological function or necessity.
+ node_decisions:
+ - node: Four-Stage Maize Biofertilization
+ rationale: Retain the field-treatment input with correct evidence source and unresolved timing boundary.
+ - node: Biofertilizer-Linked Soil and Yield Response
+ rationale: Retain reported agronomic outcomes without typing host benefit as microbial mutualism or measured
+ nitrogen fixation.
+ - node: Treatment-associated soil microbiome shifts
+ rationale: Keep soil relative-abundance responses separate from inoculant establishment and absolute growth.
+ - node: Statistical Bacillus-centered soil association network
+ rationale: Represent Bacillus centrality as computational association, not validated ecological function or
+ necessity.
+ removed_node_decisions:
+ - node: PGP-Trait SynCom7 Formulation
+ rationale: Strain selection or equal-volume inoculum preparation is workflow, not an ecological interaction.
+ Source-supported preparation remains in engineering_design and growth_media.
+ - node: Equal-Volume Field Inoculum
+ rationale: Strain selection or equal-volume inoculum preparation is workflow, not an ecological interaction.
+ Source-supported preparation remains in engineering_design and growth_media.
+ renamed_nodes:
+ Beneficial-Taxon Soil Microbiome Shift: Treatment-associated soil microbiome shifts
+ Bacillus-Centered Nutrient-Cycling Network: Statistical Bacillus-centered soil association network
+ edges_before:
+ - &id013
+ source: Four-Stage Maize Biofertilization
+ target: Biofertilizer-Linked Soil and Yield Response
+ description: 'Repeated teosinte SynCom delivery drove the measured soil, maize physiology, yield, and disease-protection
+ responses.
+
+ '
+ - &id015
+ source: Four-Stage Maize Biofertilization
+ target: Beneficial-Taxon Soil Microbiome Shift
+ description: 'Repeated teosinte SynCom delivery restructured bacterial and fungal communities over the field
+ season.
+
+ '
+ edges_after:
+ - &id014
+ source: Four-Stage Maize Biofertilization
+ target: Biofertilizer-Linked Soil and Yield Response
+ description: The repeated biofertilizer treatment is the manipulated input compared with control and conventional-fertilizer
+ arms in the reported field design. The resulting agronomic differences support a treatment-level effect, not
+ proof that a particular strain, nitrogen-fixation route or within-consortium mutualism mediated it.
+ - &id016
+ source: Four-Stage Maize Biofertilization
+ target: Treatment-associated soil microbiome shifts
+ description: The biofertilizer application arms produced distinct soil-community profiles across the sampled
+ season. This treatment-to-profile link does not establish absolute taxon growth, tracking of the introduced
+ strains, or causation by the individual edges of the co-occurrence network.
+ retained_edge_decisions:
+ - before: *id013
+ after: *id014
+ rationale: The repeated biofertilizer treatment is the manipulated input compared with control and conventional-fertilizer
+ arms in the reported field design. The resulting agronomic differences support a treatment-level effect, not
+ proof that a particular strain, nitrogen-fixation route or within-consortium mutualism mediated it.
+ - before: *id015
+ after: *id016
+ rationale: The biofertilizer application arms produced distinct soil-community profiles across the sampled season.
+ This treatment-to-profile link does not establish absolute taxon growth, tracking of the introduced strains,
+ or causation by the individual edges of the co-occurrence network.
+ removed_edge_decisions: []
+ references:
+ - PMID:40270813
+ issues:
+ - 1924
+ - 1928
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Teosinte_Maize_Biofertilizer_SynCom7/2026-10-08T133243Z-codex-d993e7.yaml
+- path: kb/communities/mCAFEs_Brachypodium_RCC.yaml
+ id: CommunityMech:000078
+ original_sha256: 6ebcd44301ad777dedee863d8542f6efea0ebba9dbe290e2df4a2da7fc368f8d
+ record_sha256: 273500dc8bec3a1e35cea5c32a9ac77be1c36ed5f5d01cd5f7861dfe65e40ecb
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain the abiotic enrichment design and its two selection arrows without asserting niche partitioning.;
+ Preserve carbon-associated ASV sorting with representative participants and no inferred substrate flux.; Define
+ fast/slow as operational abundance classes rather than growth-rate measurements or hub membership.; Keep transfer-specific
+ hubs computational and distinguish centrality from ecological necessity.; Keep recurring hubs as statistical
+ observations without assigning validated PGP or stability function.; Retain reproducible revival only for the
+ five selected stocks and separate it from initial enrichment stability.
+ node_decisions:
+ - node: Root Exudate-Mimicking Enrichment Assembly
+ rationale: Retain the abiotic enrichment design and its two selection arrows without asserting niche partitioning.
+ - node: Carbon-Source ASV Sorting
+ rationale: Preserve carbon-associated ASV sorting with representative participants and no inferred substrate
+ flux.
+ - node: Transfer-interval ASV abundance classification
+ rationale: Define fast/slow as operational abundance classes rather than growth-rate measurements or hub membership.
+ - node: Transfer-interval association-network hubs
+ rationale: Keep transfer-specific hubs computational and distinguish centrality from ecological necessity.
+ - node: Recurring association-network hubs
+ rationale: Keep recurring hubs as statistical observations without assigning validated PGP or stability function.
+ - node: 1/10 R2A Glycerol Stock Revival
+ rationale: Retain reproducible revival only for the five selected stocks and separate it from initial enrichment
+ stability.
+ removed_node_decisions: []
+ renamed_nodes:
+ Transfer-Interval Growth-Rate Sorting: Transfer-interval ASV abundance classification
+ Growth-Rate Hub Network Divergence: Transfer-interval association-network hubs
+ Generational Keystone Persistence: Recurring association-network hubs
+ edges_before:
+ - &id017
+ source: Root Exudate-Mimicking Enrichment Assembly
+ target: Carbon-Source ASV Sorting
+ description: 'The 768 enrichments crossed rhizosphere inocula with root-exudate carbon substrates, allowing
+ carbon chemistry to sort enriched ASVs.
+
+ '
+ - &id019
+ source: Root Exudate-Mimicking Enrichment Assembly
+ target: Transfer-Interval Growth-Rate Sorting
+ description: 'The same enrichment design used serial 3-day and 7-day transfers to separate ASVs favored by fast
+ and slow subculture intervals.
+
+ '
+ edges_after:
+ - &id018
+ source: Root Exudate-Mimicking Enrichment Assembly
+ target: Carbon-Source ASV Sorting
+ description: Changing the supplied carbon condition alters the ASV composition of enrichment cultures, with
+ inoculum source accounted for in comparisons. This experimentally imposed selection does not demonstrate reciprocal
+ niche partitioning or consumption of distinct substrates by each named organism.
+ - &id020
+ source: Root Exudate-Mimicking Enrichment Assembly
+ target: Transfer-interval ASV abundance classification
+ description: Changing serial-transfer interval alters which ASVs are relatively enriched at later generations.
+ The resulting 3-day/7-day abundance classification is a response to the transfer regime, not a direct per-ASV
+ growth-rate measurement.
