From 1142516cda3a9a61e23f9db131ab6477c84172d4 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Thu, 8 Oct 2026 08:31:03 -0700
Subject: [PATCH] Preserve plant outcomes and mixture assay contrasts
(batch121)
---
docs/communities/Tomato_Oxylipin_SynCom3.html | 125 +-
docs/communities/Wheat_Consortium_C1.html | 173 ++-
docs/communities/Wheat_Consortium_C6.html | 286 ++--
...t_CrownRot_SixStrain_CrossKingdom_SMC.html | 139 +-
.../2026-10-08T150228Z-codex-b1572f.yaml | 27 +
.../2026-10-08T150228Z-codex-ff737c.yaml | 26 +
.../2026-10-08T150229Z-codex-b61a7a.yaml | 29 +
.../2026-10-08T150229Z-codex-fc0ee7.yaml | 26 +
kb/communities/Tomato_Oxylipin_SynCom3.yaml | 112 +-
kb/communities/Wheat_Consortium_C1.yaml | 98 +-
kb/communities/Wheat_Consortium_C6.yaml | 231 +--
...t_CrownRot_SixStrain_CrossKingdom_SMC.yaml | 83 +-
references_cache/PMID_41504167.txt | 8 +
reports/causal_graph_review/README.md | 37 +
.../adversarial-review-20261008-batch121.yaml | 830 +++++++++++
.../cache-provenance-20261008-batch121.json | 350 +++++
.../20261008-four-records-batch121.yaml | 854 +++++++++++
reports/causal_graph_review/inventory.tsv | 8 +-
reports/causal_graph_review/summary.json | 6 +-
.../validation-20261008-batch121.json | 1293 +++++++++++++++++
tests/test_causal_review_batch121.py | 199 +++
21 files changed, 4411 insertions(+), 529 deletions(-)
create mode 100644 history/records/Tomato_Oxylipin_SynCom3/2026-10-08T150228Z-codex-b1572f.yaml
create mode 100644 history/records/Wheat_Consortium_C1/2026-10-08T150228Z-codex-ff737c.yaml
create mode 100644 history/records/Wheat_Consortium_C6/2026-10-08T150229Z-codex-b61a7a.yaml
create mode 100644 history/records/Wheat_CrownRot_SixStrain_CrossKingdom_SMC/2026-10-08T150229Z-codex-fc0ee7.yaml
create mode 100644 reports/causal_graph_review/adversarial-review-20261008-batch121.yaml
create mode 100644 reports/causal_graph_review/cache-provenance-20261008-batch121.json
create mode 100644 reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
create mode 100644 reports/causal_graph_review/validation-20261008-batch121.json
create mode 100644 tests/test_causal_review_batch121.py
diff --git a/docs/communities/Tomato_Oxylipin_SynCom3.html b/docs/communities/Tomato_Oxylipin_SynCom3.html
index 9f78630db..e1aa48006 100644
--- a/docs/communities/Tomato_Oxylipin_SynCom3.html
+++ b/docs/communities/Tomato_Oxylipin_SynCom3.html
@@ -600,7 +600,7 @@ Ecological Interactions
Ecological interaction network for Tomato Oxylipin-Protective SynCom3
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -608,8 +608,8 @@
Ecological Interactions
@@ -617,10 +617,9 @@ Ecological Interactions
-
The three-species tomato rhizosphere community combines one phytopathogen-inducible Asticcacaulis member that triggers plant defense responses with two stably colonizing Arachidicoccus and Phenylobacterium members that promote biofilm formation.
+
The three-genus tomato-root inoculum combines pathogen-inducible Asticcacaulis with stably colonizing Arachidicoccus and Phenylobacterium. The abstract attributes host-defense triggering to the inducible member and biofilm promotion to the stable colonizers, with protection similar to the 38-member precursor. These positive complementary phenotypes do not measure reciprocal bacterial fitness or metabolite exchange. Exact strain identities and selective biofilm mediation are not resolved by the inspected abstract.
@@ -646,8 +645,8 @@
Simplified Community Synergistic Protection
Downstream Effects:
-
→ Oxylipin-Mediated Disease Resistance
-
The synergistic three-species community intensifies oxylipin pathway activation in phytopathogen-infected tomato leaves.
+
→ SynCom3-induced leaf oxylipin responses
+
SynCom3 treatment intensified oxylipin responses in infected tomato leaves. PARTIAL for biofilm formation as the mediator: the abstract links complementary community functions to protection but does not isolate biofilm formation as the unique cause of leaf pathway activation.
Evidence
PMID:37549573
- - SUPPORT (IN_VITRO)
+ - SUPPORT (OTHER)
"the phytopathogen-inducible species triggering plant defense responses and the stably-colonizing species promoting biofilm formation"
+
+
+
+ "The simplified community exhibited similar protective effects as the 38-species community"
+
+
+
-
Inducible and stable colonizers synergize to trigger host defense and biofilm-mediated protection.
+
The simplified community intensified oxylipin-pathway activation in Botrytis-infected tomato leaves. This is a host response to the bacterial treatment, not microbial mutualism or evidence that the bacteria themselves synthesize the listed divinyl ethers. The downstream biosynthesis perturbation provides stronger mechanistic evidence than association alone.
@@ -711,7 +722,7 @@
Oxylipin-Mediated Disease Resistance
→ Divinyl Ether-Dependent Botrytis Protection
-
Intensified oxylipin-pathway activation feeds production of antimicrobial divinyl ethers required for community-induced protection against Botrytis cinerea.
+
The host oxylipin branch supplies divinyl ethers implicated in protection: inhibiting their biosynthesis abolished the community-induced resistance, while SlLOX5/SlDES1 overexpression with higher divinyl-ether levels increased resistance. Retain this pathway-level perturbation evidence without claiming separate necessity of each compound or bacterial-to-plant transfer.
Evidence
PMID:37549573
- - SUPPORT (IN_VITRO)
-
-
- "Through the analysis of the rhizosphere bacterial community, we established a synthetic community harboring 8 phytopathogen-inducible and 30 stably-colonizing bacteria species."
-
-
-
-
-
"the activation of oxylipin pathways in the phytopathogen-infected leaves was significantly intensified by the simplified community"
@@ -754,9 +752,8 @@ Evidence
-
The community-induced tomato defense requires biosynthesis of the antimicrobial divinyl ethers colneleic acid and colnelenic acid; when this branch is blocked, the SynCom no longer protects against Botrytis.
+
Inhibiting divinyl-ether biosynthesis abolished SynCom-induced tomato resistance to Botrytis cinerea. Conversely, SlLOX5/SlDES1-overexpressing plants with higher divinyl-ether levels had stronger resistance than wild type. Preserve this positive pathway-level evidence for colneleic/colnelenic-acid-associated defense. The abstract does not specify the inhibition method or establish that each named compound is independently indispensable, sufficient alone, or transferred from bacteria.
@@ -790,13 +787,26 @@
Evidence
PMID:37549573
- - SUPPORT (IN_VITRO)
+ - SUPPORT (IN_VIVO)
"the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic and colnelenic acid, fully abolished the community-induced plant disease resistance"
+
+
+
+ "transgenic plants overexpressing SlLOX5 and SlDES1, with higher levels of divinyl ethers, displayed stronger resistance against B. cinerea compared to wild-type plants"
+
+
+
@@ -806,6 +816,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which microbial contributions and individual divinyl ethers mediate SynCom3 protection?
+
+
The abstract supports complementary functions, host oxylipin activation and a real biosynthesis perturbation, not merely correlation. Detailed primary methods would resolve the inhibition target, individual-compound necessity and biofilm mediation. Reciprocal bacterial benefit and cross-feeding are not established. Preserve both existing directions and positive protection without inventing a new mechanism.
+
+
Attaches to: ecological_interactions#SynCom3-associated biofilm and host defense, ecological_interactions#SynCom3-induced leaf oxylipin responses, ecological_interactions#Divinyl Ether-Dependent Botrytis Protection
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic and colnelenic acid, fully abolished the community-induced plant disease resistance
+
+
+
+
+
@@ -951,7 +1000,7 @@ Environmental Factors
(function() {
var intId = "interaction:0";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -960,11 +1009,11 @@ Environmental Factors
processes.push("biofilm formation");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Simplified Community Synergistic Protection",
+ label: "SynCom3-associated biofilm and host defense",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -979,7 +1028,7 @@ Environmental Factors
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -992,11 +1041,11 @@ Environmental Factors
var processes = [];
- var evidenceCount = 2;
+ var evidenceCount = 1;
nodes.push({
id: intId,
- label: "Oxylipin-Mediated Disease Resistance",
+ label: "SynCom3-induced leaf oxylipin responses",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1011,7 +1060,7 @@ Environmental Factors
(function() {
var intId = "interaction:2";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1022,7 +1071,7 @@ Environmental Factors
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
diff --git a/docs/communities/Wheat_Consortium_C1.html b/docs/communities/Wheat_Consortium_C1.html
index 6a42d6636..db683b5cc 100644
--- a/docs/communities/Wheat_Consortium_C1.html
+++ b/docs/communities/Wheat_Consortium_C1.html
@@ -643,7 +643,7 @@ Ecological Interactions
Ecological interaction network for Wheat Synthetic Consortium C1
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for competition, colonization facilitation.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -651,13 +651,8 @@
Ecological Interactions
-
-
@@ -665,14 +660,24 @@ Ecological Interactions
-
Pseudomonas sp. B5, Pseudomonas sp. B11, Pseudomonas sp. B12, and Pseudomonas sp. P25 were combined at equal ratios as the same-genus C1 consortium within the ten-SynCom wheat-rhizosphere design.
-
+
The assembled C1 inhibited Rhizoctonia solani AG8 radial growth in dual culture, with reported inhibition of 37.00% (SD 6.57) in Table 2. This is a positive fungal-growth outcome, not evidence that both bacterial and fungal fitness declined. Plate inhibition does not establish the mediator or guarantee host protection.
+
+
+
+
Participating Taxa:
+
+ Pseudomonas sp. B5,
+
+ Pseudomonas sp. B11,
+
+ Pseudomonas sp. B12,
+ Pseudomonas sp. P25
+
@@ -682,7 +687,7 @@
Equal-Ratio Pseudomonas C1 Assembly
- biological process involved in interspecies interaction between organisms
+ interspecies interaction
(GO:0044419 )
@@ -705,7 +710,7 @@ Evidence
- SUPPORT (IN_VITRO)
"SynCom 1(C1) Pseudomonas sp. B5, Pseudomonas sp. B11, Pseudomonas sp. B12, Pseudomonas sp. P25"
+ "In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8, and C10, inhibited the growth of R. solani AG8 to varying degrees"
@@ -718,7 +723,7 @@ Evidence
- SUPPORT (IN_VITRO)
- "SynComs were obtained by mixing the individuals in equal ratios"
+ "SynCom 1(C1)37.00 ± 6.57"
@@ -728,10 +733,9 @@ Evidence
-
The four-Pseudomonas C1 SynCom inhibited Rhizoctonia solani AG8 radial growth in the in vitro dual-culture assay.
+
C1 reduced root-rot scores and increased fresh root weight of AG8-challenged Alpowa wheat in the three-week greenhouse soil assay. Preserve this positive whole-mixture benefit. The study did not show superiority over the best individual strain or establish reciprocal microbial benefit, bilateral competition, inoculum persistence, or a unique IAA/volatile mechanism. Only B5 among the four C1 members significantly reduced disease when tested individually.
@@ -756,7 +760,7 @@
C1 SynCom inhibition of R. solani AG8 radial growth
- interspecies interaction
+ biological process involved in interspecies interaction between organisms
(GO:0044419 )
@@ -776,10 +780,23 @@ Evidence
PMID:36118206
- - SUPPORT (IN_VITRO)
+ - SUPPORT (IN_VIVO)
"In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8, and C10, inhibited the growth of R. solani AG8 to varying degrees"
+ "SynCom C1, composed of four different Pseudomonas members, significantly reduced wheat root rot and increased root weight, compared with the controls"
+
+
+
+
+
+
+ "None of them was significantly better than a single strain"
@@ -787,72 +804,80 @@ Evidence
-
-
-
C1 significantly reduced wheat root rot scores and increased wheat fresh root weight relative to AG8-challenged controls in greenhouse soil.
+
+
+
+ Knowledge gaps & discussions (1)
- Participating Taxa:
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which processes explain C1 protection beyond its separate laboratory phenotypes?
+
+
C1 is protective in soil, yet individual-versus-mixture phenotypes differ. The paper reports no antifungal activity from any SynCom cell-free supernatant and identifies C2-C4/C7, not C1, as significant volatile mixtures. Lower C1 auxin and volatile outputs are not selective proof that these routes are impossible. Inoculum persistence was explicitly not assessed. Equal-ratio preparation remains in metadata and the earlier removal of workflow arrows remains intact.
- Pseudomonas sp. B5,
+
Attaches to: ecological_interactions#C1 SynCom inhibition of R. solani AG8 radial growth, ecological_interactions#C1 SynCom protection of wheat under AG8 challenge
- Pseudomonas sp. B11,
- Pseudomonas sp. B12,
- Pseudomonas sp. P25
+
+ 3 evidence item(s)
-
+
+
-
Biological Processes:
-
+
+
None of them was significantly better than a single strain
+
+
-
Evidence
-
-
-
+ the cell-free supernatants from the rest of the eight bacteria and 10 SynComs did not show any antifungal activities
- "SynCom C1, composed of four different Pseudomonas members, significantly reduced wheat root rot and increased root weight, compared with the controls"
+
-
+
+
While not assessed here, investigation of the fate of those inoculations in the soil after plant growth is needed to address their persistence and stability
+
+
+
+
@@ -1068,35 +1093,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "COLONIZATION_FACILITATION";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("biological process involved in interspecies interaction between organisms");
-
-
- var evidenceCount = 2;
-
- nodes.push({
- id: intId,
- label: "Equal-Ratio Pseudomonas C1 Assembly",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:1";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1105,7 +1102,7 @@
Evidence
processes.push("interspecies interaction");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1140,8 +1137,8 @@
Evidence
})();
(function() {
- var intId = "interaction:2";
- var intType = "COMPETITION";
+ var intId = "interaction:1";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1150,7 +1147,7 @@
Evidence
processes.push("biological process involved in interspecies interaction between organisms");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1203,7 +1200,7 @@
Evidence
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
- var nodeCount = 7;
+ var nodeCount = 6;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/Wheat_Consortium_C6.html b/docs/communities/Wheat_Consortium_C6.html
index cc1331a15..30093b018 100644
--- a/docs/communities/Wheat_Consortium_C6.html
+++ b/docs/communities/Wheat_Consortium_C6.html
@@ -643,7 +643,7 @@
Ecological Interactions
Ecological interaction network for Wheat Synthetic Consortium C6
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism, competition, colonization facilitation.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -651,18 +651,8 @@
Ecological Interactions
-
-
-
-
Ecological Interactions
-
Streptomyces sp. B6, Chryseobacterium sp. B7, Pseudomonas sp. B12, and Sphingomonas sp. B17 were combined at equal ratios as the random mixed-genus C6 consortium within a broader ten-SynCom wheat-rhizosphere design.
-
+
The assembled C6 inhibited Rhizoctonia solani AG8 radial growth in dual culture, with reported inhibition of 34.48% (SD 5.91) in Table 2. This is a positive fungal-growth outcome, not evidence that both bacterial and fungal fitness declined. Plate inhibition does not establish the mediator or guarantee host protection.
+
Participating Taxa:
+
+ Streptomyces sp. B6,
+
+ Chryseobacterium sp. B7,
+
+ Pseudomonas sp. B12,
+
+ Sphingomonas sp. B17
+
+
+
@@ -710,8 +710,7 @@
Evidence
- SUPPORT (IN_VITRO)
"SynCom 6(C6) Streptomyces sp. B6, Chryseobacterium sp. B7, Pseudomonas sp. B12, Sphingomonas sp. B17
-"
+ "In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8, and C10, inhibited the growth of R. solani AG8 to varying degrees"
@@ -724,8 +723,7 @@ Evidence
- SUPPORT (IN_VITRO)
- "SynComs were obtained by mixing the individuals in equal ratios
-"
+ "SynCom 6(C6)34.48 ± 5.91"
@@ -735,24 +733,20 @@ Evidence
-
C6 inhibited Rhizoctonia solani AG8 radial growth in the direct dual-culture agar assay, placing it among the eight inhibitory SynComs in the ten-consortium panel.
-
+
C6 culture supernatant gave an IAA-calibrated Salkowski estimate of 11.76 ug/mL (SD 2.83) in Table 3. This is a whole-mixture colorimetric output, not structural identification of every reactive compound, member-resolved synthesis, delivery to plant roots or mutualism. No selective hormone perturbation links it to the separate Arabidopsis root-length result.
-
Participating Taxa:
-
- Streptomyces sp. B6,
- Chryseobacterium sp. B7,
- Pseudomonas sp. B12,
+
Metabolites:
- Sphingomonas sp. B17
+ indole-3-acetic acid
+ (CHEBI:16411 )
@@ -760,19 +754,6 @@
C6 Dual-Culture AG8 Radial Inhibition
-
Biological Processes:
-
-
-
- biological process involved in interspecies interaction between organisms
- (GO:0044419 )
-
-
-
-
-
-
Evidence
@@ -787,55 +768,11 @@
Evidence
- SUPPORT (IN_VITRO)
"In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8, and C10, inhibited the growth of R. solani AG8 to varying degrees"
-
-
-
-
-
-
-
-
-
-
C6 culture supernatant contained indole-3-acetic acid in the whole-SynCom auxin assay, one of the plant-growth-modulating phenotypes measured across all ten consortia.