+ retained_edge_decisions:
+ - before: *id017
+ after: *id018
+ rationale: Changing the supplied carbon condition alters the ASV composition of enrichment cultures, with inoculum
+ source accounted for in comparisons. This experimentally imposed selection does not demonstrate reciprocal
+ niche partitioning or consumption of distinct substrates by each named organism.
+ - before: *id019
+ after: *id020
+ rationale: Changing serial-transfer interval alters which ASVs are relatively enriched at later generations.
+ The resulting 3-day/7-day abundance classification is a response to the transfer regime, not a direct per-ASV
+ growth-rate measurement.
+ removed_edge_decisions: []
+ references:
+ - PMID:38846575
+ issues:
+ - 1925
+ - 1929
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/mCAFEs_Brachypodium_RCC/2026-10-08T133243Z-codex-458ed6.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 3bb2c1893..49409289b 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -415,9 +415,9 @@ kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml CommunityMech:0000
kb/communities/Syntrophus_Benzoate_Degrader.yaml CommunityMech:000071 dffafcca6d385007e70e5d2024cc75f959ad3e442f5f9e27a7bdf145fe8d58d1 3 2 96.7 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml CommunityMech:000187 3584798fce68b6699f57471b38d2a5e7778e154ff5dbbbb63c3f98f92a2f3451 3 2 93.3 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml CommunityMech:000437 0d96313dbd7866dd7d642e83eab9956ff03a6c7f6a867de6ffb91ce1a3796382 2 0 60.0 pending
-kb/communities/THOR_Rhizosphere_Model_Community.yaml CommunityMech:000079 ec95272c2b0ded1ac096cd9e9a53509ae052e7316d4c88b9ef51ceefb58b9f71 4 2 100.0 pending
-kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml CommunityMech:000072 01cbb6970852dad836fce77b480e680a086b088a5ad488aeedfd4788e96f64dc 4 4 100.0 pending
-kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml CommunityMech:000100 1c99ca183a340680a90fcfa14327288bb8dac56f57733c219bc19902dbb5abac 6 2 100.0 pending
+kb/communities/THOR_Rhizosphere_Model_Community.yaml CommunityMech:000079 1d75a279b70b1ece18d4453f8576a849996e712bfb2f4a0ea9542db2f22f0dca 3 2 90.0 reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml reviewed
+kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml CommunityMech:000072 a5c33db18b80a233099b80289b173c8c57e1420ced3a4f282ef99bb9100d0f11 4 4 92.5 reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml reviewed
+kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml CommunityMech:000100 d2b51e34f56530cb2992a40d195eae0f2395925e9d4f39b135d77a8822309320 4 2 87.5 reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml reviewed
kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml CommunityMech:000259 8b79efb0b04a43548b3c73ac280ac987b83c4e97f2531b55da5c940f29485eae 4 2 90.0 reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml reviewed
kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml CommunityMech:000162 f1e51614a8c4a7856a2669afe12574d1c982f12dcebf9f53f49c65d470f747d6 3 0 68.3 reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml needs_research
kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml CommunityMech:000182 f45e52ffbf76a2c295b73efb10bf183a01ecc03056cc11f018afe3c6e3723992 3 2 100.0 reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml reviewed
@@ -458,4 +458,4 @@ kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml Commu
kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml CommunityMech:000164 49f5a5749a60d2f6b314cd487f84c5c6c609d23657faf7342daad53833dc9ec2 4 2 100.0 pending
kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml CommunityMech:000210 5640166eed0e15b269178e292e4e63066adb88cd20d82e65b3dd05938ae49be3 3 2 100.0 pending
kb/communities/hCom2_Complex_Gut_Microbiome.yaml CommunityMech:000123 e707fdc5f03ae9a01cb7a71c7892d093e3211dbb99159cbbd9c57d25f921c036 3 2 100.0 pending
-kb/communities/mCAFEs_Brachypodium_RCC.yaml CommunityMech:000078 6ebcd44301ad777dedee863d8542f6efea0ebba9dbe290e2df4a2da7fc368f8d 6 2 100.0 pending
+kb/communities/mCAFEs_Brachypodium_RCC.yaml CommunityMech:000078 273500dc8bec3a1e35cea5c32a9ac77be1c36ed5f5d01cd5f7861dfe65e40ecb 6 2 87.5 reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml reviewed
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index e2f60da21..b122ffa73 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": 1378,
+ "nodes": 1375,
"edges": 531,
"records_without_nodes": 10,
"records_without_edges": 189,
"review_status_counts": {
"needs_research": 54,
- "pending": 26,
- "reviewed": 380
+ "pending": 22,
+ "reviewed": 384
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch119.json b/reports/causal_graph_review/validation-20261008-batch119.json
new file mode 100644
index 000000000..d7059b965
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch119.json
@@ -0,0 +1,1125 @@
+{
+ "base_commit": "97c48512fb91a69598093e9d097e84341ffdfae0",
+ "scope": [
+ "kb/communities/THOR_Rhizosphere_Model_Community.yaml",
+ "kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml",
+ "kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml",
+ "kb/communities/mCAFEs_Brachypodium_RCC.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch119.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/focused.log",
+ "log_sha256": "8ac47df58727bbf4ebe68b3473faf2500cb1f30fac09881fa6290b6ac6ce96c6",
+ "output_tail": "............... [100%]\n15 passed in 3.82s\n"
+ },
+ {
+ "check": "THOR_Rhizosphere_Model_Community-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/THOR_Rhizosphere_Model_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/THOR_Rhizosphere_Model_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "THOR_Rhizosphere_Model_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch119/THOR_Rhizosphere_Model_Community-strict.tsv",
+ "kb/communities/THOR_Rhizosphere_Model_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/THOR_Rhizosphere_Model_Community-strict.log",
+ "log_sha256": "87f2e494b38e5c3d23506990ef88df238d20c8ce1c2b476c47df4292cb5816c2",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch119/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-batch119/THOR_Rhizosphere_Model_Community-strict.tsv\n"
+ },
+ {
+ "check": "THOR_Rhizosphere_Model_Community-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/THOR_Rhizosphere_Model_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/THOR_Rhizosphere_Model_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "THOR_Rhizosphere_Model_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/THOR_Rhizosphere_Model_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/THOR_Rhizosphere_Model_Community-references.log",
+ "log_sha256": "4d6c07c54007d96a4f78410f2faf43b9ffd0258b6198adeff36ed27134e28682",
+ "output_tail": "Validating kb/communities/THOR_Rhizosphere_Model_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/THOR_Rhizosphere_Model_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": "THOR_Rhizosphere_Model_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/THOR_Rhizosphere_Model_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/THOR_Rhizosphere_Model_Community-snippets.log",
+ "log_sha256": "96a23c88588d68e990af5d62f9c27df12879566b4125e7703a275c3bfa7adcd7",
+ "output_tail": "# 22 evidence snippets scanned across 1 files\n MATCH 22\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": "THOR_Rhizosphere_Model_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/THOR_Rhizosphere_Model_Community.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/THOR_Rhizosphere_Model_Community-rank.log",
+ "log_sha256": "cbfa60cb416b91076fa1a341a290f211bd851cff9f7e3ee736d28f55818fba72",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000079\",\n \"name\": \"THOR Rhizosphere Model Community\",\n \"score\": 90.0,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 7,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/THOR_Rhizosphere_Model_Community.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "THOR_Rhizosphere_Model_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/THOR_Rhizosphere_Model_Community/2026-10-08T133242Z-codex-305b58.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/THOR_Rhizosphere_Model_Community-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "TYQ1_Nematode_Biocontrol_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/TYQ1_Nematode_Biocontrol_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "TYQ1_Nematode_Biocontrol_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch119/TYQ1_Nematode_Biocontrol_SynCom-strict.tsv",
+ "kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/TYQ1_Nematode_Biocontrol_SynCom-strict.log",
+ "log_sha256": "55a883f5e6201abba3ee4a6e833a31604f80cf59a77a6cd4e4b270abed35b741",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch119/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-batch119/TYQ1_Nematode_Biocontrol_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "TYQ1_Nematode_Biocontrol_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/TYQ1_Nematode_Biocontrol_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "TYQ1_Nematode_Biocontrol_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/TYQ1_Nematode_Biocontrol_SynCom-references.log",
+ "log_sha256": "3bafce1776b6086b9ffa4831707255b53842df25d64f96a33d0e32c54a1d5d3a",
+ "output_tail": "Validating kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "TYQ1_Nematode_Biocontrol_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/TYQ1_Nematode_Biocontrol_SynCom-snippets.log",
+ "log_sha256": "c72869c3cfa80d3275b80461e8b721727d9e301213f59836200303704b4482a6",
+ "output_tail": "# 27 evidence snippets scanned across 1 files\n MATCH 27\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": "TYQ1_Nematode_Biocontrol_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/TYQ1_Nematode_Biocontrol_SynCom-rank.log",
+ "log_sha256": "9d4cf7f7a4c5d76ac84935a86d3acd051f8fe5bc7310d8f1fb8e8ad19be106ce",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000072\",\n \"name\": \"TYQ1 Nematode Biocontrol SynCom\",\n \"score\": 92.5,\n \"taxonomy\": 8,\n \"connected_taxa\": 8,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 4,\n \"interaction_evidence\": 10,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "TYQ1_Nematode_Biocontrol_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/TYQ1_Nematode_Biocontrol_SynCom/2026-10-08T133242Z-codex-3eb620.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/TYQ1_Nematode_Biocontrol_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Teosinte_Maize_Biofertilizer_SynCom7-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/Teosinte_Maize_Biofertilizer_SynCom7-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Teosinte_Maize_Biofertilizer_SynCom7-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch119/Teosinte_Maize_Biofertilizer_SynCom7-strict.tsv",
+ "kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/Teosinte_Maize_Biofertilizer_SynCom7-strict.log",
+ "log_sha256": "b523b3130ff8a7e1bd85b471ae9b4e037cc8985e2ad9506a4dfafae3a09de1b4",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch119/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-batch119/Teosinte_Maize_Biofertilizer_SynCom7-strict.tsv\n"
+ },
+ {
+ "check": "Teosinte_Maize_Biofertilizer_SynCom7-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/Teosinte_Maize_Biofertilizer_SynCom7-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Teosinte_Maize_Biofertilizer_SynCom7-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/Teosinte_Maize_Biofertilizer_SynCom7-references.log",
+ "log_sha256": "76d266fd7474d3e738788f26aeb55bbad2c87d09e67a0f030f9d17fc84effae1",
+ "output_tail": "Validating kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.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/Teosinte_Maize_Biofertilizer_SynCom7.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": "Teosinte_Maize_Biofertilizer_SynCom7-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/Teosinte_Maize_Biofertilizer_SynCom7-snippets.log",
+ "log_sha256": "d6441c5dcfaf6a072d70e8708d5fe1bbd2c2a2d31da61b3014fb014108c34cef",
+ "output_tail": "# 18 evidence snippets scanned across 1 files\n MATCH 18\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": "Teosinte_Maize_Biofertilizer_SynCom7-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/Teosinte_Maize_Biofertilizer_SynCom7-rank.log",
+ "log_sha256": "58a5b9184d61ebe4ebe1dae63417bc8d5a0b2bdea6e945e1cfbb5c7156ffcd77",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000100\",\n \"name\": \"Teosinte-Derived Maize Biofertilizer SynCom7\",\n \"score\": 87.5,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 9,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Teosinte_Maize_Biofertilizer_SynCom7-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Teosinte_Maize_Biofertilizer_SynCom7/2026-10-08T133243Z-codex-d993e7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/Teosinte_Maize_Biofertilizer_SynCom7-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "mCAFEs_Brachypodium_RCC-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/mCAFEs_Brachypodium_RCC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/mCAFEs_Brachypodium_RCC-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "mCAFEs_Brachypodium_RCC-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch119/mCAFEs_Brachypodium_RCC-strict.tsv",
+ "kb/communities/mCAFEs_Brachypodium_RCC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/mCAFEs_Brachypodium_RCC-strict.log",
+ "log_sha256": "19c296750371eeac4a9eeb2937fe5bfd06bc57ec3f19f23c4f5c1f9016814b7e",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch119/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-batch119/mCAFEs_Brachypodium_RCC-strict.tsv\n"
+ },
+ {
+ "check": "mCAFEs_Brachypodium_RCC-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/mCAFEs_Brachypodium_RCC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/mCAFEs_Brachypodium_RCC-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "mCAFEs_Brachypodium_RCC-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/mCAFEs_Brachypodium_RCC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/mCAFEs_Brachypodium_RCC-references.log",
+ "log_sha256": "2687578f17fb7c45f14f66ac5a1944b8ba1e2d22be41da2fbb63107fcd820bcd",
+ "output_tail": "Validating kb/communities/mCAFEs_Brachypodium_RCC.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/mCAFEs_Brachypodium_RCC.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": "mCAFEs_Brachypodium_RCC-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/mCAFEs_Brachypodium_RCC.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/mCAFEs_Brachypodium_RCC-snippets.log",
+ "log_sha256": "e8fe5a6250456e2c30f1d505e351e747d7545f77929e05a8d20e9212e652c822",
+ "output_tail": "# 30 evidence snippets scanned across 1 files\n MATCH 30\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": "mCAFEs_Brachypodium_RCC-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/mCAFEs_Brachypodium_RCC.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/mCAFEs_Brachypodium_RCC-rank.log",
+ "log_sha256": "b7397126d4a2e40106894dc7107e016bc0e3be9dc1f51a4c21488b9749b0b6c7",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000078\",\n \"name\": \"m-CAFEs Brachypodium Reduced Complexity Consortia\",\n \"score\": 87.5,\n \"taxonomy\": 10,\n \"connected_taxa\": 10,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 6,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 12,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/mCAFEs_Brachypodium_RCC.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "mCAFEs_Brachypodium_RCC-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/mCAFEs_Brachypodium_RCC/2026-10-08T133243Z-codex-458ed6.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/mCAFEs_Brachypodium_RCC-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-batch119/verification/inventory.log",
+ "log_sha256": "a4addd8b6a2c2217fce0ac5e25c56814ec64219acca2115c157418d36b91f767",
+ "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\": 1375,\n \"edges\": 531,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 189,\n \"review_status_counts\": {\n \"needs_research\": 54,\n \"pending\": 22,\n \"reviewed\": 384\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-batch119/verification/network.log",
+ "log_sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9",