-
-
-
-
-
-
-
-
Metabolites:
-
- indole-3-acetic acid
- (CHEBI:16411 )
-
-
-
-
-
-
Biological Processes:
-
+ "including 10 single strains and all 10 SynComs, produced auxin at various concentrations
+"
-
- growth
- (GO:0040007 )
-
-
-
-
-
-
-
Evidence
-
-
@@ -845,8 +782,7 @@
Evidence
- SUPPORT (IN_VITRO)
- "including 10 single strains and all 10 SynComs, produced auxin at various concentrations
-"
+ "SynCom 6(C6)11.76 ± 2.83"
@@ -856,11 +792,9 @@ Evidence
-
The SynCom panel, including C6, altered primary root length in a controlled Arabidopsis plate assay used to connect bacterial auxin production with plant-root phenotypes.
-
+
C6 was among the nine mixtures that significantly shortened primary roots of plate-grown Arabidopsis after cocultivation. Shorter primary roots are the measured endpoint, not demonstrated growth promotion or reciprocal benefit. The across-treatment association with a separate auxin assay does not establish IAA as the necessary mediator. This Arabidopsis phenotype is not a wheat disease-protection result; C6 was not among the mixtures with significant greenhouse root-rot reduction or fresh-root-weight improvement.
@@ -901,7 +835,7 @@
Evidence
PMID:36118206
- - SUPPORT (IN_VITRO)
+ - SUPPORT (IN_VIVO)
"Similar reductions in the primary root length of Arabidopsis seedlings were observed in all SynComs except C5
@@ -915,11 +849,9 @@
Evidence
-
Cell-free supernatants from Streptomyces B6, Chryseobacterium B7, Pseudomonas B12, and Sphingomonas B17 all inhibited AG8 growth, implicating secreted products from each C6 member in contact-independent pathogen antagonism.
-
+
Cell-free cultures of each C6 member inhibited AG8 when the strains were tested separately, but the assembled C6 was among all ten mixtures whose supernatants showed no reported antifungal activity. Keep both observations: individual secretion-associated inhibition cannot be assigned to the mixed culture. This contrast does not identify an inhibitor, prove degradation of a particular fungal wall component, or show why the mixture lost the measured phenotype.
@@ -986,17 +918,28 @@
Evidence
+
+
+
+ "the cell-free supernatants from the rest of the eight bacteria and 10 SynComs did not show any antifungal activities"
+
+
+
-
Streptomyces B6, Chryseobacterium B7, Pseudomonas B12, and Sphingomonas B17 emitted volatile products that significantly inhibited AG8 in a physically separated Petri-dish assay.
-
+
Each of the four C6 member strains inhibited AG8 in the physically separated volatile assay, but C6 was not one of the four significantly inhibitory mixtures, identified as C2-C4 and C7. Retain the individual positives and mixture contrast without assigning a positive volatile mechanism to C6, identifying particular emitted compounds, or claiming that volatile effects are absent under every possible condition.
@@ -1063,6 +1006,19 @@
Evidence
+
+
+
+ "Rhodococcus erythropolis B43, and SynComs C2-4, C7"
+
+
+
@@ -1072,6 +1028,60 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Why do C6 individual-member phenotypes differ from the assembled mixture and host assays?
+
+
All four members showed individual secretion-associated and volatile inhibition, but the corresponding positive mixture results were absent under the tested conditions. C6 retained direct plate inhibition and a measured Salkowski signal; it shortened Arabidopsis primary roots but was not among the significant wheat-protection mixtures. These contrasts need mechanistic resolution, not erased nulls or invented assay-to-assay causal arrows. The paper labels a negative correlation as r-squared; this notation is not copied as a valid variance-explained statistic or silently repaired.
+
+
Attaches to: ecological_interactions#C6 Dual-Culture AG8 Radial Inhibition, ecological_interactions#C6 Salkowski auxin-assay output, ecological_interactions#C6-associated Arabidopsis primary-root shortening, ecological_interactions#C6 cell-free contrast with inhibitory member cultures, ecological_interactions#C6 volatile contrast with inhibitory member cultures
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
SynComs (C1, C3, C4, C7, C8, C9, and C10) significantly reduced wheat root rot score
+
+
+
+
the cell-free supernatants from the rest of the eight bacteria and 10 SynComs did not show any antifungal activities
+
+
+
+
+
@@ -1287,7 +1297,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1298,34 +1308,6 @@
Evidence
var evidenceCount = 2;
- nodes.push({
- id: intId,
- label: "Equal-Ratio Mixed-Genus C6 Assembly",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:1";
- var intType = "COMPETITION";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("biological process involved in interspecies interaction between organisms");
-
-
- var evidenceCount = 1;
-
nodes.push({
id: intId,
label: "C6 Dual-Culture AG8 Radial Inhibition",
@@ -1359,8 +1341,8 @@
Evidence
})();
(function() {
- var intId = "interaction:2";
- var intType = "MUTUALISM";
+ var intId = "interaction:1";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1369,15 +1351,11 @@
Evidence
var processes = [];
-
- processes.push("growth");
-
-
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "C6 Auxin Production",
+ label: "C6 Salkowski auxin-assay output",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1391,8 +1369,8 @@
Evidence
})();
(function() {
- var intId = "interaction:3";
- var intType = "MUTUALISM";
+ var intId = "interaction:2";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1409,7 +1387,7 @@
Evidence
nodes.push({
id: intId,
- label: "SynCom Arabidopsis Root-Length Response",
+ label: "C6-associated Arabidopsis primary-root shortening",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1423,8 +1401,8 @@
Evidence
})();
(function() {
- var intId = "interaction:4";
- var intType = "COMPETITION";
+ var intId = "interaction:3";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1433,11 +1411,11 @@
Evidence
processes.push("biological process involved in interspecies interaction between organisms");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
- label: "C6-Member Cell-Free AG8 Antagonism",
+ label: "C6 cell-free contrast with inhibitory member cultures",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1468,8 +1446,8 @@
Evidence
})();
(function() {
- var intId = "interaction:5";
- var intType = "COMPETITION";
+ var intId = "interaction:4";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1478,11 +1456,11 @@
Evidence
processes.push("biological process involved in interspecies interaction between organisms");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
- label: "C6-Member Volatile AG8 Antagonism",
+ label: "C6 volatile contrast with inhibitory member cultures",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1531,7 +1509,7 @@
Evidence
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
- var nodeCount = 10;
+ var nodeCount = 9;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html b/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html
index 86567a3ca..6aad91349 100644
--- a/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html
+++ b/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html
@@ -805,7 +805,7 @@
Ecological Interactions
Ecological interaction network for Wheat Crown-Rot Six-Strain Cross-Kingdom SMC
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for competition, colonization facilitation.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -813,13 +813,8 @@
Ecological Interactions
-
-
Ecological Interactions
-
The complete six-strain SMC was soil-drenched into nonsterile wheat pots after Fusarium pseudograminearum challenge and reduced the disease severity index relative to the pathogen-only treatment while sustaining plant growth.
+
The six-strain T19-plus-Bacillus SMC reduced the reported crown-rot DSI from 86.45% in pathogen-only pots to 25.93% with SMC, a 70.01% relative reduction, in nonsterile soil. Plant growth and thousand-kernel weight also improved. Preserve these controlled-pot treatment benefits without equating lower disease with bilateral competition or uniquely resolved immune, nutrient or microbial mediators. The design does not isolate the necessity of each SMC strain, and it is not multilocation field validation.
@@ -870,6 +864,19 @@
Evidence
+
+
+
+ "SMC+Fp increased TKW by 10.39% relative to Fp"
+
+
+
Evidence
-
The SMC shifted the resident wheat rhizosphere toward fungal and bacterial genera associated with antagonism, plant growth promotion, and nutrient supply under Fusarium challenge.
+
SMC treatment altered resident rhizosphere DNA-based composition, including higher relative abundances of Chaetomium, Trichoderma and Mortierella. Relative abundance is not absolute viable abundance or strain-resolved establishment of the inoculum. Functional assignments to enriched taxa and correlation-network associations are not direct measurements of nutrient transfer, mutualism, ecological necessity or stability after perturbation. These observations do not isolate remodeling as the causal mediator of the positive plant outcome.
@@ -888,17 +894,6 @@
SMC-associated wheat rhizosphere remodeling
-
Biological Processes:
-
-
-
- regulation of defense response
- (GO:0031347 )
-
-
-
-
@@ -925,10 +920,10 @@
Evidence
PMID:41504167
- - SUPPORT (IN_VIVO)
+ - SUPPORT (OTHER)
"Full-length ITS and 16S profiling revealed that SMC suppressed pathogenic Fusarium in favor of beneficial fungi (Mortierella, Trichoderma, Chaetomium) and plant growth-promoting bacteria (Pseudomonas, Paenibacillus)."
+ "Total DNA was extracted from soil using a commercial soil DNA extraction kit"
@@ -941,6 +936,90 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which SMC-dependent routes cause protection beyond community and metabolite associations?
+
+
Compatibility tests support nonantagonism, not demonstrated cross-feeding. The source reports positive plant responses to added allantoin and dihydrodaidzein and no direct antifungal activity of those compounds in the tested assay. This supports candidate host-mediated effects, not their necessity in the intact SMC or proof of a specific immune pathway. Community correlations likewise do not isolate the responsible taxa. Fresh primary text differs from existing cache wording; graph quotes use verified passages and the broader provenance discrepancy is tracked separately.
+
+
Attaches to: ecological_interactions#Six-strain SMC suppression of Fusarium crown rot, ecological_interactions#SMC-associated wheat rhizosphere remodeling
+
+
+
+
+ 4 evidence item(s)
+
+
+
+
functional validation at the molecular and genetic levels remains limited
+
+
+
+
showed no direct antifungal activity of either compound
+
+
+
+
significantly reduced DSI
+
+
+
+
These data demonstrate that the Bacillus supernatants are nonantagonistic to T19
+
+
+
+
+
@@ -1277,7 +1356,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1286,7 +1365,7 @@ Evidence
processes.push("defense response to fungus");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1305,15 +1384,11 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("regulation of defense response");
-
-
var evidenceCount = 2;
nodes.push({
diff --git a/history/records/Tomato_Oxylipin_SynCom3/2026-10-08T150228Z-codex-b1572f.yaml b/history/records/Tomato_Oxylipin_SynCom3/2026-10-08T150228Z-codex-b1572f.yaml
new file mode 100644
index 000000000..068a4440e
--- /dev/null
+++ b/history/records/Tomato_Oxylipin_SynCom3/2026-10-08T150228Z-codex-b1572f.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Tomato_Oxylipin_SynCom3.yaml
+ slug: Tomato_Oxylipin_SynCom3
+session:
+ id: 2026-10-08T150228Z-codex-b1572f
+ timestamp: '2026-10-08T15:02:28Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1939
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain complementary biofilm and defense phenotypes without asserting reciprocal
+ microbial benefit.; Keep treatment-induced host oxylipin activation distinct from bacterial
+ production or transfer.; Preserve biosynthesis-inhibition and overexpression evidence
+ at pathway rather than individual-compound scope.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
diff --git a/history/records/Wheat_Consortium_C1/2026-10-08T150228Z-codex-ff737c.yaml b/history/records/Wheat_Consortium_C1/2026-10-08T150228Z-codex-ff737c.yaml
new file mode 100644
index 000000000..9debcf466
--- /dev/null
+++ b/history/records/Wheat_Consortium_C1/2026-10-08T150228Z-codex-ff737c.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wheat_Consortium_C1.yaml
+ slug: Wheat_Consortium_C1
+session:
+ id: 2026-10-08T150228Z-codex-ff737c
+ timestamp: '2026-10-08T15:02:28Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1940
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Keep measured whole-C1 fungal inhibition without a bilateral-competition interpretation.;
+ Retain positive greenhouse protection and root weight without claiming superiority or
+ identified mediation.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
diff --git a/history/records/Wheat_Consortium_C6/2026-10-08T150229Z-codex-b61a7a.yaml b/history/records/Wheat_Consortium_C6/2026-10-08T150229Z-codex-b61a7a.yaml
new file mode 100644
index 000000000..0395907a4
--- /dev/null
+++ b/history/records/Wheat_Consortium_C6/2026-10-08T150229Z-codex-b61a7a.yaml
@@ -0,0 +1,29 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wheat_Consortium_C6.yaml
+ slug: Wheat_Consortium_C6
+session:
+ id: 2026-10-08T150229Z-codex-b61a7a
+ timestamp: '2026-10-08T15:02:29Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1941
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain whole-C6 plate inhibition without bilateral competition or automatic greenhouse
+ benefit.; Bound auxin production to the calibrated colorimetric assay without assigning
+ reciprocal benefit or plant delivery.; Preserve measured Arabidopsis root shortening without
+ turning a correlation into a hormone-mediated growth benefit.; Keep positive member supernatants
+ and the negative whole-C6 supernatant outcome together.; Keep positive member volatile
+ assays distinct from the non-significant whole-C6 mixture result.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
diff --git a/history/records/Wheat_CrownRot_SixStrain_CrossKingdom_SMC/2026-10-08T150229Z-codex-fc0ee7.yaml b/history/records/Wheat_CrownRot_SixStrain_CrossKingdom_SMC/2026-10-08T150229Z-codex-fc0ee7.yaml
new file mode 100644
index 000000000..db989be79
--- /dev/null
+++ b/history/records/Wheat_CrownRot_SixStrain_CrossKingdom_SMC/2026-10-08T150229Z-codex-fc0ee7.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml
+ slug: Wheat_CrownRot_SixStrain_CrossKingdom_SMC
+session:
+ id: 2026-10-08T150229Z-codex-fc0ee7
+ timestamp: '2026-10-08T15:02:29Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1942
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve the positive SMC disease and grain outcomes without an unsupported bilateral-competition
+ mechanism.; Keep relative community-profile observations distinct from colonization facilitation
+ and inferred ecological functions.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
diff --git a/kb/communities/Tomato_Oxylipin_SynCom3.yaml b/kb/communities/Tomato_Oxylipin_SynCom3.yaml
index 4492a7714..443943811 100644
--- a/kb/communities/Tomato_Oxylipin_SynCom3.yaml
+++ b/kb/communities/Tomato_Oxylipin_SynCom3.yaml
@@ -92,12 +92,12 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: Simplified Community Synergistic Protection
- description: The three-species tomato rhizosphere community combines one
- phytopathogen-inducible Asticcacaulis member that triggers plant defense
- responses with two stably colonizing Arachidicoccus and Phenylobacterium
- members that promote biofilm formation.
- interaction_type: MUTUALISM
+- name: SynCom3-associated biofilm and host defense
+ description: The three-genus tomato-root inoculum combines pathogen-inducible Asticcacaulis with stably colonizing
+ Arachidicoccus and Phenylobacterium. The abstract attributes host-defense triggering to the inducible member
+ and biofilm promotion to the stable colonizers, with protection similar to the 38-member precursor. These positive
+ complementary phenotypes do not measure reciprocal bacterial fitness or metabolite exchange. Exact strain identities
+ and selective biofilm mediation are not resolved by the inspected abstract.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biofilm formation
@@ -105,21 +105,27 @@ ecological_interactions:
id: GO:0042710
label: biofilm formation
downstream:
- - target: Oxylipin-Mediated Disease Resistance
- description: The synergistic three-species community intensifies oxylipin
- pathway activation in phytopathogen-infected tomato leaves.
+ - target: SynCom3-induced leaf oxylipin responses
+ description: 'SynCom3 treatment intensified oxylipin responses in infected tomato leaves. PARTIAL for biofilm
+ formation as the mediator: the abstract links complementary community functions to protection but does not
+ isolate biofilm formation as the unique cause of leaf pathway activation.'
evidence:
- reference: PMID:37549573
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: the phytopathogen-inducible species triggering plant defense responses and the
- stably-colonizing species promoting biofilm formation
- explanation: Supports the two complementary functions that make the
- simplified rhizosphere community protective.
-- name: Oxylipin-Mediated Disease Resistance
- description: Inducible and stable colonizers synergize to trigger host defense and biofilm-mediated
- protection.
- interaction_type: MUTUALISM
+ evidence_source: OTHER
+ snippet: the phytopathogen-inducible species triggering plant defense responses and the stably-colonizing species
+ promoting biofilm formation
+ explanation: Abstract-level attribution of complementary functions; detailed biofilm assay context was not available.
+ - reference: PMID:37549573
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: The simplified community exhibited similar protective effects as the 38-species community
+ explanation: Preserves the positive protection comparison while distinguishing the final inoculum from its precursor.
+- name: SynCom3-induced leaf oxylipin responses
+ description: The simplified community intensified oxylipin-pathway activation in Botrytis-infected tomato leaves.
+ This is a host response to the bacterial treatment, not microbial mutualism or evidence that the bacteria themselves
+ synthesize the listed divinyl ethers. The downstream biosynthesis perturbation provides stronger mechanistic
+ evidence than association alone.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: oxylipin
@@ -136,23 +142,24 @@ ecological_interactions:
label: colnelenic acid
downstream:
- target: Divinyl Ether-Dependent Botrytis Protection
- description: Intensified oxylipin-pathway activation feeds production of
- antimicrobial divinyl ethers required for community-induced protection
- against Botrytis cinerea.