+ "output_tail": "\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ],\n \"Tinto_River_Iron_Cycling_Community\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Basidiomycota\",\n \"taxon_id\": \"NCBITaxon:5204\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Basidiomycota\",\n \"term\": {\n \"id\": \"NCBITaxon:5204\",\n \"label\": \"Basidiomycota\"\n },\n \"gtdb_grounding_status\": \"NO_GTDB_EQUIVALENT\",\n \"notes\": \"Acidophilic fungi including Hortaea werneckii (black yeast) detected in Rio Tinto sediments and water. Fungi contribute to organic matter degradation, biofilm formation, and nutrient cycling through extracellular enzyme secretion.\\n\"\n },\n \"functional_role\": [\n \"PRIMARY_DEGRADER\"\n ],\n \"abundance_level\": \"RARE\",\n \"evidence\": [\n {\n \"reference\": \"PMID:25369810\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons\",\n \"explanation\": \"Documents fungal presence\"\n }\n ]\n },\n \"message\": \"Taxon 'Basidiomycota' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch119/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-batch119/verification/rank-all.log",
+ "log_sha256": "c05a4807c6dcde02a74e0b08c380c94393c4304de973301f6f0ca7372ff118ec",
+ "output_tail": "Consortia (DIETsimp)\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n404\t96.7\tkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml\tCommunityMech:000023\tDesulfovibrio-Methanococcus Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n405\t96.7\tkb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml\tCommunityMech:000340\tPelagerythrobacter-Salinicola PES Pyrene-Degradation SynCom\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n406\t96.7\tkb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml\tCommunityMech:000291\tPseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium\t2\t2\t0\t3\t2\t3\tinteraction_type\t0\t0\n407\t96.7\tkb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml\tCommunityMech:000083\tStreptococcus mutans - Candida albicans ECC Biofilm Model\t2\t2\t0\t3\t2\t4\tinteraction_type\t0\t0\n408\t96.7\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n409\t96.7\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n410\t96.7\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\tinteraction_type\t0\t0\n411\t96.7\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t9\tinteraction_type\t0\t0\n412\t96.7\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t9\tinteraction_type\t0\t0\n413\t96.7\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\tinteraction_type\t0\t0\n414\t96.7\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n415\t96.7\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n416\t96.7\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n417\t97.5\tkb/communities/Anammox_Granule_Metabolic_Interaction_Community.yaml\tCommunityMech:000146\tAnammox Granule Metabolic Interaction Community\t3\t3\t0\t4\t3\t5\tinteraction_type\t0\t0\n418\t97.5\tkb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml\tCommunityMech:000176\tORNL Clostridium-Desulfovibrio-Geobacter Trophic Model Community\t3\t3\t0\t4\t2\t8\tinteraction_type\t0\t0\n419\t97.5\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t8\tinteraction_type\t0\t0\n420\t97.5\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t8\tinteraction_type\t0\t0\n421\t97.9\tkb/communities/Maize_Drought_Response_SynCom.yaml\tCommunityMech:000103\tMaize Drought Response SynCom\t1\t1\t0\t7\t7\t8\tmetabolites_or_biological_processes\t0\t0\n422\t98.3\tkb/communities/Populus_Salt_Tolerant_SynComs.yaml\tCommunityMech:000090\tPopulus Salt-Tolerant Rhizosphere SynComs\t1\t1\t0\t3\t2\t3\tmetabolites_or_biological_processes\t0\t0\n423\t98.3\tkb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml\tCommunityMech:000404\tWollastonite Ramichloridium-Talaromyces Fungal Consortium\t2\t2\t0\t3\t2\t5\tmetabolites_or_biological_processes\t0\t0\n424\t98.8\tdata/isolates/Chromobacterium_Gold_Biocyanidation.yaml\tCommunityMech:000273\tChromobacterium Gold Biocyanidation Platform\t1\t1\t0\t4\t2\t7\tmetabolites_or_biological_processes\t0\t0\n425\t100.0\tdata/isolates/Aspergillus_Indium_LED_Recovery.yaml\tCommunityMech:000320\tAspergillus Indium LCD Recovery Platform\t1\t1\t0\t5\t4\t6\t\t0\t0\n426\t100.0\tdata/isolates/Methylobacterium_REE_Ewaste_Platform.yaml\tCommunityMech:000322\tMethylobacterium REE E-waste Platform\t1\t1\t0\t4\t2\t6\t\t0\t0\n427\t100.0\tkb/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.yaml\tCommunityMech:000276\tANME/SRB Anaerobic Methanotrophic Syntrophic Consortia\t6\t6\t0\t3\t2\t7\t\t0\t0\n428\t100.0\tkb/communities/Anabaena_MGS1_Anaerobic_Digestion_Methanogen_Consortium.yaml\tCommunityMech:000307\tAnabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium\t1\t1\t0\t5\t2\t7\t\t0\t0\n429\t100.0\tkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml\tCommunityMech:000245\tAvena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds\t1\t1\t0\t5\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml\tCommunityMech:000142\tBacteroides-Methanobrevibacter Gnotobiotic Mouse Mutualism\t2\t2\t0\t3\t2\t3\t\t0\t0\n431\t100.0\tkb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml\tCommunityMech:000012\tBioModels MODEL2405300001 Infant Gut HMO SynCom\t13\t13\t0\t3\t2\t6\t\t0\t0\n432\t100.0\tkb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml\tCommunityMech:000215\tCalifornia Grassland Precipitation Legacy Soil Community\t1\t1\t0\t3\t2\t6\t\t0\t0\n433\t100.0\tkb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml\tCommunityMech:000089\tCellulose-to-Methane Quad-Culture SynCom\t4\t4\t0\t6\t5\t9\t\t0\t0\n434\t100.0\tkb/communities/DVM_Triculture.yaml\tCommunityMech:000021\tDVM Tri-culture\t3\t3\t0\t4\t2\t7\t\t0\t0\n435\t100.0\tkb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml\tCommunityMech:000301\tDehalococcoides mccartyi CWV2 Dechlorinating Consortium\t1\t1\t0\t5\t2\t6\t\t0\t0\n436\t100.0\tkb/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.yaml\tCommunityMech:000296\tEscherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture\t2\t2\t0\t3\t2\t6\t\t0\t0\n437\t100.0\tkb/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.yaml\tCommunityMech:000350\tHigh-Ammonia Biogas 0B Butyrate-Oxidizing Enrichment\t4\t4\t0\t3\t2\t6\t\t0\t0\n438\t100.0\tkb/communities/Honeybee_Core20_Defined_Microbiota.yaml\tCommunityMech:000124\tHoneybee Core-20 Defined Microbiota\t1\t1\t0\t3\t2\t3\t\t0\t0\n439\t100.0\tkb/communities/Microbacterium_Terrabacter_Sulfadiazine_CrossFeeding_Coculture.yaml\tCommunityMech:000462\tMicrobacterium-Terrabacter Sulfadiazine Cross-Feeding Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n440\t100.0\tkb/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.yaml\tCommunityMech:000157\tMicrocoleus-Massilia Cyanosphere Urea Mutualism\t2\t2\t0\t3\t2\t5\t\t0\t0\n441\t100.0\tkb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml\tCommunityMech:000119\tMultiomics Corn Straw Degradation SynCom\t1\t1\t0\t4\t3\t9\t\t0\t0\n442\t100.0\tkb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml\tCommunityMech:000156\tNeocallimastix-Methanobrevibacter Xylanolytic Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n443\t100.0\tkb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml\tCommunityMech:000190\tPelotomaculum-Methanocella Propionate RNA-Seq Coculture\t2\t2\t0\t4\t2\t9\t\t0\t0\n444\t100.0\tkb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\tCommunityMech:000052\tPelotomaculum-Methanothermobacter Syntrophic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Phenol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n446\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\n447\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\n448\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\n449\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\n450\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\n451\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\n452\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\n453\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n454\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n455\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\n456\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\n457\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n458\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n459\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n460\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "output_tail": "unitymech-causal-batch119/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 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Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch119/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch119/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch119/docs/index.html\n"
+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
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+ "exit_code": 0,
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+ "output_tail": "unitymech-causal-batch119/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch119/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch119/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch119/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch119/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']()))"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/connectivity-survey.log",
+ "log_sha256": "6dba3d2251cf8431c1fc7f04f3c0806d8a8c166c0901fd6be1fcbc268a1730a4",
+ "output_tail": "{\"records\": 460, \"with_community_level\": 414, \"mixed\": 136, \"community_level_only\": 278, \"taxa\": 1568, \"credited_solely_by_the_rule\": 1281}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_batch107.py",
+ "tests/test_causal_review_batch108.py",
+ "tests/test_causal_review_batch109.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch110.py",
+ "tests/test_causal_review_batch111.py",
+ "tests/test_causal_review_batch112.py",
+ "tests/test_causal_review_batch113.py",
+ "tests/test_causal_review_batch114.py",
+ "tests/test_causal_review_batch115.py",
+ "tests/test_causal_review_batch116.py",
+ "tests/test_causal_review_batch117.py",
+ "tests/test_causal_review_batch118.py",
+ "tests/test_causal_review_batch119.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_network_palette.py",
+ "tests/test_datamodel.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/regressions.log",
+ "log_sha256": "9a434e81e9fba6def0f50bbf96dbe77f1ec28d27e39dbcb63858ba02c7b8b009",
+ "output_tail": "........................................................................ [ 6%]\n........................................................................ [ 12%]\n........................................................................ [ 19%]\n........................................................................ [ 25%]\n........................................................................ [ 32%]\n........................................................................ [ 38%]\n........................................................................ [ 45%]\n........................................................................ [ 51%]\n........................................................................ [ 58%]\n........................................................................ [ 64%]\n........................................................................ [ 70%]\n........................................................................ [ 77%]\n........................................................................ [ 83%]\n........................................................................ [ 90%]\n........................................................................ [ 96%]\n.................................... [100%]\n1116 passed in 319.85s (0:05:19)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/just-lint.log",
+ "log_sha256": "52583cff803ab95a188a83a2c90acf0711ddad704f3e1046d4dd2b7779cc84f2",
+ "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\n372 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-batch119/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-batch119/verification/audit-snippets-all.log",
+ "log_sha256": "19debbd44244dfd187d76c8e32eff8b83772195dfa4bfac9cf26ca949f202694",
+ "output_tail": "# 9046 evidence snippets scanned across 460 files\n MATCH 8901\n RENDERING 28\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch119/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects. All20existing nodes/10arrows reviewed across four whole records. Retain17nodes/10arrows,remove three nodes,rename nine,no new topology.",
+ "Five fresh EuropePMC abstracts and Crossref identities checked; all five complete main-body XML texts read including methods/results/discussion,table text and captions. No original figure pixels,separate supplementary files,raw data or analysis code audited. Literal matching is not entailment proof.",
+ "THOR founding study uses CI04,whereas2022Methods explicitly name UW101. Keep UW101 inhibition,expression and protection; CI04 biofilm remains contextual discussion,not a UW101 node. CI04 accumulation and spo0H results only partially support UW101 chemical mediation. Non-graph strain/cultivation reconciliation remains1926.",
+ "TYQ1 positive pairwise biofilm,medium-specific filtrate assays and actual biological omission retained. SX attraction and AS reverse-use exceptions preserved. Fitted network weights and in-silico node removal are not measured flux or biological omission. Root mechanism mediation remains PARTIAL; metadata/AF-role follow-up1927.",
+ "Teosinte field-treatment effects retained as reported,not independently reproduced statistics. Two formulation-workflow nodes removed while preparation remains in non-graph fields. Relative abundance and correlation centrality do not establish mutualism,nitrogen flux or necessary inoculant strains. Seven-strain roster and source-design ambiguities remain1928.",
+ "mCAFEs is a collection of enrichments,not a fixed ten-member consortium. Keep carbon/transfer selection arrows,operational abundance classes,computational hubs and revival of five selected stocks. No niche-partitioning or keystone-necessity claim. Metadata/carbon-arm reconciliation remains1929.",
+ "Fresh all-state1160issue titles/bodies searched initially; pre-creation receipt records fresh count. Matching1288/615/497/258/25/14/12 bodies read and distinct. Hidden/ignored-inclusive local search found130paths excluding.git,docs,site,references_cache,.env; not a historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,922unchanged caches,unrelated raw YAML blocks,all prior histories/decisions. One CC-BY4.0 cache gains four source-checked selected excerpts append-only; no whole-body import. Four append-only record histories and curation events. Taxon identities unchanged; shared evidence aliases detached.",
+ "Existing-graph repair with no new nodes/directions: no Edison run,provider submission or credit spend. Prior authorized Ruegeria1883 authentication blocker not retried without state change; no credential inspected. Self-adversarial review is not independent approval. Overall review,protected merge and branch deletion remain incomplete."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/THOR_Rhizosphere_Model_Community.yaml": {
+ "MATCH": 22,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
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+ "NOCONTENT": 0
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+ "MISMATCH": 0,
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+ },
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+ {
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+ "the growth of P. koreensis and B. cereus was not affected by coculture",
+ "Bacillus cereus UW85 (B), Flavobacterium johnsoniae UW101 (F), Pseudomonas koreensis CI12 (P)",
+ "likely a combination of direct effects from koreenceine and indirect effects due to slower growth rate of F. johnsoniae in the presence of an antibiotic",
+ "P. koreensis reduced growth of F. johnsoniae when they were grown as a pair, but F. johnsoniae abundance was higher when B. cereus was also present"
+ ],
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+ "primary_sha256": "b9a9f6c077c7d82c95f3f3fe393c68986aa2765d614c95361f3b1e036b7e4362",
+ "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9239112/",
+ "license": "CC BY 4.0",
+ "license_url": "https://creativecommons.org/licenses/by/4.0/",
+ "scope": "Append-only selected literal excerpts; not full-paper import or entailment certification."