+ description: 'The host oxylipin branch supplies divinyl ethers implicated in protection: inhibiting their biosynthesis
+ abolished the community-induced resistance, while SlLOX5/SlDES1 overexpression with higher divinyl-ether levels
+ increased resistance. Retain this pathway-level perturbation evidence without claiming separate necessity
+ of each compound or bacterial-to-plant transfer.'
evidence:
- - *id001
- reference: PMID:37549573
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: the activation of oxylipin pathways in the phytopathogen-infected leaves was significantly
- intensified by the simplified community
- explanation: Supports oxylipin-pathway activation as the plant defense
- mechanism intensified by the simplified tomato rhizosphere community.
+ evidence_source: IN_VIVO
+ snippet: the activation of oxylipin pathways in the phytopathogen-infected leaves was significantly intensified
+ by the simplified community
+ explanation: Supports oxylipin-pathway activation as the plant defense mechanism intensified by the simplified
+ tomato rhizosphere community.
- name: Divinyl Ether-Dependent Botrytis Protection
- description: The community-induced tomato defense requires biosynthesis of
- the antimicrobial divinyl ethers colneleic acid and colnelenic acid; when
- this branch is blocked, the SynCom no longer protects against Botrytis.
- interaction_type: MUTUALISM
+ description: Inhibiting divinyl-ether biosynthesis abolished SynCom-induced tomato resistance to Botrytis cinerea.
+ Conversely, SlLOX5/SlDES1-overexpressing plants with higher divinyl-ether levels had stronger resistance than
+ wild type. Preserve this positive pathway-level evidence for colneleic/colnelenic-acid-associated defense. The
+ abstract does not specify the inhibition method or establish that each named compound is independently indispensable,
+ sufficient alone, or transferred from bacteria.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: colneleic acid
@@ -166,11 +173,17 @@ ecological_interactions:
evidence:
- reference: PMID:37549573
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic
- and colnelenic acid, fully abolished the community-induced plant disease resistance
- explanation: Supports colneleic and colnelenic acid biosynthesis as
- required downstream chemistry for SynCom-induced gray mold resistance.
+ evidence_source: IN_VIVO
+ snippet: the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic and colnelenic acid,
+ fully abolished the community-induced plant disease resistance
+ explanation: Supports dependence on the perturbed biosynthetic branch, not separate necessity of each listed
+ compound.
+ - reference: PMID:37549573
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: transgenic plants overexpressing SlLOX5 and SlDES1, with higher levels of divinyl ethers, displayed
+ stronger resistance against B. cinerea compared to wild-type plants
+ explanation: Preserves the complementary positive host perturbation reported in the abstract.
environmental_factors:
- name: defined synthetic community design
value: A 38-species community was simplified to Asticcacaulis, Arachidicoccus, and Phenylobacterium
@@ -224,3 +237,30 @@ related_ingredients:
and colnelenic acid, fully abolished the community-induced plant disease resistance
explanation: Names colnelenic acid as an antimicrobial divinyl ether essential to the
community's disease resistance.
+discussions:
+- discussion_id: tomato_causal_scope_batch121
+ prompt: Which microbial contributions and individual divinyl ethers mediate SynCom3 protection?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#SynCom3-associated biofilm and host defense
+ - ecological_interactions#SynCom3-induced leaf oxylipin responses
+ - ecological_interactions#Divinyl Ether-Dependent Botrytis Protection
+ rationale: The abstract supports complementary functions, host oxylipin activation and a real biosynthesis perturbation,
+ not merely correlation. Detailed primary methods would resolve the inhibition target, individual-compound necessity
+ and biofilm mediation. Reciprocal bacterial benefit and cross-feeding are not established. Preserve both existing
+ directions and positive protection without inventing a new mechanism.
+ evidence:
+ - reference: PMID:37549573
+ snippet: the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic and colnelenic acid,
+ fully abolished the community-induced plant disease resistance
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T15:02:26Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain complementary biofilm and defense phenotypes without asserting reciprocal microbial benefit.;
+ Keep treatment-induced host oxylipin activation distinct from bacterial production or transfer.; Preserve biosynthesis-inhibition
+ and overexpression evidence at pathway rather than individual-compound scope. Issue#1939; reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
+ llm_assisted: true
diff --git a/kb/communities/Wheat_Consortium_C1.yaml b/kb/communities/Wheat_Consortium_C1.yaml
index aaf210469..a586442ad 100644
--- a/kb/communities/Wheat_Consortium_C1.yaml
+++ b/kb/communities/Wheat_Consortium_C1.yaml
@@ -157,36 +157,10 @@ taxonomy:
sp. B12, Pseudomonas sp. P25
explanation: Identifies Pseudomonas sp. P25 as a C1 member.
ecological_interactions:
-- name: Equal-Ratio Pseudomonas C1 Assembly
- description: >
- Pseudomonas sp. B5, Pseudomonas sp. B11, Pseudomonas sp. B12, and
- Pseudomonas sp. P25 were combined at equal ratios as the same-genus C1
- consortium within the ten-SynCom wheat-rhizosphere design.
- 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:36118206
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: SynCom 1(C1) Pseudomonas sp. B5, Pseudomonas sp. B11, Pseudomonas
- sp. B12, Pseudomonas sp. P25
- explanation: Table 1 names the four Pseudomonas isolates that make up SynCom
- 1.
- - reference: PMID:36118206
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: SynComs were obtained by mixing the individuals in equal ratios
- explanation: Supports the equal-ratio inoculum construction used for C1 and
- the other wheat-rhizosphere SynComs.
- name: C1 SynCom inhibition of R. solani AG8 radial growth
- description: The four-Pseudomonas C1 SynCom inhibited Rhizoctonia solani AG8
- radial growth in the in vitro dual-culture assay.
- interaction_type: COMPETITION
+ description: The assembled C1 inhibited Rhizoctonia solani AG8 radial growth in dual culture, with reported inhibition
+ of 37.00% (SD 6.57) in Table 2. This is a positive fungal-growth outcome, not evidence that both bacterial and
+ fungal fitness declined. Plate inhibition does not establish the mediator or guarantee host protection.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Pseudomonas sp. B5
@@ -214,15 +188,21 @@ ecological_interactions:
- reference: PMID:36118206
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8,
- and C10, inhibited the growth of R. solani AG8 to varying degrees
- explanation: Places C1 among the SynComs with significant AG8 radial-growth
- inhibition.
+ snippet: In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8, and C10, inhibited the growth
+ of R. solani AG8 to varying degrees
+ explanation: Places C1 among the SynComs with significant AG8 radial-growth inhibition.
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: SynCom 1(C1)37.00 ± 6.57
+ explanation: Table 2 reports the whole-mixture plate inhibition estimate and standard deviation.
- name: C1 SynCom protection of wheat under AG8 challenge
- description: C1 significantly reduced wheat root rot scores and increased wheat
- fresh root weight relative to AG8-challenged controls in greenhouse soil.
+ description: C1 reduced root-rot scores and increased fresh root weight of AG8-challenged Alpowa wheat in the
+ three-week greenhouse soil assay. Preserve this positive whole-mixture benefit. The study did not show superiority
+ over the best individual strain or establish reciprocal microbial benefit, bilateral competition, inoculum persistence,
+ or a unique IAA/volatile mechanism. Only B5 among the four C1 members significantly reduced disease when tested
+ individually.
scope: COMMUNITY_LEVEL
- interaction_type: COMPETITION
participating_taxa:
- preferred_term: Pseudomonas sp. B5
term:
@@ -249,10 +229,14 @@ ecological_interactions:
- reference: PMID:36118206
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SynCom C1, composed of four different Pseudomonas members, significantly
- reduced wheat root rot and increased root weight, compared with the controls
- explanation: Supports the host-protection outcome measured for the whole C1
- consortium.
+ snippet: SynCom C1, composed of four different Pseudomonas members, significantly reduced wheat root rot and
+ increased root weight, compared with the controls
+ explanation: Supports the host-protection outcome measured for the whole C1 consortium.
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: None of them was significantly better than a single strain
+ explanation: Bounds claims of emergent superiority without erasing the significant C1 host outcome.
environmental_factors:
- name: Host plant
value: Triticum aestivum
@@ -314,6 +298,36 @@ curation_history:
- timestamp: '2026-10-02T06:10:22Z'
curator: codex
action: REVIEW_CAUSAL_GRAPH
- changes: Removed three downstream edges that linked Wheat C1 equal-ratio
- assembly and dual-culture AG8 inhibition to subsequent assay endpoints.
+ changes: Removed three downstream edges that linked Wheat C1 equal-ratio assembly and dual-culture AG8 inhibition
+ to subsequent assay endpoints.
llm_assisted: true
+- timestamp: '2026-10-08T15:02:27Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Keep measured whole-C1 fungal inhibition without a bilateral-competition interpretation.; Retain positive
+ greenhouse protection and root weight without claiming superiority or identified mediation. Issue#1940; reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
+ llm_assisted: true
+discussions:
+- discussion_id: c1_causal_scope_batch121
+ prompt: Which processes explain C1 protection beyond its separate laboratory phenotypes?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#C1 SynCom inhibition of R. solani AG8 radial growth
+ - ecological_interactions#C1 SynCom protection of wheat under AG8 challenge
+ rationale: C1 is protective in soil, yet individual-versus-mixture phenotypes differ. The paper reports no antifungal
+ activity from any SynCom cell-free supernatant and identifies C2-C4/C7, not C1, as significant volatile mixtures.
+ Lower C1 auxin and volatile outputs are not selective proof that these routes are impossible. Inoculum persistence
+ was explicitly not assessed. Equal-ratio preparation remains in metadata and the earlier removal of workflow
+ arrows remains intact.
+ evidence:
+ - reference: PMID:36118206
+ snippet: None of them was significantly better than a single strain
+ - reference: PMID:36118206
+ snippet: the cell-free supernatants from the rest of the eight bacteria and 10 SynComs did not show any antifungal
+ activities
+ - reference: PMID:36118206
+ snippet: While not assessed here, investigation of the fate of those inoculations in the soil after plant growth
+ is needed to address their persistence and stability
+ posed_by: codex
+ posed_date: '2026-10-08'
diff --git a/kb/communities/Wheat_Consortium_C6.yaml b/kb/communities/Wheat_Consortium_C6.yaml
index b9132e112..30f062278 100644
--- a/kb/communities/Wheat_Consortium_C6.yaml
+++ b/kb/communities/Wheat_Consortium_C6.yaml
@@ -155,41 +155,10 @@ taxonomy:
Pseudomonas sp. B12, Sphingomonas sp. B17
explanation: Identifies Sphingomonas sp. B17 as a C6 member.
ecological_interactions:
-- name: Equal-Ratio Mixed-Genus C6 Assembly
- description: >
- Streptomyces sp. B6, Chryseobacterium sp. B7, Pseudomonas sp. B12,
- and Sphingomonas sp. B17 were combined at equal ratios as the random
- mixed-genus C6 consortium within a broader ten-SynCom wheat-rhizosphere
- design.
- 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:36118206
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- SynCom 6(C6) Streptomyces sp. B6, Chryseobacterium sp. B7,
- Pseudomonas sp. B12, Sphingomonas sp. B17
- explanation: Table 1 names the four bacterial isolates that make up SynCom 6.
- - reference: PMID:36118206
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- SynComs were obtained by mixing the individuals in equal ratios
- explanation: >
- Supports the mixed inoculum construction used for C6 and the other
- wheat-rhizosphere SynComs.
- name: C6 Dual-Culture AG8 Radial Inhibition
- description: >
- C6 inhibited Rhizoctonia solani AG8 radial growth in the direct
- dual-culture agar assay, placing it among the eight inhibitory SynComs in
- the ten-consortium panel.
- interaction_type: COMPETITION
+ description: The assembled C6 inhibited Rhizoctonia solani AG8 radial growth in dual culture, with reported inhibition
+ of 34.48% (SD 5.91) in Table 2. This is a positive fungal-growth outcome, not evidence that both bacterial and
+ fungal fitness declined. Plate inhibition does not establish the mediator or guarantee host protection.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Streptomyces sp. B6
@@ -217,48 +186,52 @@ ecological_interactions:
- reference: PMID:36118206
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8,
- and C10, inhibited the growth of R. solani AG8 to varying degrees
- explanation: Places C6 among the SynComs with significant AG8 radial-growth
- inhibition.
-- name: C6 Auxin Production
- description: >
- C6 culture supernatant contained indole-3-acetic acid in the whole-SynCom
- auxin assay, one of the plant-growth-modulating phenotypes measured across
- all ten consortia.
+ snippet: In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8, and C10, inhibited the growth
+ of R. solani AG8 to varying degrees
+ explanation: Places C6 among the SynComs with significant AG8 radial-growth inhibition.
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: SynCom 6(C6)34.48 ± 5.91
+ explanation: Table 2 reports the whole-mixture plate inhibition estimate and standard deviation.
+- name: C6 Salkowski auxin-assay output
+ description: C6 culture supernatant gave an IAA-calibrated Salkowski estimate of 11.76 ug/mL (SD 2.83) in Table
+ 3. This is a whole-mixture colorimetric output, not structural identification of every reactive compound, member-resolved
+ synthesis, delivery to plant roots or mutualism. No selective hormone perturbation links it to the separate
+ Arabidopsis root-length result.
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
metabolites:
- preferred_term: indole-3-acetic acid
term:
id: CHEBI:16411
label: indole-3-acetic acid
- biological_processes:
- - preferred_term: growth
- term:
- id: GO:0040007
- label: growth
+ notes: IAA-calibrated Salkowski interpretation; not independently resolved molecular identity or plant delivery.
evidence:
- reference: PMID:36118206
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- including 10 single strains and all 10 SynComs, produced auxin at various
- concentrations
- explanation: >
- Supports IAA production by C6 in the whole-SynCom auxin panel.
-- name: SynCom Arabidopsis Root-Length Response
- description: >
- The SynCom panel, including C6, altered primary root length in a controlled
- Arabidopsis plate assay used to connect bacterial auxin production with
- plant-root phenotypes.
+ snippet: 'including 10 single strains and all 10 SynComs, produced auxin at various concentrations
+
+ '
+ explanation: Reports the authors auxin interpretation; Methods specify colorimetry calibrated with IAA.
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: SynCom 6(C6)11.76 ± 2.83
+ explanation: Table 3 gives the C6 assay estimate and standard deviation.
+- name: C6-associated Arabidopsis primary-root shortening
+ description: C6 was among the nine mixtures that significantly shortened primary roots of plate-grown Arabidopsis
+ after cocultivation. Shorter primary roots are the measured endpoint, not demonstrated growth promotion or reciprocal
+ benefit. The across-treatment association with a separate auxin assay does not establish IAA as the necessary
+ mediator. This Arabidopsis phenotype is not a wheat disease-protection result; C6 was not among the mixtures
+ with significant greenhouse root-rot reduction or fresh-root-weight improvement.
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
metabolites:
- preferred_term: indole-3-acetic acid
term:
id: CHEBI:16411
label: indole-3-acetic acid
+ notes: Candidate explanation from a separate assay correlation, not demonstrated hormone mediation.
biological_processes:
- preferred_term: growth
term:
@@ -267,20 +240,18 @@ ecological_interactions:
evidence:
- reference: PMID:36118206
supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- Similar reductions in the primary root length of Arabidopsis seedlings
- were observed in all SynComs except C5
- explanation: >
- Supports C6 as one of the SynComs with a measured Arabidopsis primary
- root-length effect.
-- name: C6-Member Cell-Free AG8 Antagonism
- description: >
- Cell-free supernatants from Streptomyces B6, Chryseobacterium B7,
- Pseudomonas B12, and Sphingomonas B17 all inhibited AG8 growth, implicating
- secreted products from each C6 member in contact-independent pathogen
- antagonism.
- interaction_type: COMPETITION
+ evidence_source: IN_VIVO
+ snippet: 'Similar reductions in the primary root length of Arabidopsis seedlings were observed in all SynComs
+ except C5
+
+ '
+ explanation: Reports the primary-root reduction in the living Arabidopsis plate assay; not increased wheat growth.
+- name: C6 cell-free contrast with inhibitory member cultures
+ description: 'Cell-free cultures of each C6 member inhibited AG8 when the strains were tested separately, but
+ the assembled C6 was among all ten mixtures whose supernatants showed no reported antifungal activity. Keep
+ both observations: individual secretion-associated inhibition cannot be assigned to the mixed culture. This
+ contrast does not identify an inhibitor, prove degradation of a particular fungal wall component, or show why
+ the mixture lost the measured phenotype.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Streptomyces sp. B6
@@ -308,29 +279,34 @@ ecological_interactions:
- reference: PMID:36118206
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- three Pseudomonas sp. strains (B5, B11, and B12), Streptomyces sp. B6,
- Chryseobacterium sp. B7, and Sphingomonas sp. B17 became irregular shaped
- and creamy colored
- explanation: >
- Identifies Pseudomonas B12, Streptomyces B6, Chryseobacterium B7, and
- Sphingomonas B17 among the strains whose cell-free supernatants visibly
- altered AG8 margins.