+ }
+ ],
+ "edison": {
+ "required_for_this_repair": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "new_nodes_or_directions": 0,
+ "prior_extension_blocker": "Ruegeria1883: configured authentication unavailable in prior approved invocation; no unchanged-state retry."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch119/baseline.json": "934b2a66a6b4e2cf32378820bd0efe6b83a7142153311829380e666d53aad95e",
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+ "/private/tmp/communitymech-batch119/mcafes-crossref.json": "0330f6d22e37bdf969b9c91ecbecc189c49a617c7a82f16070297cf2d3ca8895",
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+ "/private/tmp/communitymech-batch119/teosinte-abstract.txt": "1786cb570a19790190afbb711b3a59d7d67e638b3bdb31503ce95fa6ab665978",
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+ "/private/tmp/communitymech-batch119/teosinte-metadata.json": "92e515c4f9d6920b311ca8bb4d4a03421ff688d560bc3714179cb009cadd56dc",
+ "/private/tmp/communitymech-batch119/teosinte-primary.txt": "9429a36c9a2f5aba42cca117de33b6e84d038b0d140fe2b360ccc49529f21a63",
+ "/private/tmp/communitymech-batch119/teosinte-primary.xml": "16952d1a74ea4f4c32b18738c1ae81002b5afb8a963570af976ca19f9c21494e",
+ "/private/tmp/communitymech-batch119/thor-abstract.txt": "aba0a9eb50423bb6b946b6967d8af78458d08c08554c5b17aee0338321020188",
+ "/private/tmp/communitymech-batch119/thor-crossref.json": "f40bc596050e40dd6d86c7fda159a1a734aaae3110c8f25f723228ec7202aedd",
+ "/private/tmp/communitymech-batch119/thor-metadata.json": "1bd54c130797ed4e39c3cfffa7811a8249141d10d58ae25f6114b665bf758513",
+ "/private/tmp/communitymech-batch119/thor-primary.txt": "19977f829c30cd8e501768b69217b49b9adfdcb07c388b70824b340da22c5e24",
+ "/private/tmp/communitymech-batch119/thor-primary.xml": "c663e5119014062be939d6f25a3f31434f5bfbbc7e5c7acbfd062592bc8711ef",
+ "/private/tmp/communitymech-batch119/thor_transcript-abstract.txt": "53539b846730e3982b83ea8a50b09e9c3e5a58ac6b230afea51cbef8d6c4553a",
+ "/private/tmp/communitymech-batch119/thor_transcript-crossref.json": "162f8f635424cc0debbd549d79a47e11f0f80f0b1e84ffc9ac92ad3f1ce91ed4",
+ "/private/tmp/communitymech-batch119/thor_transcript-metadata.json": "f65ac38bab962e8778365530766cbc8f6ca5c29d77500c637e7fc784156acbf0",
+ "/private/tmp/communitymech-batch119/thor_transcript-primary.txt": "b9a9f6c077c7d82c95f3f3fe393c68986aa2765d614c95361f3b1e036b7e4362",
+ "/private/tmp/communitymech-batch119/thor_transcript-primary.xml": "1bad9ec1b49b84443f7e8124afdd6088e7c453d914ce8558e532db3d42cd151b",
+ "/private/tmp/communitymech-batch119/tyq1-abstract.txt": "12dbff0f276f4b4ac7171ad8211ed026e242e26666640cc21f32fe815bb15876",
+ "/private/tmp/communitymech-batch119/tyq1-crossref.json": "d7c14368903ca8af9dcfb12ade9faaed2e23c7719d530509d2f4aae89e9ebea2",
+ "/private/tmp/communitymech-batch119/tyq1-metadata.json": "d8677749fe15356890bf0925f4cddd846b2353cbb6989abf59ff0257a906fc0f",
+ "/private/tmp/communitymech-batch119/tyq1-primary.txt": "eb456f3033f2233ac13f686b54d3c9b34c221b290d0ecae000fcd9d9f1acd160",
+ "/private/tmp/communitymech-batch119/tyq1-primary.xml": "2b7f977d7da5531e3f1a4fa4a1c2b5a81aeb2f5b5baccc0ac43da4ba675be828",
+ "references_cache/PMID_30837345.md": "9bd0c3fd2d1c9191184c1e9212fc38ad956b09c7d1c126f4a7df947afb977c7c",
+ "references_cache/PMID_35435700.md": "4c801186b23c80af1db7a38872e597f00d709a7406768fcece1dd640c1bbf7eb",
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+ "references_cache/PMID_40270813.txt": "4d5eb9bba8bc7d0e92212075395581a151e5580d95c59f71ec0dec87874cdba0",
+ "references_cache/PMID_41660888.md": "1500925aca34ba63cb4d76d3d4d8fdcdc0f038555eaeb4528600119e390e164c"
+ },
+ "immutable_prior_history_and_decision_files": 884,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 38,
+ "discussion_quotations": 5,
+ "fresh_primary_literal_matches": 43,
+ "all_cached_literal_matches": 43,
+ "retained_nodes": 17,
+ "removed_nodes": 3,
+ "renamed_nodes": 9,
+ "retained_arrows": 10,
+ "removed_arrows": 0,
+ "new_nodes_or_directions": 0
+ },
+ "network_delta": {
+ "existing_findings_preserved": 57,
+ "added_findings": {},
+ "removed_findings": {},
+ "structural_defects": 0
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1361,
+ "arrows": 523
+ },
+ "render_scope": "Deterministic rendering and exact HTML description parsing, not screenshots; postcommit docs-current still required.",
+ "participant_census": {
+ "current": {
+ "records": 460,
+ "with_community_level": 414,
+ "mixed": 136,
+ "community_level_only": 278,
+ "taxa": 1568,
+ "credited_solely_by_the_rule": 1281
+ },
+ "delta_from_batch118": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 1
+ },
+ "explanation": "One explicit participant-list user added for THOR three-member protection;299total. Bacillus cereus UW85 leaves the incorrectly assigned pairwise protection node and is explicitly named in the three-member node. Sole-credit rises1280to1281; record-scope counts remain unchanged. Sole-credit does not certify actual participant coverage. Connectivity logic and thresholds are unchanged."