+ snippet: 'three Pseudomonas sp. strains (B5, B11, and B12), Streptomyces sp. B6, Chryseobacterium sp. B7, and
+ Sphingomonas sp. B17 became irregular shaped and creamy colored
+
+ '
+ explanation: 'Identifies Pseudomonas B12, Streptomyces B6, Chryseobacterium B7, and Sphingomonas B17 among the
+ strains whose cell-free supernatants visibly altered AG8 margins.
+
+ '
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 'The growth of AG8 treated with these bacterial strains was significantly inhibited
+
+ '
+ explanation: 'Supports significant AG8 inhibition by the C6-member cell-free supernatants.
+
+ '
- reference: PMID:36118206
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- The growth of AG8 treated with these bacterial strains was significantly
- inhibited
- explanation: >
- Supports significant AG8 inhibition by the C6-member cell-free
- supernatants.
-- name: C6-Member Volatile AG8 Antagonism
- description: >
- Streptomyces B6, Chryseobacterium B7, Pseudomonas B12, and Sphingomonas B17
- emitted volatile products that significantly inhibited AG8 in a physically
- separated Petri-dish assay.
- interaction_type: COMPETITION
+ snippet: the cell-free supernatants from the rest of the eight bacteria and 10 SynComs did not show any antifungal
+ activities
+ explanation: Direct whole-mixture null result contrasted with the positive individual-member cultures.
+- name: C6 volatile contrast with inhibitory member cultures
+ description: Each of the four C6 member strains inhibited AG8 in the physically separated volatile assay, but
+ C6 was not one of the four significantly inhibitory mixtures, identified as C2-C4 and C7. Retain the individual
+ positives and mixture contrast without assigning a positive volatile mechanism to C6, identifying particular
+ emitted compounds, or claiming that volatile effects are absent under every possible condition.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Streptomyces sp. B6
@@ -358,20 +334,26 @@ ecological_interactions:
- reference: PMID:36118206
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- the volatiles emitted by nine single strains and four SynComs
- significantly inhibited the growth of AG8
- explanation: >
- Supports volatile-mediated AG8 growth inhibition in the assay panel.
+ snippet: 'the volatiles emitted by nine single strains and four SynComs significantly inhibited the growth of
+ AG8
+
+ '
+ explanation: Panel-level positive count; it does not identify C6 as an inhibitory mixture.
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 'They included four Pseudomonas spp. B5, B11, B12, and P25, Streptomyces sp. B6, Chryseobacterium sp.
+ B7, Sphingomonas sp. B17
+
+ '
+ explanation: 'Identifies all four C6 member genera or strains in the volatile-producing strain set.
+
+ '
- reference: PMID:36118206
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- They included four Pseudomonas spp. B5, B11, B12, and P25,
- Streptomyces sp. B6, Chryseobacterium sp. B7, Sphingomonas sp. B17
- explanation: >
- Identifies all four C6 member genera or strains in the volatile-producing
- strain set.
+ snippet: Rhodococcus erythropolis B43, and SynComs C2-4, C7
+ explanation: The end of the explicit positive list identifies the four mixtures and excludes C6 from that list.
environmental_factors:
- name: Host plant
value: Triticum aestivum
@@ -432,7 +414,40 @@ curation_history:
- timestamp: '2026-10-02T06:04:09Z'
curator: codex
action: REPAIR_CAUSAL_GRAPH
- changes: Removed five Wheat C6 assay workflow edges linking consortium
- assembly and aggregate auxin or AG8 antagonism phenotypes to later
- dual-culture, cell-free, volatile, and Arabidopsis root-length assays.
+ changes: Removed five Wheat C6 assay workflow edges linking consortium assembly and aggregate auxin or AG8 antagonism
+ phenotypes to later dual-culture, cell-free, volatile, and Arabidopsis root-length assays.
+ llm_assisted: true
+- timestamp: '2026-10-08T15:02:27Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain whole-C6 plate inhibition without bilateral competition or automatic greenhouse benefit.; Bound
+ auxin production to the calibrated colorimetric assay without assigning reciprocal benefit or plant delivery.;
+ Preserve measured Arabidopsis root shortening without turning a correlation into a hormone-mediated growth benefit.;
+ Keep positive member supernatants and the negative whole-C6 supernatant outcome together.; Keep positive member
+ volatile assays distinct from the non-significant whole-C6 mixture result. Issue#1941; reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
llm_assisted: true
+discussions:
+- discussion_id: c6_causal_scope_batch121
+ prompt: Why do C6 individual-member phenotypes differ from the assembled mixture and host assays?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#C6 Dual-Culture AG8 Radial Inhibition
+ - ecological_interactions#C6 Salkowski auxin-assay output
+ - ecological_interactions#C6-associated Arabidopsis primary-root shortening
+ - ecological_interactions#C6 cell-free contrast with inhibitory member cultures
+ - ecological_interactions#C6 volatile contrast with inhibitory member cultures
+ rationale: All four members showed individual secretion-associated and volatile inhibition, but the corresponding
+ positive mixture results were absent under the tested conditions. C6 retained direct plate inhibition and a
+ measured Salkowski signal; it shortened Arabidopsis primary roots but was not among the significant wheat-protection
+ mixtures. These contrasts need mechanistic resolution, not erased nulls or invented assay-to-assay causal arrows.
+ The paper labels a negative correlation as r-squared; this notation is not copied as a valid variance-explained
+ statistic or silently repaired.
+ evidence:
+ - reference: PMID:36118206
+ snippet: SynComs (C1, C3, C4, C7, C8, C9, and C10) significantly reduced wheat root rot score
+ - reference: PMID:36118206
+ snippet: the cell-free supernatants from the rest of the eight bacteria and 10 SynComs did not show any antifungal
+ activities
+ posed_by: codex
+ posed_date: '2026-10-08'
diff --git a/kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml b/kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml
index da0f5291a..1fb0efdec 100644
--- a/kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml
+++ b/kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml
@@ -238,9 +238,11 @@ taxonomy:
explanation: Identifies strain S8 as Bacillus halotolerans and lists its CCTCC deposit.
ecological_interactions:
- name: Six-strain SMC suppression of Fusarium crown rot
- description: The complete six-strain SMC was soil-drenched into nonsterile wheat pots after Fusarium pseudograminearum challenge
- and reduced the disease severity index relative to the pathogen-only treatment while sustaining plant growth.
- interaction_type: COMPETITION
+ description: The six-strain T19-plus-Bacillus SMC reduced the reported crown-rot DSI from 86.45% in pathogen-only
+ pots to 25.93% with SMC, a 70.01% relative reduction, in nonsterile soil. Plant growth and thousand-kernel weight
+ also improved. Preserve these controlled-pot treatment benefits without equating lower disease with bilateral
+ competition or uniquely resolved immune, nutrient or microbial mediators. The design does not isolate the necessity
+ of each SMC strain, and it is not multilocation field validation.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: defense response to fungus
@@ -251,32 +253,33 @@ ecological_interactions:
- reference: PMID:41504167
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: With SMC treatment, the DSI decreased to 25.93%, a 70.01% reduction relative to Fp, demonstrating marked control
- efficacy.
+ snippet: With SMC treatment, the DSI decreased to 25.93%, a 70.01% reduction relative to Fp, demonstrating marked
+ control efficacy.
explanation: Reports the Fusarium crown-rot disease-severity reduction in the SMC+Fp treatment.
+ - reference: PMID:41504167
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: SMC+Fp increased TKW by 10.39% relative to Fp
+ explanation: Preserves the positive measured grain-development outcome in the challenged treatment.
- name: SMC-associated wheat rhizosphere remodeling
- description: The SMC shifted the resident wheat rhizosphere toward fungal and bacterial genera associated with antagonism,
- plant growth promotion, and nutrient supply under Fusarium challenge.
- interaction_type: COLONIZATION_FACILITATION
+ description: SMC treatment altered resident rhizosphere DNA-based composition, including higher relative abundances
+ of Chaetomium, Trichoderma and Mortierella. Relative abundance is not absolute viable abundance or strain-resolved
+ establishment of the inoculum. Functional assignments to enriched taxa and correlation-network associations
+ are not direct measurements of nutrient transfer, mutualism, ecological necessity or stability after perturbation.
+ These observations do not isolate remodeling as the causal mediator of the positive plant outcome.
scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: regulation of defense response
- term:
- id: GO:0031347
- label: regulation of defense response
evidence:
- reference: PMID:41504167
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SMC and SMC+Fp increased the relative abundances of growth-promoting and antagonistic genera, including Chaetomium,
- Trichoderma, and Mortierella.
+ snippet: SMC and SMC+Fp increased the relative abundances of growth-promoting and antagonistic genera, including
+ Chaetomium, Trichoderma, and Mortierella.
explanation: Supports SMC-associated remodeling of the resident fungal rhizosphere community.
- reference: PMID:41504167
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Full-length ITS and 16S profiling revealed that SMC suppressed pathogenic Fusarium in favor of beneficial fungi
- (Mortierella, Trichoderma, Chaetomium) and plant growth-promoting bacteria (Pseudomonas, Paenibacillus).
- explanation: Supports SMC-associated enrichment of resident fungal and bacterial taxa with plant-beneficial trait annotations.
+ evidence_source: OTHER
+ snippet: Total DNA was extracted from soil using a commercial soil DNA extraction kit
+ explanation: Defines the DNA-based profiling context, not viable-cell or inoculum-strain tracking.
growth_media:
- name: nonsterile wheat soil pot assay
temperature: 25
@@ -365,13 +368,45 @@ curation_history:
- timestamp: '2026-09-22T00:20:14Z'
curator: codex
action: CREATE_RECORD
- changes: Created CommunityMech:000414 for the six-strain Trichoderma/Bacillus cross-kingdom wheat Fusarium crown-rot SMC
- from PMID:41504167, including strain membership, SynCom assembly design, nonsterile wheat-pot cultivation, Fusarium challenge,
- and SMC disease-suppression and rhizosphere-remodeling outcomes.
+ changes: Created CommunityMech:000414 for the six-strain Trichoderma/Bacillus cross-kingdom wheat Fusarium crown-rot
+ SMC from PMID:41504167, including strain membership, SynCom assembly design, nonsterile wheat-pot cultivation,
+ Fusarium challenge, and SMC disease-suppression and rhizosphere-remodeling outcomes.
llm_assisted: true
- timestamp: '2026-09-22T00:33:44Z'
curator: codex
action: FIX_REVIEW_FINDING
- changes: Fixed CommunityMech#1035 by removing redundant participating_taxa from the whole-community Fusarium crown-rot suppression
- edge; omitted participating_taxa already credits every SMC member.
+ changes: Fixed CommunityMech#1035 by removing redundant participating_taxa from the whole-community Fusarium crown-rot
+ suppression edge; omitted participating_taxa already credits every SMC member.
llm_assisted: true
+- timestamp: '2026-10-08T15:02:27Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Preserve the positive SMC disease and grain outcomes without an unsupported bilateral-competition mechanism.;
+ Keep relative community-profile observations distinct from colonization facilitation and inferred ecological
+ functions. Issue#1942; reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
+ llm_assisted: true
+discussions:
+- discussion_id: crown_causal_scope_batch121
+ prompt: Which SMC-dependent routes cause protection beyond community and metabolite associations?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Six-strain SMC suppression of Fusarium crown rot
+ - ecological_interactions#SMC-associated wheat rhizosphere remodeling
+ rationale: Compatibility tests support nonantagonism, not demonstrated cross-feeding. The source reports positive
+ plant responses to added allantoin and dihydrodaidzein and no direct antifungal activity of those compounds
+ in the tested assay. This supports candidate host-mediated effects, not their necessity in the intact SMC or
+ proof of a specific immune pathway. Community correlations likewise do not isolate the responsible taxa. Fresh
+ primary text differs from existing cache wording; graph quotes use verified passages and the broader provenance
+ discrepancy is tracked separately.
+ evidence:
+ - reference: PMID:41504167
+ snippet: functional validation at the molecular and genetic levels remains limited
+ - reference: PMID:41504167
+ snippet: showed no direct antifungal activity of either compound
+ - reference: PMID:41504167
+ snippet: significantly reduced DSI
+ - reference: PMID:41504167
+ snippet: These data demonstrate that the Bacillus supernatants are nonantagonistic to T19
+ posed_by: codex
+ posed_date: '2026-10-08'
diff --git a/references_cache/PMID_41504167.txt b/references_cache/PMID_41504167.txt
index 6dfbc6829..07c2e19d3 100644
--- a/references_cache/PMID_41504167.txt
+++ b/references_cache/PMID_41504167.txt
@@ -59,3 +59,11 @@ Total DNA was extracted from soil using a commercial soil DNA extraction kit acc
Soil Metabolomics Analysis
Metabolites were profiled on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 120 mass spectrometer (Thermo) using methanol-extracted samples that were ultrasonicated, centrifuged, and filtered prior to injection. Chromatographic separation was performed on an ACQUITY UPLC HSS T3 column with gradient elution using 0.1% formic acid in water and 0.1% formic acid in acetonitrile. The mass spectrometer operated in both positive and negative ion modes with a full-scan range of m/z 70-1000, and data-dependent acquisition was used for MS/MS fragmentation. Metabolomic data were processed in MS-DIAL and annotated against multiple reference libraries, including the PerSonalbio Next-Generation Metabolomics Database, mzCloud, LIPID MAPS, HMDB0000003, MoNA, and NIST_2020_MSMS, as well as AI-predicted MS/MS spectral libraries. Peaks with a detection frequency below 50% in quality control samples were removed, and the resulting metabolite relative abundance matrix was used for statistical analyses.
+
+Selected discussion excerpts verified 2026-10-08
+Source: Zhou et al., Cross-Kingdom Synthetic Microbiota Suppresses Wheat Fusarium Crown Rot by Remodeling the Rhizosphere Microbiome and Metabolome, DOI:10.1021/acs.jafc.5c11786; https://pmc.ncbi.nlm.nih.gov/articles/PMC12833866/
+License: CC BY-NC-ND 4.0. These three short excerpts are not a full-text import. Earlier cache wording is preserved; source discrepancies remain tracked in issue #1945.
+
+functional validation at the molecular and genetic levels remains limited
+showed no direct antifungal activity of either compound
+significantly reduced DSI
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 4acb4fe5b..483518cae 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,43 @@ 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`.
+## Batch121: Plant Outcomes And Mixture Contrasts
+
+[Decisions](decisions/20261008-four-records-batch121.yaml),
+[provenance](cache-provenance-20261008-batch121.json),
+[validation](validation-20261008-batch121.json), and
+[self-adversarial review](adversarial-review-20261008-batch121.yaml) cover
+tomato oxylipin SynCom3, wheat C1 and C6, and the six-strain wheat crown-rot SMC.
+Twelve of fourteen nodes and both existing arrows remain, with six renames.
+Two wheat inoculum-preparation nodes are removed; no new topology is introduced.
+
+Tomato retains positive biosynthesis-inhibition and overexpression evidence
+at host-pathway scope, without claiming reciprocal bacterial mutualism.
+C1 retains plate inhibition and greenhouse protection, not superiority over
+the best single strain. C6 keeps direct plate inhibition and Salkowski output,
+Arabidopsis root shortening, and the contrasts between positive individual
+strains and negative assembled-mixture cell-free/volatile assays.
+Crown-rot treatment benefits remain, while relative DNA profiles and correlation
+networks do not establish viable colonization or causal ecological necessity.
+Positive added-compound plant effects and negative direct fungal assays remain
+distinct from necessity in the intact SMC.
+
+Four whole records and three unique primary studies were reviewed. Wheat C1/C6
+and crown-rot complete main bodies, methods, tables and captions were read;
+tomato is abstract-bounded. Original figure pixels, external supplements, raw
+data and analysis code were not audited. All 34 graph/discussion quotations
+match primary text and local caches. Three short crown-rot excerpts, 21 words,
+are appended with attribution and its CC BY-NC-ND 4.0 license; earlier cache
+bytes are preserved for the provenance follow-up. The other 922 caches,
+456 records and unrelated raw fields are unchanged. Four append-only histories
+record the repairs. No Edison submission or spend was needed.
+
+Repairs #1939-#1942 await protected-main merge. Non-graph member/role,
+metal/abundance and source-provenance follow-ups #1943-#1945 remain open.
+This is source-based self-review, not independent approval or completion of
+the overall review and protected merge.
+
+
## Batch120: Measured Outcomes And Inferred Routes
[Decisions](decisions/20261008-four-records-batch120.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch121.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch121.yaml
new file mode 100644
index 000000000..b4a888235
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch121.yaml
@@ -0,0 +1,830 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 5afca28e40023b10e05db1c228ec70ecbaf5d7a9
+scope:
+- kb/communities/Tomato_Oxylipin_SynCom3.yaml
+- kb/communities/Wheat_Consortium_C1.yaml
+- kb/communities/Wheat_Consortium_C6.yaml
+- kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch121.json
+findings:
+- issue: 1939
+ severity: P2
+ finding: Keep tomato SynCom3 divinyl-ether causality without reciprocal-mutualism claims
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1940
+ severity: P2
+ finding: Separate wheat C1 inoculum assembly and measured protection from ecological mechanism
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1941
+ severity: P2
+ finding: Preserve wheat C6 mixture-versus-member assay contrasts and null outcomes
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1942
+ severity: P2
+ finding: Distinguish wheat crown-rot SMC protection from inferred rhizosphere mechanisms
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1943
+ severity: P2
+ finding: Ground tomato SynCom3 member evidence and cross-feeder roles to the exact community
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1944
+ severity: P2
+ finding: Verify incidental-metal attribution and abundance scope in wheat C1 and C6 records
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1945
+ severity: P2
+ finding: Reconcile wheat crown-rot source-cache discrepancies and experimental timing
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+adversarial_checks:
+- 'All 14 original nodes and two arrows accounted for: 12 nodes and both directions retained, two inoculum-preparation
+ nodes removed, six renames, no new topology. Targets and discussion anchors resolve. Prior C1/C6 workflow-arrow
+ deletions are not undone.'