+ },
+ "verification_corrections": [
+ {
+ "check": "connectivity-survey",
+ "initial_assertion": "Expected1280sole-credit but observed1281; first verifier invocation stopped here before regressions.",
+ "resolution": "Inspected old/new THOR pairwise credit: Bacillus moves to explicit three-member protection. Updated exact census expectation in the verifier and current-corpus regression,not a threshold or graph change.",
+ "original_survey_log": "/private/tmp/communitymech-batch119/verification/connectivity-survey.log",
+ "original_survey_log_sha256": "6dba3d2251cf8431c1fc7f04f3c0806d8a8c166c0901fd6be1fcbc268a1730a4"
+ }
+ ],
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary established Python3.13 lint environment; project dependencies unchanged."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 9046,
+ "categories": {
+ "MATCH": 8901,
+ "RENDERING": 28,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 40,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Informational audit exit0 is not clean-corpus or entailment certification.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1375,
+ "edges": 531,
+ "records_without_nodes": 10,
+ "records_without_edges": 189,
+ "review_status_counts": {
+ "needs_research": 54,
+ "pending": 22,
+ "reviewed": 384
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml": "f8bdcb0de3409627788a931ea8c49717dfd9aeba50fb061fde838f6d7b67b955",
+ "tests/test_causal_review_batch119.py": "f917f104f5b09dd7a98dcd9cf967a44962b410e6722443ec880e29c1d55cdc14",
+ "tests/test_participating_taxa.py": "f438815b4a028c0f38a077df53c95f685f98b3c2b523593896a124b544269db1",
+ "tests/test_community_level_connectivity_credit.py": "996cc631423bfa7adc5d8e693d67d55b374a24379d119ab0fa8f1802f38f216a",
+ "tests/test_causal_review_batch109.py": "ff8e9e26771545e1ace22b3c1d42076789c99cc4bc83e588b6a4b9ad698d3d73",
+ "tests/test_datamodel.py": "f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25",
+ "reports/causal_graph_review/cache-provenance-20261008-batch119.json": "c01b47ab2bb142eb1db61e7faaf5572da929325e7fae67b6a4a36477582b2a61",
+ "kb/communities/THOR_Rhizosphere_Model_Community.yaml": "1d75a279b70b1ece18d4453f8576a849996e712bfb2f4a0ea9542db2f22f0dca",
+ "kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml": "a5c33db18b80a233099b80289b173c8c57e1420ced3a4f282ef99bb9100d0f11",
+ "kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml": "d2b51e34f56530cb2992a40d195eae0f2395925e9d4f39b135d77a8822309320",
+ "kb/communities/mCAFEs_Brachypodium_RCC.yaml": "273500dc8bec3a1e35cea5c32a9ac77be1c36ed5f5d01cd5f7861dfe65e40ecb"
+ },
+ "pre_research_baseline": {
+ "base_commit": "97c48512fb91a69598093e9d097e84341ffdfae0",
+ "base_tree": "1055d3cbe986e3fb1ada11583113930aac4adf2c",
+ "research_worktree": "/private/tmp/communitymech-causal-batch119",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch119/baseline-rank.log",
+ "sha256": "8e25bb1f6265c3922fddfcb336ed79d5508c26466483274a6a80403ed26aae67"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch119/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-batch119/baseline-network.log",
+ "sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch119/baseline-downstream.log",
+ "sha256": "0ce6a1336abc252b7cc66c67d7d0de28a55a89131888edb8029735903e012b7f"
+ }
+ ],
+ "baseline_sha256": "934b2a66a6b4e2cf32378820bd0efe6b83a7142153311829380e666d53aad95e"
+ },
+ "reference_validator_caveat": "Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment. Total checks in the reference CLI counts issues, not examined snippets.",
+ "status": "verified_existing_graph_repairs",
+ "total_recorded_gate_outputs": 41
+}
diff --git a/tests/test_causal_review_batch109.py b/tests/test_causal_review_batch109.py
index d33387151..2130ea9b3 100644
--- a/tests/test_causal_review_batch109.py
+++ b/tests/test_causal_review_batch109.py
@@ -176,7 +176,7 @@ def test_hashes_histories_and_canonical_identity_only_scope_are_explicit():
def test_current_scope_census_tracks_later_source_bounded_repairs():
- # Batch117 narrows vitamin provision to the tested pair; no sole credit changes.
+ # Batch119 moves Bacillus protection to all three THOR members: one more sole credit.
survey = runpy.run_path(str(ROOT / "tests/test_community_level_connectivity_credit.py"))[
"_survey"
]()
@@ -186,5 +186,5 @@ def test_current_scope_census_tracks_later_source_bounded_repairs():
"mixed": 136,
"community_level_only": 278,
"taxa": 1568,
- "credited_solely_by_the_rule": 1280,
+ "credited_solely_by_the_rule": 1281,
}
diff --git a/tests/test_causal_review_batch119.py b/tests/test_causal_review_batch119.py
new file mode 100644
index 000000000..0abdc5ffe
--- /dev/null
+++ b/tests/test_causal_review_batch119.py
@@ -0,0 +1,194 @@
+"""Preserve measured results without mixing strains, assay roles or causal levels."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / row["path"]).read_text()) for row in rows]
+
+
+def test_thor_inhibition_is_locus_dependent_not_bilateral_competition():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][0]
+ assert "UW101" in node["name"] and "interaction_type" not in node
+ assert "deletion of the koreenceine locus" in node["evidence"][0]["snippet"]
+ assert "was not affected by coculture" in node["evidence"][1]["snippet"]
+ assert all(e["reference"] == "PMID:35435700" for e in node["evidence"])
+
+
+def test_thor_expression_retains_the_correct_denominator_and_indirect_limit():
+ _, _, docs = records()
+ first, expression, _ = docs[0]["ecological_interactions"]
+ assert "interaction_type" not in expression
+ assert "greater-than-twofold pairwise response" in expression["description"]
+ assert "not of each whole genome" in expression["description"]
+ assert expression["evidence"][1]["supports"] == "PARTIAL"
+ assert "indirect effects" in expression["evidence"][1]["snippet"]
+ assert first["downstream"][0]["target"] == expression["name"]
+ assert "PARTIAL" in first["downstream"][0]["description"]
+
+
+def test_thor_protection_has_three_participants_and_variant_bounded_chemistry():
+ _, _, docs = records()
+ first, _, protection = docs[0]["ecological_interactions"]
+ assert protection["scope"] == "COMMUNITY_LEVEL"
+ assert "interaction_type" not in protection
+ assert "source_taxon" not in protection and "target_taxon" not in protection
+ assert len(protection["participating_taxa"]) == 3
+ assert "not facilitation of P. koreensis colonization" in protection["description"]
+ assert protection["evidence"][0]["reference"] == "PMID:35435700"
+ assert protection["evidence"][1]["reference"] == "PMID:30837345"
+ assert protection["evidence"][1]["supports"] == "PARTIAL"
+ assert protection["downstream"][0]["target"] == first["name"]
+ assert "CI04, not UW101" in protection["downstream"][0]["description"]
+
+
+def test_thor_ci04_biofilm_is_context_not_a_uw101_node():
+ _, rows, docs = records()
+ doc = docs[0]
+ assert len(doc["ecological_interactions"]) == 3
+ assert len(rows[0]["removed_node_decisions"]) == 1