+- Tomato complementary biofilm/host-defense functions are not reciprocal microbial fitness. Keep positive protection
+ comparable to the 38-member precursor and intensified host oxylipin responses. Biofilm mediation remains PARTIAL.
+ Biosynthesis inhibition abolishes protection and SlLOX5/SlDES1 overexpression increases resistance; do not erase
+ these stronger causal experiments or promote separate necessity of each divinyl ether.
+- C1 retains 37.00% plate inhibition and positive greenhouse root-rot/root-weight effects. Equal-ratio assembly
+ is preparation, not colonization facilitation. No demonstrated superiority over the best single strain; persistence
+ was explicitly unassessed. Whole-mixture cell-free and volatile results are not inferred from individual members.
+- C6 retains 34.48% direct plate inhibition and 11.76 ug/mL IAA-calibrated Salkowski output. Colorimetry is not
+ resolved compound identity or plant delivery. Arabidopsis primary-root shortening is not growth promotion or significant
+ wheat protection. The source negative-r-squared notation is not copied as a valid statistic.
+- C6 individual members have positive cell-free and volatile results, but assembled-mixture supernatants are null
+ and C6 is absent from the significant volatile-mixture list. Both positive members and null mixture observations
+ stay together. No universal inefficacy claim and no new assay-to-assay causal arrows.
+- Crown-rot SMC retains positive disease reduction from 86.45% to 25.93% and challenged TKW +10.39%. Relative DNA
+ profiles and correlation networks are not viability, colonization, nutrient flux, reciprocal cooperation or ecological
+ necessity. Added allantoin/dihydrodaidzein positive host assays and negative direct fungal assays remain explicit,
+ not erased or promoted to intact-SMC necessity.
+- 'Twenty-four graph and 10 discussion quotes match fresh primary and caches. Three unique studies: complete wheat
+ C1/C6 and crown-rot main bodies, methods, results, discussion, tables and captions read; tomato abstract-bounded.
+ No original figure pixels, external supplements, raw data or code audit. Crown-rot license CC BY-NC-ND 4.0, not
+ unrestricted CC BY. Three short excerpts, 21 words, appended with verified Zhou attribution; old cache prefix
+ preserved. Cache/source wording and treatment-assignment discrepancies remain #1945.'
+- 'Four guarded writes and append-only histories preserve 456 other records, 922 unchanged caches, unrelated raw
+ YAML blocks and previous histories/decisions. Canonical taxa, participant lists and scopes unchanged. Shared evidence
+ aliases detached. Non-graph member/role, metal/abundance and provenance/timing findings remain #1943-#1945.'
+- Fifteen focused tests and 12 control/mutation/restored-control probes pass. Mutations reject tomato mutualism,
+ unique-biofilm promotion, erased biosynthesis/overexpression positives, restored C1 assembly, best-single superiority,
+ C6 auxin mutualism, root-growth promotion, erased supernatant/volatile nulls, erased crown-rot grain benefit and
+ profile-to-colonization promotion. No canonical writes in probes.
+- 'All four records pass schema, strict, terms, full-record references, snippets, rank and history. 1146 selected
+ tests including palette pass; not full Linux CI certification. Network: 57 unchanged warnings, zero structural
+ defects. Exact descriptions on 456 pages, 1359 nodes and 522 arrows and deterministic rendering verified, not
+ screenshot QA.'
+- 'Participant lists and scopes unchanged: 299 list users, 414 community-level, 136 mixed, 278 community-only, 1568
+ taxa, 1281 solely credited. Scope credit is not certification of actual participant coverage. Connectivity logic
+ and thresholds unchanged.'
+- 'Issues #1939-#1942 addressed pending protected-main merge; #1943-#1945 remain open. No Edison extension or credits.
+ Prior Ruegeria #1883 configured-authentication blocker not retried unchanged. Source-based self-review is not
+ independent approval; root #1836 and actual exact-head protected checks still required.'
+- 'Corpus: 392 reviewed, 14 pending, 54 needs_research across 460 records. Overall goal, protected merge and branch
+ deletion remain incomplete. Postcommit docs-current and exact-head publication are separate gates, not preasserted
+ here.'
+- The initial 1146-test run passed, then lint identified two SIM300 assertion-operand-order violations. Only operand
+ order was corrected. Original gate/probe outputs are preserved; focused tests, all1146selected tests, all12mutation
+ probes and lint were rerun successfully against the corrected file. No assertion or canonical-data weakening.
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Restore unsupported tomato mutualism
+ test: test_tomato_complementarity_is_not_reciprocal_mutualism
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 21
+ assertion: assert all("interaction_type" not in n for n in nodes)
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/interaction_type
+ before: null
+ after: MUTUALISM
+ - mutation: Promote biofilm to the proven unique mediator
+ test: test_tomato_biofilm_mediation_remains_partial
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 33
+ assertion: assert "PARTIAL for biofilm formation as the mediator" in a["downstream"][0]["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/downstream/0/description
+ before: 'SynCom3 treatment intensified oxylipin responses in infected tomato leaves. PARTIAL for biofilm
+ formation as the mediator: the abstract links complementary community functions to protection but does
+ not isolate biofilm formation as the unique cause of leaf pathway activation.'
+ after: Biofilm is the proven unique mediator.
+ - mutation: Erase positive biosynthesis perturbation
+ test: test_tomato_retains_positive_biosynthesis_perturbation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 41
+ assertion: assert "fully abolished" in evidence["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/2/evidence/0/snippet
+ before: the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic and colnelenic acid,
+ fully abolished the community-induced plant disease resistance
+ after: Only correlation was measured.
+ - mutation: Erase complementary overexpression benefit
+ test: test_tomato_retains_complementary_overexpression_evidence
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 51
+ assertion: assert "overexpressing SlLOX5 and SlDES1" in node["evidence"][1]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/2/evidence/1/snippet
+ before: transgenic plants overexpressing SlLOX5 and SlDES1, with higher levels of divinyl ethers, displayed
+ stronger resistance against B. cinerea compared to wild-type plants
+ after: Overexpression had no benefit.
+ - mutation: Restore C1 assembly as an ecological node
+ test: test_wheat_c1_assembly_is_metadata_not_an_ecological_node
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 60
+ assertion: assert len(nodes) == 2 and len(rows[1]["removed_node_decisions"]) == 1
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions
+ before:
+ - name: C1 SynCom inhibition of R. solani AG8 radial growth
+ description: The assembled C1 inhibited Rhizoctonia solani AG8 radial growth in dual culture, with reported
+ inhibition of 37.00% (SD 6.57) in Table 2. This is a positive fungal-growth outcome, not evidence that
+ both bacterial and fungal fitness declined. Plate inhibition does not establish the mediator or guarantee
+ host protection.
+ scope: COMMUNITY_LEVEL
+ participating_taxa:
+ - preferred_term: Pseudomonas sp. B5
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. B11
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. B12
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. P25
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ biological_processes:
+ - preferred_term: interspecies interaction
+ term:
+ id: GO:0044419
+ label: biological process involved in interspecies interaction between organisms
+ evidence:
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8, and C10, inhibited
+ the growth of R. solani AG8 to varying degrees
+ explanation: Places C1 among the SynComs with significant AG8 radial-growth inhibition.
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: "SynCom 1(C1)37.00 \xB1 6.57"
+ explanation: Table 2 reports the whole-mixture plate inhibition estimate and standard deviation.
+ - name: C1 SynCom protection of wheat under AG8 challenge
+ description: C1 reduced root-rot scores and increased fresh root weight of AG8-challenged Alpowa wheat
+ in the three-week greenhouse soil assay. Preserve this positive whole-mixture benefit. The study did
+ not show superiority over the best individual strain or establish reciprocal microbial benefit, bilateral
+ competition, inoculum persistence, or a unique IAA/volatile mechanism. Only B5 among the four C1 members
+ significantly reduced disease when tested individually.
+ scope: COMMUNITY_LEVEL
+ participating_taxa:
+ - preferred_term: Pseudomonas sp. B5
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. B11
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. B12
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. P25
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ 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:36118206
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: SynCom C1, composed of four different Pseudomonas members, significantly reduced wheat root
+ rot and increased root weight, compared with the controls
+ explanation: Supports the host-protection outcome measured for the whole C1 consortium.
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: None of them was significantly better than a single strain
+ explanation: Bounds claims of emergent superiority without erasing the significant C1 host outcome.
+ after:
+ - name: C1 SynCom inhibition of R. solani AG8 radial growth
+ description: The assembled C1 inhibited Rhizoctonia solani AG8 radial growth in dual culture, with reported
+ inhibition of 37.00% (SD 6.57) in Table 2. This is a positive fungal-growth outcome, not evidence that
+ both bacterial and fungal fitness declined. Plate inhibition does not establish the mediator or guarantee
+ host protection.
+ scope: COMMUNITY_LEVEL
+ participating_taxa:
+ - preferred_term: Pseudomonas sp. B5
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. B11
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. B12
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. P25
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ biological_processes:
+ - preferred_term: interspecies interaction
+ term:
+ id: GO:0044419
+ label: biological process involved in interspecies interaction between organisms
+ evidence:
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: In vitro dual-culture assay showed eight SynComs, including C1-C4, C6-C8, and C10, inhibited
+ the growth of R. solani AG8 to varying degrees
+ explanation: Places C1 among the SynComs with significant AG8 radial-growth inhibition.
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: "SynCom 1(C1)37.00 \xB1 6.57"
+ explanation: Table 2 reports the whole-mixture plate inhibition estimate and standard deviation.
+ - name: C1 SynCom protection of wheat under AG8 challenge
+ description: C1 reduced root-rot scores and increased fresh root weight of AG8-challenged Alpowa wheat
+ in the three-week greenhouse soil assay. Preserve this positive whole-mixture benefit. The study did
+ not show superiority over the best individual strain or establish reciprocal microbial benefit, bilateral
+ competition, inoculum persistence, or a unique IAA/volatile mechanism. Only B5 among the four C1 members
+ significantly reduced disease when tested individually.
+ scope: COMMUNITY_LEVEL
+ participating_taxa:
+ - preferred_term: Pseudomonas sp. B5
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. B11
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. B12
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ - preferred_term: Pseudomonas sp. P25
+ term:
+ id: NCBITaxon:286
+ label: Pseudomonas
+ 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:36118206
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: SynCom C1, composed of four different Pseudomonas members, significantly reduced wheat root
+ rot and increased root weight, compared with the controls
+ explanation: Supports the host-protection outcome measured for the whole C1 consortium.
+ - reference: PMID:36118206
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: None of them was significantly better than a single strain
+ explanation: Bounds claims of emergent superiority without erasing the significant C1 host outcome.
+ - name: Inoculum assembly
+ - mutation: Promote C1 to superior-to-best-single performance
+ test: test_wheat_c1_host_benefit_is_not_best_strain_superiority
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 79
+ assertion: node["evidence"][1]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/1/evidence/1/snippet
+ before: None of them was significantly better than a single strain
+ after: The mixture outperformed the best single strain.
+ - mutation: Turn C6 colorimetry into mutualism
+ test: test_wheat_c6_salkowski_is_not_resolved_delivery_or_mutualism
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 98
+ assertion: assert "interaction_type" not in node and "biological_processes" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/1/interaction_type
+ before: null
+ after: MUTUALISM
+ - mutation: Convert root shortening into growth promotion
+ test: test_wheat_c6_primary_root_shortening_is_not_growth_promotion
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 112
+ assertion: assert "not demonstrated growth promotion" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/2/description
+ before: C6 was among the nine mixtures that significantly shortened primary roots of plate-grown Arabidopsis
+ after cocultivation. Shorter primary roots are the measured endpoint, not demonstrated growth promotion
+ or reciprocal benefit. The across-treatment association with a separate auxin assay does not establish
+ IAA as the necessary mediator. This Arabidopsis phenotype is not a wheat disease-protection result; C6
+ was not among the mixtures with significant greenhouse root-rot reduction or fresh-root-weight improvement.
+ after: C6 demonstrated IAA-mediated growth promotion.
+ - mutation: Erase whole-C6 cell-free null
+ test: test_wheat_c6_cell_free_member_positives_do_not_erase_mixture_null
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 123
+ assertion: assert "10 SynComs did not show any antifungal activities" in node["evidence"][2]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/3/evidence/2/snippet
+ before: the cell-free supernatants from the rest of the eight bacteria and 10 SynComs did not show any antifungal
+ activities
+ after: All SynCom supernatants were inhibitory.
+ - mutation: Insert C6 into positive volatile mixture list
+ test: test_wheat_c6_volatile_positive_list_is_not_a_mixture_benefit
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 134
+ assertion: assert "SynComs C2-4, C7" in node["evidence"][2]["snippet"]
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/4/evidence/2/snippet
+ before: Rhodococcus erythropolis B43, and SynComs C2-4, C7
+ after: SynComs C2-4, C6, C7
+ - mutation: Erase crown-rot grain benefit
+ test: test_crown_rot_retains_positive_disease_and_grain_outcomes
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 145
+ assertion: assert node["evidence"][1]["snippet"] == "SMC+Fp increased TKW by 10.39% relative to Fp"
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/0/evidence/1/snippet
+ before: SMC+Fp increased TKW by 10.39% relative to Fp
+ after: No grain benefit occurred.
+ - mutation: Promote relative profiles to colonization facilitation
+ test: test_crown_rot_profiles_and_compound_assays_do_not_prove_necessity
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 152
+ assertion: assert "interaction_type" not in node and "biological_processes" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/1/interaction_type
+ before: null
+ after: COLONIZATION_FACILITATION
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Tomato_Oxylipin_SynCom3.yaml: 228468ac43630c33939dd4b0708476ef4006c9af7dbf1f108e7f88c36b0962c3
+ kb/communities/Wheat_Consortium_C1.yaml: 96fe252612fed33b257aed133760e929462f7021eef085750dfbb4469b1e6f26
+ kb/communities/Wheat_Consortium_C6.yaml: e0fca5ba8eedf1676949159803aa46771fa28af92dab641d102f531d3adc2c87
+ kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml: cf2ae08aab3fed7a94f5a0068db6d108baf734b22152547241ebe258f52d15ce
+ tests/test_causal_review_batch121.py: ac1e4196de6c948bc26632cc5b53ddf3e0e59a3eb9570340ae4e21fbc771a6cb
+ probe_script_sha256: ff36c48b3d7e84c51a8511846051408b929a0722a5c104a7f7e9c0ea3b0f29aa
+ scope: In-memory control/mutation/restored-control; no canonical writes and not additional pytest tests.
+ artifact: /private/tmp/communitymech-batch121/adversarial-regression-proof.json
+ sha256: daf0c2ac8b3e513f2f0539dcf8a9082c6e870c437a1f27a46cb4c7c22239fe7a
+lint_correction:
+ description: Two SIM300 equality-operand-order fixes in the new test only. Assertions retain identical string-equality
+ semantics. Original focused/regression passes and failed lint retained; focused,combined regressions,lint and
+ all12probes rerun on the corrected test. No canonical data or validation thresholds changed.
+ superseded_gate_outputs:
+ - check: focused
+ command:
+ - /Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3
+ - -m
+ - pytest
+ - -q
+ - tests/test_causal_review_batch121.py
+ exit_code: 0
+ expected_exit_codes:
+ - 0
+ log: /private/tmp/communitymech-batch121/verification/focused.log
+ log_sha256: 1bb220465fb38a66322df21f319c57ddc286c948f1dbd9ed95e5f16c3dbf57e7
+ output_tail: '............... [100%]
+
+ 15 passed in 4.01s
+
+ '
+ - check: regressions
+ command:
+ - /Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3
+ - -m
+ - pytest
+ - -q
+ - tests/test_causal_review_batch10.py
+ - tests/test_causal_review_batch100.py
+ - tests/test_causal_review_batch101.py
+ - tests/test_causal_review_batch102.py
+ - tests/test_causal_review_batch103.py
+ - tests/test_causal_review_batch104.py
+ - tests/test_causal_review_batch105.py
+ - tests/test_causal_review_batch106.py
+ - tests/test_causal_review_batch107.py
+ - tests/test_causal_review_batch108.py
+ - tests/test_causal_review_batch109.py
+ - tests/test_causal_review_batch11.py
+ - tests/test_causal_review_batch110.py
+ - tests/test_causal_review_batch111.py
+ - tests/test_causal_review_batch112.py
+ - tests/test_causal_review_batch113.py
+ - tests/test_causal_review_batch114.py
+ - tests/test_causal_review_batch115.py
+ - tests/test_causal_review_batch116.py
+ - tests/test_causal_review_batch117.py
+ - tests/test_causal_review_batch118.py
+ - tests/test_causal_review_batch119.py
+ - tests/test_causal_review_batch12.py
+ - tests/test_causal_review_batch120.py
+ - tests/test_causal_review_batch121.py
+ - tests/test_causal_review_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-batch121/verification/regressions.log
+ log_sha256: 873297760b8f8ff58434193e806da505e241c10d71fd4b5606e07069b36f0923
+ output_tail: '........................................................................ [ 6%]
+
+ ........................................................................ [ 12%]
+
+ ........................................................................ [ 18%]
+
+ ........................................................................ [ 25%]
+
+ ........................................................................ [ 31%]
+
+ ........................................................................ [ 37%]
+
+ ........................................................................ [ 43%]
+
+ ........................................................................ [ 50%]
+
+ ........................................................................ [ 56%]
+
+ ........................................................................ [ 62%]
+
+ ........................................................................ [ 69%]
+
+ ........................................................................ [ 75%]
+
+ ........................................................................ [ 81%]
+
+ ........................................................................ [ 87%]
+
+ ........................................................................ [ 94%]
+
+ .................................................................. [100%]
+
+ 1146 passed in 390.61s (0:06:30)
+
+ '
+ - check: just-lint
+ command:
+ - just
+ - lint
+ exit_code: 1
+ expected_exit_codes:
+ - 0
+ log: /private/tmp/communitymech-batch121/verification/just-lint.log
+ log_sha256: 2fe8d75b0a76266199cfe190c9be5f96ccb92a6fafa1204a15db38f851ab6f2f
+ output_tail: "SIM300 [*] Yoda condition detected\n --> tests/test_causal_review_batch121.py:79:9\n |\n77\
+ \ | assert \"reduced root-rot scores and increased fresh root weight\" in node[\"description\"]\n78\
+ \ | assert (\n79 | / \"None of them was significantly better than a single strain\"\n80 | |\
+ \ == node[\"evidence\"][1][\"snippet\"]\n | |_________________________________________^\n81 | \
+ \ )\n82 | assert \"Only B5\" in node[\"description\"]\n |\n |\n78 | assert (\n - \
+ \ \"None of them was significantly better than a single strain\"\n - == node[\"evidence\"][1][\"\
+ snippet\"]\n79 + node[\"evidence\"][1][\"snippet\"]\n80 + == \"None of them was significantly\
+ \ better than a single strain\"\n81 | )\n |\n\nSIM300 [*] Yoda condition detected\n --> tests/test_causal_review_batch121.py:145:12\n\
+ \ |\n143 | assert \"interaction_type\" not in node\n144 | assert \"86.45%\" in node[\"description\"\
+ ] and \"25.93%\" in node[\"description\"]\n145 | assert \"SMC+Fp increased TKW by 10.39% relative to Fp\"\
+ \ == node[\"evidence\"][1][\"snippet\"]\n | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\
+ 146 | assert \"not multilocation field validation\" in node[\"description\"]\n |\n |\n144 | \
+ \ assert \"86.45%\" in node[\"description\"] and \"25.93%\" in node[\"description\"]\n - assert \"\
+ SMC+Fp increased TKW by 10.39% relative to Fp\" == node[\"evidence\"][1][\"snippet\"]\n145 + assert node[\"\
+ evidence\"][1][\"snippet\"] == \"SMC+Fp increased TKW by 10.39% relative to Fp\"\n146 | assert \"not multilocation\
+ \ field validation\" in node[\"description\"]\n |\n\nFound 2 errors.\n[*] 2 fixable with the `--fix` option.\n\
+ uv run black --check src/ tests/ scripts/\nAll done! \u2728 \U0001F370 \u2728\n374 files would be left unchanged.\n\
+ uv 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`)\nerror: recipe `lint`\
+ \ failed on line 518 with exit code 1\n"
+ prior_probe_artifact: /private/tmp/communitymech-batch121/adversarial-regression-proof-before-lint-fix.json
+ prior_probe_sha256: 6af8a2078d2804b963e2293514fb721e0c7b1df16b43c951aa8431e3daa6d305
+verification:
+ combined_regressions: 1146 passed in 406.93s (0:06:46)
+ new_regression_tests: 15
+ total_recorded_gate_outputs: 41
+ primary_graph_snippet_proof:
+ graph_quotations: 24
+ discussion_quotations: 10
+ fresh_primary_literal_matches: 34
+ all_cached_literal_matches: 34
+ retained_nodes: 12
+ removed_nodes: 2
+ renamed_nodes: 6
+ retained_arrows: 2
+ removed_arrows: 0
+ new_nodes_or_directions: 0
+ references: Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment.
+ Total checks in the reference CLI counts issues, not examined snippets.
+ snippet_counts_by_record:
+ kb/communities/Tomato_Oxylipin_SynCom3.yaml:
+ MATCH: 14
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wheat_Consortium_C1.yaml:
+ MATCH: 14
+ RENDERING: 1
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wheat_Consortium_C6.yaml:
+ MATCH: 19
+ RENDERING: 2
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml:
+ MATCH: 33
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9073
+ categories:
+ MATCH: 8925
+ RENDERING: 31
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 76
+ caveat: Informational audit exit0 is not clean-corpus or entailment certification.
+ network:
+ existing_findings_preserved: 57
+ added_findings: {}
+ removed_findings: {}
+ structural_defects: 0
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml: e6545894c4182a28cb36818c71a5d2958dd7d5494fba58b101f4a478a6f0eed5
+ tests/test_causal_review_batch121.py: ac1e4196de6c948bc26632cc5b53ddf3e0e59a3eb9570340ae4e21fbc771a6cb
+ 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-batch121.json: 52293a3b4509be41d05b369a019fd0b99a2f4144b2f978b986eb2a911cb54d18
+ kb/communities/Tomato_Oxylipin_SynCom3.yaml: 228468ac43630c33939dd4b0708476ef4006c9af7dbf1f108e7f88c36b0962c3
+ kb/communities/Wheat_Consortium_C1.yaml: 96fe252612fed33b257aed133760e929462f7021eef085750dfbb4469b1e6f26
+ kb/communities/Wheat_Consortium_C6.yaml: e0fca5ba8eedf1676949159803aa46771fa28af92dab641d102f531d3adc2c87
+ kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml: cf2ae08aab3fed7a94f5a0068db6d108baf734b22152547241ebe258f52d15ce
+ history_sha256:
+ history/records/Tomato_Oxylipin_SynCom3/2026-10-08T150228Z-codex-b1572f.yaml: 6ba7a6ebd8bf8265071204827b11af6f071dfd5e10ad96c04ff657e297518ea3
+ history/records/Wheat_Consortium_C1/2026-10-08T150228Z-codex-ff737c.yaml: b0376f6cb7bc63570018a97ba08ead611c9ed773920b1ed0315be9c0ef75a916
+ history/records/Wheat_Consortium_C6/2026-10-08T150229Z-codex-b61a7a.yaml: d5b973cc60054869f95d2eda524821d86d189566e304ed5b2c4b885eafa7dd54
+ history/records/Wheat_CrownRot_SixStrain_CrossKingdom_SMC/2026-10-08T150229Z-codex-fc0ee7.yaml: 9a91fe60edf1f4e0b3c6f4d66f56651dac882ca5eb88ac1bd0d835690a641482
+ unchanged_records: 456
+ unchanged_caches: 922
+ immutable_prior_history_and_decision_files: 894
+ cache_changes:
+ - path: references_cache/PMID_41504167.txt
+ before_sha256: 4d486d1a61d439b27b58e26f089b287540ce49b0dfea5ff74b9d4c45b9d3b2ff
+ after_sha256: 09dbe7338cb653bdfec20d7103d2510e252b08f70b9166b38c193199e7e6e2fd
+ old_prefix_preserved: true
+ added_bytes: 606
+ added_quotation_words: 21
+ source_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC12833866/
+ source_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ source_sha256: 5473ae75df36a381dc6f107afe7cd3d93851565378b25de0baccca019d8ee36c
+ license: CC BY-NC-ND 4.0
+ scope: Three short selected discussion excerpts, not a full-text import. Existing provenance discrepancies retained
+ for issue1945.
+ quotations:
+ - functional validation at the molecular and genetic levels remains limited
+ - showed no direct antifungal activity of either compound
+ - significantly reduced DSI
+ 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_batch120:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ explanation: All participant lists and scopes are unchanged;299participant-list users. Scope credit is not certification
+ of actual participant coverage. Connectivity logic and thresholds are unchanged.
+corpus:
+ records: 460
+ nodes: 1373
+ edges: 530
+ review_status_counts:
+ needs_research: 54
+ pending: 14
+ reviewed: 392
+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.
+ All four whole records and14existing nodes/two arrows reviewed. Retain12nodes/two arrows,remove two inoculum-assembly
+ nodes,rename six nodes,no new topology.
+- Four fresh EuropePMC abstract/metadata and Crossref retrievals cover three unique primary studies. Complete wheat
+ C1/C6 and crown-rot main bodies read including methods,results,discussion,tables and captions. C1/C6 XML/body
+ hashes are identical. No original figure pixels,separate supplementary files,raw data or analysis code audited.
+- Tomato changes are abstract-bounded. EuropePMC has no PMC identifier and lists subscription-required DOI access;
+ DOI open was unavailable and ScienceDirect PII S0981942823004527 returned403. No exhaustive full-text absence
+ claim,access bypass or author contact. No full article-body import.
+- Tomato retains positive complementary community functions,leaf oxylipin activation,biosynthesis-inhibition loss
+ of protection,and SlLOX5/SlDES1 overexpression benefit. This supports pathway-level causality,not reciprocal bacterial
+ fitness,unique biofilm mediation or independent necessity of each divinyl ether. Exact member/role metadata remains1943.
+- Wheat C1/C6 primary is CC BY4.0. Equal-ratio assembly is preparation,not ecological colonization; prior workflow-arrow
+ removals remain intact. C1 retains significant greenhouse benefits but no demonstrated superiority over the best
+ single strain. C6 retains positive dual-plate inhibition and Salkowski output but Arabidopsis root shortening
+ is not growth promotion. Positive individual-member secretion/volatile assays do not override whole-mixture nulls.
+ Persistence explicitly was not assessed. Negative r-squared notation is not silently repaired. Non-graph abundance/metal
+ scope remains1944.
+- Crown-rot primary is CC BY-NC-ND4.0,not unrestricted CC BY. Preserve measured pot disease and grain benefits.
+ Relative DNA profiles are not viable-cell colonization or functional flux; correlation networks do not establish
+ cooperation or ecological necessity. Added allantoin/dihydrodaidzein have positive plant outcomes and negative
+ direct fungal assays; do not erase these positives or infer intact-SMC necessity. Old cache wording differs from
+ fresh abstract and bacterial-treatment assignments; timing and provenance remain1945.
+- Exactly three short crown-rot discussion excerpts,21quoted words,are appended with source/license attribution.
+ Old cache bytes remain an unchanged prefix. No protocol addition or full-body import. All24graph and10discussion
+ quotes independently matched to fresh primary and authoritative local caches; literal matches are not entailment
+ proof. Existing selected caches and primary text read; no claim to manual whole-reading of the very long C1 markdown
+ cache.
+- Initial and fresh pre-creation all-state1175issue titles/bodies searched,seven matching bodies read,161matching
+ local paths found including ignored/hidden files except.git,docs,site,references_cache,.env.1035/1037 address
+ crown-rot participants/CI;615 host-cultivation schema;1521,1378,1375,981 other records. Not a historical PR-comment
+ audit.
+- Four guarded writes preserve456otherrecords,922unchangedcaches,unrelated raw YAML blocks and all prior histories/decisions.
+ Four append-only histories and curation events. Taxon identities,participant lists and scopes unchanged; evidence
+ aliases detached. No experimental optimization.
+- 'Existing-graph repair with no new nodes/directions: no Edison run,provider submission or spend. Prior authorized
+ Ruegeria1883 authentication blocker not retried unchanged; no credential inspected. Source-based 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-batch121.json b/reports/causal_graph_review/cache-provenance-20261008-batch121.json
new file mode 100644
index 000000000..be6aec73c
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch121.json
@@ -0,0 +1,350 @@
+{
+ "changes": [
+ {
+ "path": "references_cache/PMID_41504167.txt",
+ "before_sha256": "4d486d1a61d439b27b58e26f089b287540ce49b0dfea5ff74b9d4c45b9d3b2ff",
+ "after_sha256": "09dbe7338cb653bdfec20d7103d2510e252b08f70b9166b38c193199e7e6e2fd",
+ "old_prefix_preserved": true,
+ "added_bytes": 606,
+ "added_quotation_words": 21,
+ "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12833866/",
+ "source_artifact": "/private/tmp/communitymech-batch121/crown-primary.txt",
+ "source_sha256": "5473ae75df36a381dc6f107afe7cd3d93851565378b25de0baccca019d8ee36c",
+ "license": "CC BY-NC-ND 4.0",
+ "scope": "Three short selected discussion excerpts, not a full-text import. Existing provenance discrepancies retained for issue1945.",
+ "quotations": [
+ "functional validation at the molecular and genetic levels remains limited",
+ "showed no direct antifungal activity of either compound",
+ "significantly reduced DSI"
+ ]
+ }
+ ],
+ "unchanged_cache_files": 922,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch121/baseline.json": "e92b45d03d6c465de8302b503b81336144391a7179c1c56de54b1b0e64245493",
+ "/private/tmp/communitymech-batch121/c1-abstract.txt": "9b252c4c3c94a7afa338c6615098c79ec89fe90cc684fc17e509ea766245d611",
+ "/private/tmp/communitymech-batch121/c1-crossref.json": "c792f94d269f646a9d7d0f9f234de848623ad76a5ce3aa505775615a3d13ca79",
+ "/private/tmp/communitymech-batch121/c1-metadata.json": "434bf6f8f3d784a8c75b37dc9f0136447a673bc68c49da5ddc665230c275015e",
+ "/private/tmp/communitymech-batch121/c1-primary.txt": "3c36c4e7d883c60a96ae0a33027d1f1bfcaef52793e453ae3383b3b73071dbd9",
+ "/private/tmp/communitymech-batch121/c1-primary.xml": "cc69d3ea571e2bdf4f416df2f4185725c01989357333a0a0db4b084fcf014d8e",
+ "/private/tmp/communitymech-batch121/c6-abstract.txt": "9b252c4c3c94a7afa338c6615098c79ec89fe90cc684fc17e509ea766245d611",
+ "/private/tmp/communitymech-batch121/c6-crossref.json": "c792f94d269f646a9d7d0f9f234de848623ad76a5ce3aa505775615a3d13ca79",
+ "/private/tmp/communitymech-batch121/c6-metadata.json": "10c50b850e2f7a1f15d45cfdc428de4200f1f2f960c05e3ffbc277b670f827b0",
+ "/private/tmp/communitymech-batch121/c6-primary.txt": "3c36c4e7d883c60a96ae0a33027d1f1bfcaef52793e453ae3383b3b73071dbd9",
+ "/private/tmp/communitymech-batch121/c6-primary.xml": "cc69d3ea571e2bdf4f416df2f4185725c01989357333a0a0db4b084fcf014d8e",
+ "/private/tmp/communitymech-batch121/cache-append.json": "2b8a00668844860f4d1a6cf0008be793cd1c5b3b0df674fb7c43de0dcff074be",
+ "/private/tmp/communitymech-batch121/crown-abstract.txt": "16c788598453a61f000910a5e0f8a4008ba8519ee5701ae3a3e17d18e825810b",
+ "/private/tmp/communitymech-batch121/crown-crossref.json": "617800ca4aaf5db73b90bc0ee491c93fe22e5c5503c0e69cb440d5bebeff61d5",
+ "/private/tmp/communitymech-batch121/crown-metadata.json": "128b9f3ad73905c118c5572a74c5f187560ab502296adc51af428b6afac8a99c",
+ "/private/tmp/communitymech-batch121/crown-primary.txt": "5473ae75df36a381dc6f107afe7cd3d93851565378b25de0baccca019d8ee36c",
+ "/private/tmp/communitymech-batch121/crown-primary.xml": "0b76802b924a03d6b2a8621bf63c8a068d565267c876bc05e7116e440ea84939",
+ "/private/tmp/communitymech-batch121/issue-dedup-current.json": "855090c628e4814fea1ca1d0a4d8f7081c3727c971fe3f2dd7b30d768ec374d8",
+ "/private/tmp/communitymech-batch121/local-matches-expanded.txt": "04facf3dcb06aa984a9d620a2d9cafe0da8f0057a5d5c12d1e7292682f65dc44",
+ "/private/tmp/communitymech-batch121/local-matches.txt": "cb931efcd842d1fafd28bbfbe63bbd88b39af4056a9d998fc69585e2a683e41e",
+ "/private/tmp/communitymech-batch121/primary-manifest.json": "ecb885005fbdbcc00b35bbcb6f894fd0ad63a3b310d764ce6af154e647aee7c3",
+ "/private/tmp/communitymech-batch121/target-baseline.json": "5c3e2c7f8253df656fc9ba1aac4d6398c43a5c4564c9cd2f515db56f08597cf9",
+ "/private/tmp/communitymech-batch121/tomato-abstract.txt": "572769f335cb9e22e9f3bfa7ace56d21697b0c5f499c5ec3c4fd8bd277382a96",
+ "/private/tmp/communitymech-batch121/tomato-crossref.json": "da0362a3f97c2b71031319206884eab8da40cf83d4df180ddf67cc8e484a5473",
+ "/private/tmp/communitymech-batch121/tomato-metadata.json": "61aa41a2b34c20f8d257ff9ec6fbab461a42907621e3a4f5c918b612315f6b95",
+ "references_cache/PMID_36118206.md": "314ea2db4d987629dc153dd408a6862de979aab0fc85cdeeef3cff44e024e0c6",
+ "references_cache/PMID_37549573.txt": "a84a280cb33625ddefb3a79de376d86d6f6fe774e0f53bf8978677e50e34ffa4",
+ "references_cache/PMID_41504167.txt": "09dbe7338cb653bdfec20d7103d2510e252b08f70b9166b38c193199e7e6e2fd"
+ },
+ "source_access": {
+ "retrieval_manifest": {