+ assert "Emergent Three-Member Biofilm Formation" not in [
+ n["name"] for n in doc["ecological_interactions"]
+ ]
+ discussion = doc["discussions"][-1]
+ assert "CI04" in discussion["prompt"] and "UW101" in discussion["prompt"]
+ assert "increased the maximum biofilm" in discussion["evidence"][1]["snippet"]
+
+
+def test_tyq1_seven_positive_biofilms_do_not_erase_the_sx_attraction_exception():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][1]
+ assert "interaction_type" not in node
+ assert "all strains" in node["evidence"][0]["snippet"]
+ assert "exception of SX" in node["evidence"][1]["snippet"]
+ assert all(e["evidence_source"] == "IN_VITRO" for e in node["evidence"])
+
+
+def test_tyq1_cross_feeding_keeps_medium_direction_and_as_limits():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][2]
+ assert node["interaction_type"] == "CROSS_FEEDING"
+ assert "all seven enriched strains" in node["evidence"][0]["snippet"]
+ assert "Except for AS" in node["evidence"][1]["snippet"]
+ assert "did not influence TYQ1growth" in node["evidence"][2]["snippet"]
+ assert node["evidence"][3]["evidence_source"] == "COMPUTATIONAL"
+ assert "not measured metabolite fluxes" in node["description"]
+ assert "in-silico" in node["description"]
+
+
+def test_tyq1_biological_omission_is_positive_but_not_specific_mediation():
+ _, _, docs = records()
+ nodes = docs[1]["ecological_interactions"]
+ assert "interaction_type" not in nodes[3]
+ assert "lost its inhibitory function" in nodes[3]["evidence"][1]["snippet"]
+ assert nodes[3]["evidence"][1]["evidence_source"] == "IN_VIVO"
+ assert nodes[3]["evidence"][2]["supports"] == "PARTIAL"
+ edges = [e for n in nodes for e in n.get("downstream", [])]
+ assert len(edges) == 4 and all(e["description"].startswith("PARTIAL:") for e in edges)
+ assert "transient" in nodes[1]["downstream"][0]["description"]
+
+
+def test_teosinte_preparation_is_not_an_ecological_node():
+ _, rows, docs = records()
+ doc = docs[2]
+ assert len(doc["ecological_interactions"]) == 4
+ assert len(rows[2]["removed_node_decisions"]) == 2
+ assert all("Formulation" not in n["name"] for n in doc["ecological_interactions"])
+ assert doc["engineering_design"] and doc["growth_media"]
+
+
+def test_teosinte_field_effects_remain_without_claiming_nitrogen_flux():
+ _, _, docs = records()
+ treatment, outcome, _, _ = docs[2]["ecological_interactions"]
+ assert "interaction_type" not in treatment and "interaction_type" not in outcome
+ assert "biological_processes" not in treatment
+ assert all(e["evidence_source"] == "IN_VIVO" for e in treatment["evidence"])
+ assert len(treatment["downstream"]) == 2
+ assert "treatment-level effect" in treatment["downstream"][0]["description"]
+ assert {p["term"]["id"] for p in outcome["biological_processes"]} == {"GO:0040007"}
+ assert "not measurements of nitrogen-fixation flux" in outcome["description"]
+
+
+def test_teosinte_soil_association_network_is_not_mutualism_or_necessity():
+ _, _, docs = records()
+ _, _, composition, network = docs[2]["ecological_interactions"]
+ assert "interaction_type" not in composition and "interaction_type" not in network
+ assert "Relative abundance does not prove absolute" in composition["description"]
+ assert "biological_processes" not in network and not network.get("downstream")
+ assert all(e["evidence_source"] == "COMPUTATIONAL" for e in network["evidence"])
+ assert network["evidence"][0]["supports"] == "PARTIAL"
+ assert "correlated changes in abundance" in network["evidence"][-1]["snippet"]
+
+
+def test_mcafes_selection_keeps_both_experimental_directions():
+ _, _, docs = records()
+ nodes = docs[3]["ecological_interactions"]
+ assert all("interaction_type" not in n for n in nodes)
+ assert "not one fixed consortium" in nodes[0]["description"]
+ assert [e["target"] for e in nodes[0]["downstream"]] == [nodes[1]["name"], nodes[2]["name"]]
+ assert len(nodes[1]["participating_taxa"]) == 3
+
+
+def test_mcafes_abundance_classes_are_not_direct_growth_rates_or_hub_membership():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][2]
+ assert "participating_taxa" not in node
+ assert "not measured isolate growth rates" in node["description"]
+ assert "generations 6 and 9" in node["description"]
+ assert "not substituted" in node["description"]
+
+
+def test_mcafes_hubs_are_computational_not_necessary_ecological_functions():
+ _, _, docs = records()
+ for node in docs[3]["ecological_interactions"][3:5]:
+ assert "interaction_type" not in node and "biological_processes" not in node
+ assert all(e["evidence_source"] == "COMPUTATIONAL" for e in node["evidence"])
+ hub = docs[3]["ecological_interactions"][3]
+ assert "90% quantile" in hub["evidence"][-1]["snippet"]
+ assert "not establish" in hub["description"]
+
+
+def test_mcafes_revival_is_positive_for_five_selected_stocks_only():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][5]
+ assert "participating_taxa" not in node
+ assert "Five selected" in node["description"]
+ assert "does not establish universal revival" in node["description"]
+ assert "less stable" in node["description"]
+ assert node["evidence"][0]["evidence_source"] == "IN_VITRO"
+ assert node["evidence"][1]["evidence_source"] == "COMPUTATIONAL"
+
+
+def test_review_accounts_for_all_nodes_arrows_and_append_only_cache():
+ ledger, rows, docs = records()
+ counts = ledger["reviewed_counts"]
+ assert (counts["original_nodes"], counts["retained_nodes"], counts["removed_nodes"]) == (
+ 20,
+ 17,
+ 3,
+ )
+ assert counts["renamed_nodes"] == 9
+ assert counts["original_arrows"] == counts["retained_arrows"] == 10
+ assert counts["removed_arrows"] == 0
+ assert (counts["graph_quotations"], counts["discussion_quotations"]) == (38, 5)
+ assert len(ledger["cache_changes"]) == 1 and not ledger["independent_approval"]
+ assert ledger["cache_changes"][0]["path"] == "references_cache/PMID_35435700.md"
+ assert len(ledger["cache_changes"][0]["quotations"]) == 4
+ assert ledger["edison"]["new_nodes_or_directions"] == 0
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ names = [n["name"] for n in doc["ecological_interactions"]]
+ assert [r["node"] for r in row["node_decisions"]] == names
+ assert len(row["history_files"]) == 1 and doc["curation_history"][-1]["llm_assisted"]
+ for node in doc["ecological_interactions"]:
+ assert "downstream" not in node or node["downstream"]
+ assert all(e["target"] in names for e in node.get("downstream", []))
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 50bb905ed..318ea57b5 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -437,6 +437,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Syntrophus_Benzoate_Degrader.yaml",
"Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml",
"TCP_NonDehalogenimonas_Groundwater_Consortium.yaml",
+ "THOR_Rhizosphere_Model_Community.yaml",
"Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml",
"Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml",
"Thermophilic_Pyrite_QS_Consortium.yaml",