+ "tomato": {
+ "pmid": "37549573",
+ "doi": "10.1016/j.plaphy.2023.107941",
+ "pmcid": null,
+ "title": "A simplified synthetic rhizosphere bacterial community steers plant oxylipin pathways for preventing foliar phytopathogens.",
+ "metadata": "/private/tmp/communitymech-batch121/tomato-metadata.json",
+ "metadata_sha256": "61aa41a2b34c20f8d257ff9ec6fbab461a42907621e3a4f5c918b612315f6b95",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A37549573+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch121/tomato-abstract.txt",
+ "abstract_sha256": "572769f335cb9e22e9f3bfa7ace56d21697b0c5f499c5ec3c4fd8bd277382a96",
+ "crossref": "/private/tmp/communitymech-batch121/tomato-crossref.json",
+ "crossref_sha256": "da0362a3f97c2b71031319206884eab8da40cf83d4df180ddf67cc8e484a5473",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2023,
+ 9,
+ 1
+ ]
+ ],
+ "date-time": "2023-09-01T00:00:00Z",
+ "timestamp": 1693526400000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2023,
+ 9,
+ 1
+ ]
+ ],
+ "date-time": "2023-09-01T00:00:00Z",
+ "timestamp": 1693526400000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://www.elsevier.com/legal/tdmrep-license"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2023,
+ 9,
+ 1
+ ]
+ ],
+ "date-time": "2023-09-01T00:00:00Z",
+ "timestamp": 1693526400000
+ },
+ "content-version": "stm-asf",
+ "delay-in-days": 0,
+ "URL": "https://doi.org/10.15223/policy-017"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2023,
+ 9,
+ 1
+ ]
+ ],
+ "date-time": "2023-09-01T00:00:00Z",
+ "timestamp": 1693526400000
+ },
+ "content-version": "stm-asf",
+ "delay-in-days": 0,
+ "URL": "https://doi.org/10.15223/policy-037"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
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+ "pmcid": "PMC9473337",
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+ "metadata_sha256": "434bf6f8f3d784a8c75b37dc9f0136447a673bc68c49da5ddc665230c275015e",
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+ "doi": "10.3389/fmicb.2022.908981",
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+ "title": "Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen.",
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+ "status": "retrieved"
+ },
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+ "abstract_sha256": "9b252c4c3c94a7afa338c6615098c79ec89fe90cc684fc17e509ea766245d611",
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+ "primary_text_sha256": "3c36c4e7d883c60a96ae0a33027d1f1bfcaef52793e453ae3383b3b73071dbd9",
+ "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-batch121/c6-crossref.json",
+ "crossref_sha256": "c792f94d269f646a9d7d0f9f234de848623ad76a5ce3aa505775615a3d13ca79",
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+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0/"
+ }
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+ },
+ "crown": {
+ "pmid": "41504167",
+ "doi": "10.1021/acs.jafc.5c11786",
+ "pmcid": "PMC12833866",
+ "title": "Cross-Kingdom Synthetic Microbiota Suppresses Wheat Fusarium Crown Rot by Remodeling the Rhizosphere Microbiome and Metabolome.",
+ "metadata": "/private/tmp/communitymech-batch121/crown-metadata.json",
+ "metadata_sha256": "128b9f3ad73905c118c5572a74c5f187560ab502296adc51af428b6afac8a99c",
+ "retrievals": [
+ {
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+ "status": "retrieved"
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12833866/fullTextXML",
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+ "xml": "/private/tmp/communitymech-batch121/crown-primary.xml",
+ "xml_sha256": "0b76802b924a03d6b2a8621bf63c8a068d565267c876bc05e7116e440ea84939",
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+ "primary_text_sha256": "5473ae75df36a381dc6f107afe7cd3d93851565378b25de0baccca019d8ee36c",
+ "license": [
+ "https://creativecommons.org/licenses/by-nc-nd/4.0/This article is licensed under CC-BY-NC-ND 4.0"
+ ],
+ "crossref": "/private/tmp/communitymech-batch121/crown-crossref.json",
+ "crossref_sha256": "617800ca4aaf5db73b90bc0ee491c93fe22e5c5503c0e69cb440d5bebeff61d5",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2026,
+ 1,
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+ ]
+ ],
+ "date-time": "2026-01-08T00:00:00Z",
+ "timestamp": 1767830400000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by-nc-nd/4.0/"
+ }
+ ]
+ }
+ },
+ "actual_read_scope": [
+ "Four fresh EuropePMC abstract/metadata and Crossref retrievals cover three unique primary studies. Complete wheat C1/C6 and crown-rot main bodies read including methods,results,discussion,tables and captions. C1/C6 XML/body hashes are identical. No original figure pixels,separate supplementary files,raw data or analysis code audited.",
+ "Tomato changes are abstract-bounded. EuropePMC has no PMC identifier and lists subscription-required DOI access; DOI open was unavailable and ScienceDirect PII S0981942823004527 returned403. No exhaustive full-text absence claim,access bypass or author contact. No full article-body import.",
+ "Tomato retains positive complementary community functions,leaf oxylipin activation,biosynthesis-inhibition loss of protection,and SlLOX5/SlDES1 overexpression benefit. This supports pathway-level causality,not reciprocal bacterial fitness,unique biofilm mediation or independent necessity of each divinyl ether. Exact member/role metadata remains1943.",
+ "Wheat C1/C6 primary is CC BY4.0. Equal-ratio assembly is preparation,not ecological colonization; prior workflow-arrow removals remain intact. C1 retains significant greenhouse benefits but no demonstrated superiority over the best single strain. C6 retains positive dual-plate inhibition and Salkowski output but Arabidopsis root shortening is not growth promotion. Positive individual-member secretion/volatile assays do not override whole-mixture nulls. Persistence explicitly was not assessed. Negative r-squared notation is not silently repaired. Non-graph abundance/metal scope remains1944.",
+ "Crown-rot primary is CC BY-NC-ND4.0,not unrestricted CC BY. Preserve measured pot disease and grain benefits. Relative DNA profiles are not viable-cell colonization or functional flux; correlation networks do not establish cooperation or ecological necessity. Added allantoin/dihydrodaidzein have positive plant outcomes and negative direct fungal assays; do not erase these positives or infer intact-SMC necessity. Old cache wording differs from fresh abstract and bacterial-treatment assignments; timing and provenance remain1945.",
+ "Exactly three short crown-rot discussion excerpts,21quoted words,are appended with source/license attribution. Old cache bytes remain an unchanged prefix. No protocol addition or full-body import. All24graph and10discussion quotes independently matched to fresh primary and authoritative local caches; literal matches are not entailment proof. Existing selected caches and primary text read; no claim to manual whole-reading of the very long C1 markdown cache."
+ ]
+ },
+ "limitations": [
+ "Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects. All four whole records and14existing nodes/two arrows reviewed. Retain12nodes/two arrows,remove two inoculum-assembly nodes,rename six nodes,no new topology.",
+ "Four fresh EuropePMC abstract/metadata and Crossref retrievals cover three unique primary studies. Complete wheat C1/C6 and crown-rot main bodies read including methods,results,discussion,tables and captions. C1/C6 XML/body hashes are identical. No original figure pixels,separate supplementary files,raw data or analysis code audited.",
+ "Tomato changes are abstract-bounded. EuropePMC has no PMC identifier and lists subscription-required DOI access; DOI open was unavailable and ScienceDirect PII S0981942823004527 returned403. No exhaustive full-text absence claim,access bypass or author contact. No full article-body import.",
+ "Tomato retains positive complementary community functions,leaf oxylipin activation,biosynthesis-inhibition loss of protection,and SlLOX5/SlDES1 overexpression benefit. This supports pathway-level causality,not reciprocal bacterial fitness,unique biofilm mediation or independent necessity of each divinyl ether. Exact member/role metadata remains1943.",
+ "Wheat C1/C6 primary is CC BY4.0. Equal-ratio assembly is preparation,not ecological colonization; prior workflow-arrow removals remain intact. C1 retains significant greenhouse benefits but no demonstrated superiority over the best single strain. C6 retains positive dual-plate inhibition and Salkowski output but Arabidopsis root shortening is not growth promotion. Positive individual-member secretion/volatile assays do not override whole-mixture nulls. Persistence explicitly was not assessed. Negative r-squared notation is not silently repaired. Non-graph abundance/metal scope remains1944.",
+ "Crown-rot primary is CC BY-NC-ND4.0,not unrestricted CC BY. Preserve measured pot disease and grain benefits. Relative DNA profiles are not viable-cell colonization or functional flux; correlation networks do not establish cooperation or ecological necessity. Added allantoin/dihydrodaidzein have positive plant outcomes and negative direct fungal assays; do not erase these positives or infer intact-SMC necessity. Old cache wording differs from fresh abstract and bacterial-treatment assignments; timing and provenance remain1945.",
+ "Exactly three short crown-rot discussion excerpts,21quoted words,are appended with source/license attribution. Old cache bytes remain an unchanged prefix. No protocol addition or full-body import. All24graph and10discussion quotes independently matched to fresh primary and authoritative local caches; literal matches are not entailment proof. Existing selected caches and primary text read; no claim to manual whole-reading of the very long C1 markdown cache.",
+ "Initial and fresh pre-creation all-state1175issue titles/bodies searched,seven matching bodies read,161matching local paths found including ignored/hidden files except.git,docs,site,references_cache,.env.1035/1037 address crown-rot participants/CI;615 host-cultivation schema;1521,1378,1375,981 other records. Not a historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,922unchangedcaches,unrelated raw YAML blocks and all prior histories/decisions. Four append-only histories and curation events. Taxon identities,participant lists and scopes unchanged; evidence aliases detached. No experimental optimization.",
+ "Existing-graph repair with no new nodes/directions: no Edison run,provider submission or spend. Prior authorized Ruegeria1883 authentication blocker not retried unchanged; no credential inspected. Source-based 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-batch121.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
new file mode 100644
index 000000000..e50b5c364
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
@@ -0,0 +1,854 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 5afca28e40023b10e05db1c228ec70ecbaf5d7a9
+baseline_commit: 5afca28e40023b10e05db1c228ec70ecbaf5d7a9
+base_tree: d78af7c5ca32b724f1a57b22ac40391989f72c89
+pre_source_baseline_sha256: e92b45d03d6c465de8302b503b81336144391a7179c1c56de54b1b0e64245493
+issues:
+- 1939
+- 1940
+- 1941
+- 1942
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1943
+- 1944
+- 1945
+source_access:
+ retrieval_manifest:
+ tomato:
+ pmid: '37549573'
+ doi: 10.1016/j.plaphy.2023.107941
+ pmcid: null
+ title: A simplified synthetic rhizosphere bacterial community steers plant oxylipin pathways for preventing
+ foliar phytopathogens.
+ metadata: /private/tmp/communitymech-batch121/tomato-metadata.json
+ metadata_sha256: 61aa41a2b34c20f8d257ff9ec6fbab461a42907621e3a4f5c918b612315f6b95
+ retrievals:
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+ status: retrieved
+ abstract: /private/tmp/communitymech-batch121/tomato-abstract.txt
+ abstract_sha256: 572769f335cb9e22e9f3bfa7ace56d21697b0c5f499c5ec3c4fd8bd277382a96
+ crossref: /private/tmp/communitymech-batch121/tomato-crossref.json
+ crossref_sha256: da0362a3f97c2b71031319206884eab8da40cf83d4df180ddf67cc8e484a5473
+ crossref_license:
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+ URL: https://www.elsevier.com/legal/tdmrep-license
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+ timestamp: 1693526400000
+ content-version: stm-asf
+ delay-in-days: 0
+ URL: https://doi.org/10.15223/policy-012
+ - start:
+ date-parts:
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+ - 9
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+ timestamp: 1693526400000
+ content-version: stm-asf
+ delay-in-days: 0
+ URL: https://doi.org/10.15223/policy-029
+ - start:
+ date-parts:
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+ - 9
+ - 1
+ date-time: '2023-09-01T00:00:00Z'
+ timestamp: 1693526400000
+ content-version: stm-asf
+ delay-in-days: 0
+ URL: https://doi.org/10.15223/policy-004
+ c1:
+ pmid: '36118206'
+ doi: 10.3389/fmicb.2022.908981
+ pmcid: PMC9473337
+ title: Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal
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+ metadata_sha256: 434bf6f8f3d784a8c75b37dc9f0136447a673bc68c49da5ddc665230c275015e
+ retrievals:
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+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9473337/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch121/c1-abstract.txt
+ abstract_sha256: 9b252c4c3c94a7afa338c6615098c79ec89fe90cc684fc17e509ea766245d611
+ xml: /private/tmp/communitymech-batch121/c1-primary.xml
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+ license:
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+ content-version: vor
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+ URL: https://creativecommons.org/licenses/by/4.0/
+ c6:
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+ doi: 10.3389/fmicb.2022.908981
+ pmcid: PMC9473337
+ title: Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal
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+ metadata_sha256: 10c50b850e2f7a1f15d45cfdc428de4200f1f2f960c05e3ffbc277b670f827b0
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+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9473337/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch121/c6-abstract.txt
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+ xml: /private/tmp/communitymech-batch121/c6-primary.xml
+ xml_sha256: cc69d3ea571e2bdf4f416df2f4185725c01989357333a0a0db4b084fcf014d8e
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+ primary_text_sha256: 3c36c4e7d883c60a96ae0a33027d1f1bfcaef52793e453ae3383b3b73071dbd9
+ 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-batch121/c6-crossref.json
+ crossref_sha256: c792f94d269f646a9d7d0f9f234de848623ad76a5ce3aa505775615a3d13ca79
+ crossref_license:
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+ timestamp: 1661904000000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0/
+ crown:
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+ doi: 10.1021/acs.jafc.5c11786
+ pmcid: PMC12833866
+ title: Cross-Kingdom Synthetic Microbiota Suppresses Wheat Fusarium Crown Rot by Remodeling the Rhizosphere
+ Microbiome and Metabolome.
+ metadata: /private/tmp/communitymech-batch121/crown-metadata.json
+ metadata_sha256: 128b9f3ad73905c118c5572a74c5f187560ab502296adc51af428b6afac8a99c
+ retrievals:
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+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12833866/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch121/crown-abstract.txt
+ abstract_sha256: 16c788598453a61f000910a5e0f8a4008ba8519ee5701ae3a3e17d18e825810b
+ xml: /private/tmp/communitymech-batch121/crown-primary.xml
+ xml_sha256: 0b76802b924a03d6b2a8621bf63c8a068d565267c876bc05e7116e440ea84939
+ primary_text: /private/tmp/communitymech-batch121/crown-primary.txt
+ primary_text_sha256: 5473ae75df36a381dc6f107afe7cd3d93851565378b25de0baccca019d8ee36c
+ license:
+ - https://creativecommons.org/licenses/by-nc-nd/4.0/This article is licensed under CC-BY-NC-ND 4.0
+ crossref: /private/tmp/communitymech-batch121/crown-crossref.json
+ crossref_sha256: 617800ca4aaf5db73b90bc0ee491c93fe22e5c5503c0e69cb440d5bebeff61d5
+ crossref_license:
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+ timestamp: 1767830400000
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+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by-nc-nd/4.0/
+ actual_read_scope:
+ - Four fresh EuropePMC abstract/metadata and Crossref retrievals cover three unique primary studies. Complete
+ wheat C1/C6 and crown-rot main bodies read including methods,results,discussion,tables and captions. C1/C6 XML/body
+ hashes are identical. No original figure pixels,separate supplementary files,raw data or analysis code audited.
+ - Tomato changes are abstract-bounded. EuropePMC has no PMC identifier and lists subscription-required DOI access;
+ DOI open was unavailable and ScienceDirect PII S0981942823004527 returned403. No exhaustive full-text absence
+ claim,access bypass or author contact. No full article-body import.
+ - Tomato retains positive complementary community functions,leaf oxylipin activation,biosynthesis-inhibition loss
+ of protection,and SlLOX5/SlDES1 overexpression benefit. This supports pathway-level causality,not reciprocal
+ bacterial fitness,unique biofilm mediation or independent necessity of each divinyl ether. Exact member/role
+ metadata remains1943.
+ - Wheat C1/C6 primary is CC BY4.0. Equal-ratio assembly is preparation,not ecological colonization; prior workflow-arrow
+ removals remain intact. C1 retains significant greenhouse benefits but no demonstrated superiority over the
+ best single strain. C6 retains positive dual-plate inhibition and Salkowski output but Arabidopsis root shortening
+ is not growth promotion. Positive individual-member secretion/volatile assays do not override whole-mixture
+ nulls. Persistence explicitly was not assessed. Negative r-squared notation is not silently repaired. Non-graph
+ abundance/metal scope remains1944.
+ - Crown-rot primary is CC BY-NC-ND4.0,not unrestricted CC BY. Preserve measured pot disease and grain benefits.
+ Relative DNA profiles are not viable-cell colonization or functional flux; correlation networks do not establish
+ cooperation or ecological necessity. Added allantoin/dihydrodaidzein have positive plant outcomes and negative
+ direct fungal assays; do not erase these positives or infer intact-SMC necessity. Old cache wording differs
+ from fresh abstract and bacterial-treatment assignments; timing and provenance remain1945.
+ - Exactly three short crown-rot discussion excerpts,21quoted words,are appended with source/license attribution.
+ Old cache bytes remain an unchanged prefix. No protocol addition or full-body import. All24graph and10discussion
+ quotes independently matched to fresh primary and authoritative local caches; literal matches are not entailment
+ proof. Existing selected caches and primary text read; no claim to manual whole-reading of the very long C1
+ markdown cache.
+primary_artifacts:
+ /private/tmp/communitymech-batch121/baseline.json: e92b45d03d6c465de8302b503b81336144391a7179c1c56de54b1b0e64245493
+ /private/tmp/communitymech-batch121/c1-abstract.txt: 9b252c4c3c94a7afa338c6615098c79ec89fe90cc684fc17e509ea766245d611
+ /private/tmp/communitymech-batch121/c1-crossref.json: c792f94d269f646a9d7d0f9f234de848623ad76a5ce3aa505775615a3d13ca79
+ /private/tmp/communitymech-batch121/c1-metadata.json: 434bf6f8f3d784a8c75b37dc9f0136447a673bc68c49da5ddc665230c275015e
+ /private/tmp/communitymech-batch121/c1-primary.txt: 3c36c4e7d883c60a96ae0a33027d1f1bfcaef52793e453ae3383b3b73071dbd9
+ /private/tmp/communitymech-batch121/c1-primary.xml: cc69d3ea571e2bdf4f416df2f4185725c01989357333a0a0db4b084fcf014d8e
+ /private/tmp/communitymech-batch121/c6-abstract.txt: 9b252c4c3c94a7afa338c6615098c79ec89fe90cc684fc17e509ea766245d611
+ /private/tmp/communitymech-batch121/c6-crossref.json: c792f94d269f646a9d7d0f9f234de848623ad76a5ce3aa505775615a3d13ca79
+ /private/tmp/communitymech-batch121/c6-metadata.json: 10c50b850e2f7a1f15d45cfdc428de4200f1f2f960c05e3ffbc277b670f827b0
+ /private/tmp/communitymech-batch121/c6-primary.txt: 3c36c4e7d883c60a96ae0a33027d1f1bfcaef52793e453ae3383b3b73071dbd9
+ /private/tmp/communitymech-batch121/c6-primary.xml: cc69d3ea571e2bdf4f416df2f4185725c01989357333a0a0db4b084fcf014d8e
+ /private/tmp/communitymech-batch121/cache-append.json: 2b8a00668844860f4d1a6cf0008be793cd1c5b3b0df674fb7c43de0dcff074be
+ /private/tmp/communitymech-batch121/crown-abstract.txt: 16c788598453a61f000910a5e0f8a4008ba8519ee5701ae3a3e17d18e825810b
+ /private/tmp/communitymech-batch121/crown-crossref.json: 617800ca4aaf5db73b90bc0ee491c93fe22e5c5503c0e69cb440d5bebeff61d5
+ /private/tmp/communitymech-batch121/crown-metadata.json: 128b9f3ad73905c118c5572a74c5f187560ab502296adc51af428b6afac8a99c
+ /private/tmp/communitymech-batch121/crown-primary.txt: 5473ae75df36a381dc6f107afe7cd3d93851565378b25de0baccca019d8ee36c
+ /private/tmp/communitymech-batch121/crown-primary.xml: 0b76802b924a03d6b2a8621bf63c8a068d565267c876bc05e7116e440ea84939
+ /private/tmp/communitymech-batch121/issue-dedup-current.json: 855090c628e4814fea1ca1d0a4d8f7081c3727c971fe3f2dd7b30d768ec374d8
+ /private/tmp/communitymech-batch121/local-matches-expanded.txt: 04facf3dcb06aa984a9d620a2d9cafe0da8f0057a5d5c12d1e7292682f65dc44
+ /private/tmp/communitymech-batch121/local-matches.txt: cb931efcd842d1fafd28bbfbe63bbd88b39af4056a9d998fc69585e2a683e41e
+ /private/tmp/communitymech-batch121/primary-manifest.json: ecb885005fbdbcc00b35bbcb6f894fd0ad63a3b310d764ce6af154e647aee7c3
+ /private/tmp/communitymech-batch121/target-baseline.json: 5c3e2c7f8253df656fc9ba1aac4d6398c43a5c4564c9cd2f515db56f08597cf9
+ /private/tmp/communitymech-batch121/tomato-abstract.txt: 572769f335cb9e22e9f3bfa7ace56d21697b0c5f499c5ec3c4fd8bd277382a96
+ /private/tmp/communitymech-batch121/tomato-crossref.json: da0362a3f97c2b71031319206884eab8da40cf83d4df180ddf67cc8e484a5473
+ /private/tmp/communitymech-batch121/tomato-metadata.json: 61aa41a2b34c20f8d257ff9ec6fbab461a42907621e3a4f5c918b612315f6b95
+ references_cache/PMID_36118206.md: 314ea2db4d987629dc153dd408a6862de979aab0fc85cdeeef3cff44e024e0c6
+ references_cache/PMID_37549573.txt: a84a280cb33625ddefb3a79de376d86d6f6fe774e0f53bf8978677e50e34ffa4
+ references_cache/PMID_41504167.txt: 09dbe7338cb653bdfec20d7103d2510e252b08f70b9166b38c193199e7e6e2fd
+reviewed_counts:
+ original_nodes: 14
+ retained_nodes: 12
+ removed_nodes: 2
+ original_arrows: 2
+ retained_arrows: 2
+ removed_arrows: 0
+ renamed_nodes: 6
+ graph_quotations: 24
+ discussion_quotations: 10
+ new_discussions: 4
+primary_graph_snippet_count: 24
+snippet_checks:
+- record: Tomato_Oxylipin_SynCom3
+ node: SynCom3-associated biofilm and host defense
+ evidence_index: 0
+ reference: PMID:37549573
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/tomato-abstract.txt
+ cache_artifact: references_cache/PMID_37549573.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tomato_Oxylipin_SynCom3
+ node: SynCom3-associated biofilm and host defense
+ evidence_index: 1
+ reference: PMID:37549573
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/tomato-abstract.txt
+ cache_artifact: references_cache/PMID_37549573.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tomato_Oxylipin_SynCom3
+ node: SynCom3-induced leaf oxylipin responses
+ evidence_index: 0
+ reference: PMID:37549573
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/tomato-abstract.txt
+ cache_artifact: references_cache/PMID_37549573.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tomato_Oxylipin_SynCom3
+ node: Divinyl Ether-Dependent Botrytis Protection
+ evidence_index: 0
+ reference: PMID:37549573
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/tomato-abstract.txt
+ cache_artifact: references_cache/PMID_37549573.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Tomato_Oxylipin_SynCom3
+ node: Divinyl Ether-Dependent Botrytis Protection
+ evidence_index: 1
+ reference: PMID:37549573
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/tomato-abstract.txt
+ cache_artifact: references_cache/PMID_37549573.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C1
+ node: C1 SynCom inhibition of R. solani AG8 radial growth
+ evidence_index: 0
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C1
+ node: C1 SynCom inhibition of R. solani AG8 radial growth
+ evidence_index: 1
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C1
+ node: C1 SynCom protection of wheat under AG8 challenge
+ evidence_index: 0
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C1
+ node: C1 SynCom protection of wheat under AG8 challenge
+ evidence_index: 1
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 Dual-Culture AG8 Radial Inhibition
+ evidence_index: 0
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 Dual-Culture AG8 Radial Inhibition
+ evidence_index: 1
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 Salkowski auxin-assay output
+ evidence_index: 0
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 Salkowski auxin-assay output
+ evidence_index: 1
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6-associated Arabidopsis primary-root shortening
+ evidence_index: 0
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 cell-free contrast with inhibitory member cultures
+ evidence_index: 0
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 cell-free contrast with inhibitory member cultures
+ evidence_index: 1
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 cell-free contrast with inhibitory member cultures
+ evidence_index: 2
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 volatile contrast with inhibitory member cultures
+ evidence_index: 0
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 volatile contrast with inhibitory member cultures
+ evidence_index: 1
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: C6 volatile contrast with inhibitory member cultures
+ evidence_index: 2
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_CrownRot_SixStrain_CrossKingdom_SMC
+ node: Six-strain SMC suppression of Fusarium crown rot
+ evidence_index: 0
+ reference: PMID:41504167
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ cache_artifact: references_cache/PMID_41504167.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_CrownRot_SixStrain_CrossKingdom_SMC
+ node: Six-strain SMC suppression of Fusarium crown rot
+ evidence_index: 1
+ reference: PMID:41504167
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ cache_artifact: references_cache/PMID_41504167.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_CrownRot_SixStrain_CrossKingdom_SMC
+ node: SMC-associated wheat rhizosphere remodeling
+ evidence_index: 0
+ reference: PMID:41504167
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ cache_artifact: references_cache/PMID_41504167.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_CrownRot_SixStrain_CrossKingdom_SMC
+ node: SMC-associated wheat rhizosphere remodeling
+ evidence_index: 1
+ reference: PMID:41504167
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ cache_artifact: references_cache/PMID_41504167.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+discussion_snippet_checks:
+- record: Tomato_Oxylipin_SynCom3
+ node: tomato_causal_scope_batch121
+ evidence_index: 0
+ reference: PMID:37549573
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/tomato-abstract.txt
+ cache_artifact: references_cache/PMID_37549573.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C1
+ node: c1_causal_scope_batch121
+ evidence_index: 0
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C1
+ node: c1_causal_scope_batch121
+ evidence_index: 1
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C1
+ node: c1_causal_scope_batch121
+ evidence_index: 2
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: c6_causal_scope_batch121
+ evidence_index: 0
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_Consortium_C6
+ node: c6_causal_scope_batch121
+ evidence_index: 1
+ reference: PMID:36118206
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/c6-primary.txt
+ cache_artifact: references_cache/PMID_36118206.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_CrownRot_SixStrain_CrossKingdom_SMC
+ node: crown_causal_scope_batch121
+ evidence_index: 0
+ reference: PMID:41504167
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ cache_artifact: references_cache/PMID_41504167.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_CrownRot_SixStrain_CrossKingdom_SMC
+ node: crown_causal_scope_batch121
+ evidence_index: 1
+ reference: PMID:41504167
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ cache_artifact: references_cache/PMID_41504167.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_CrownRot_SixStrain_CrossKingdom_SMC
+ node: crown_causal_scope_batch121
+ evidence_index: 2
+ reference: PMID:41504167
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ cache_artifact: references_cache/PMID_41504167.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Wheat_CrownRot_SixStrain_CrossKingdom_SMC
+ node: crown_causal_scope_batch121
+ evidence_index: 3
+ reference: PMID:41504167
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ cache_artifact: references_cache/PMID_41504167.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+cache_changes:
+- path: references_cache/PMID_41504167.txt
+ before_sha256: 4d486d1a61d439b27b58e26f089b287540ce49b0dfea5ff74b9d4c45b9d3b2ff
+ after_sha256: 09dbe7338cb653bdfec20d7103d2510e252b08f70b9166b38c193199e7e6e2fd
+ old_prefix_preserved: true
+ added_bytes: 606
+ added_quotation_words: 21
+ source_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC12833866/
+ source_artifact: /private/tmp/communitymech-batch121/crown-primary.txt
+ source_sha256: 5473ae75df36a381dc6f107afe7cd3d93851565378b25de0baccca019d8ee36c
+ license: CC BY-NC-ND 4.0
+ scope: Three short selected discussion excerpts, not a full-text import. Existing provenance discrepancies retained
+ for issue1945.
+ quotations:
+ - functional validation at the molecular and genetic levels remains limited
+ - showed no direct antifungal activity of either compound
+ - significantly reduced DSI
+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.
+ All four whole records and14existing nodes/two arrows reviewed. Retain12nodes/two arrows,remove two inoculum-assembly
+ nodes,rename six nodes,no new topology.
+- Four fresh EuropePMC abstract/metadata and Crossref retrievals cover three unique primary studies. Complete wheat
+ C1/C6 and crown-rot main bodies read including methods,results,discussion,tables and captions. C1/C6 XML/body
+ hashes are identical. No original figure pixels,separate supplementary files,raw data or analysis code audited.
+- Tomato changes are abstract-bounded. EuropePMC has no PMC identifier and lists subscription-required DOI access;
+ DOI open was unavailable and ScienceDirect PII S0981942823004527 returned403. No exhaustive full-text absence
+ claim,access bypass or author contact. No full article-body import.
+- Tomato retains positive complementary community functions,leaf oxylipin activation,biosynthesis-inhibition loss
+ of protection,and SlLOX5/SlDES1 overexpression benefit. This supports pathway-level causality,not reciprocal bacterial
+ fitness,unique biofilm mediation or independent necessity of each divinyl ether. Exact member/role metadata remains1943.
+- Wheat C1/C6 primary is CC BY4.0. Equal-ratio assembly is preparation,not ecological colonization; prior workflow-arrow
+ removals remain intact. C1 retains significant greenhouse benefits but no demonstrated superiority over the best
+ single strain. C6 retains positive dual-plate inhibition and Salkowski output but Arabidopsis root shortening
+ is not growth promotion. Positive individual-member secretion/volatile assays do not override whole-mixture nulls.
+ Persistence explicitly was not assessed. Negative r-squared notation is not silently repaired. Non-graph abundance/metal
+ scope remains1944.
+- Crown-rot primary is CC BY-NC-ND4.0,not unrestricted CC BY. Preserve measured pot disease and grain benefits.
+ Relative DNA profiles are not viable-cell colonization or functional flux; correlation networks do not establish
+ cooperation or ecological necessity. Added allantoin/dihydrodaidzein have positive plant outcomes and negative
+ direct fungal assays; do not erase these positives or infer intact-SMC necessity. Old cache wording differs from
+ fresh abstract and bacterial-treatment assignments; timing and provenance remain1945.
+- Exactly three short crown-rot discussion excerpts,21quoted words,are appended with source/license attribution.
+ Old cache bytes remain an unchanged prefix. No protocol addition or full-body import. All24graph and10discussion
+ quotes independently matched to fresh primary and authoritative local caches; literal matches are not entailment
+ proof. Existing selected caches and primary text read; no claim to manual whole-reading of the very long C1 markdown
+ cache.
+- Initial and fresh pre-creation all-state1175issue titles/bodies searched,seven matching bodies read,161matching
+ local paths found including ignored/hidden files except.git,docs,site,references_cache,.env.1035/1037 address
+ crown-rot participants/CI;615 host-cultivation schema;1521,1378,1375,981 other records. Not a historical PR-comment
+ audit.
+- Four guarded writes preserve456otherrecords,922unchangedcaches,unrelated raw YAML blocks and all prior histories/decisions.
+ Four append-only histories and curation events. Taxon identities,participant lists and scopes unchanged; evidence
+ aliases detached. No experimental optimization.
+- 'Existing-graph repair with no new nodes/directions: no Edison run,provider submission or spend. Prior authorized
+ Ruegeria1883 authentication blocker not retried unchanged; no credential inspected. Source-based self-adversarial
+ review is not independent approval. Overall review,protected merge and branch deletion remain incomplete.'
+records:
+- path: kb/communities/Tomato_Oxylipin_SynCom3.yaml
+ id: CommunityMech:000107
+ original_sha256: 9c5917f46de396ed1c278b2cb65ff5d6d5a78be8aa470ce09e20a9e8550ccafe
+ record_sha256: 228468ac43630c33939dd4b0708476ef4006c9af7dbf1f108e7f88c36b0962c3
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain complementary biofilm and defense phenotypes without asserting reciprocal microbial benefit.;
+ Keep treatment-induced host oxylipin activation distinct from bacterial production or transfer.; Preserve biosynthesis-inhibition
+ and overexpression evidence at pathway rather than individual-compound scope.
+ node_decisions:
+ - node: SynCom3-associated biofilm and host defense
+ rationale: Retain complementary biofilm and defense phenotypes without asserting reciprocal microbial benefit.
+ - node: SynCom3-induced leaf oxylipin responses
+ rationale: Keep treatment-induced host oxylipin activation distinct from bacterial production or transfer.
+ - node: Divinyl Ether-Dependent Botrytis Protection
+ rationale: Preserve biosynthesis-inhibition and overexpression evidence at pathway rather than individual-compound
+ scope.
+ removed_node_decisions: []
+ renamed_nodes:
+ Simplified Community Synergistic Protection: SynCom3-associated biofilm and host defense
+ Oxylipin-Mediated Disease Resistance: SynCom3-induced leaf oxylipin responses
+ edges_before:
+ - &id001
+ source: Simplified Community Synergistic Protection
+ target: Oxylipin-Mediated Disease Resistance
+ description: The synergistic three-species community intensifies oxylipin pathway activation in phytopathogen-infected
+ tomato leaves.
+ - &id003
+ source: Oxylipin-Mediated Disease Resistance
+ target: Divinyl Ether-Dependent Botrytis Protection
+ description: Intensified oxylipin-pathway activation feeds production of antimicrobial divinyl ethers required
+ for community-induced protection against Botrytis cinerea.
+ edges_after:
+ - &id002
+ source: SynCom3-associated biofilm and host defense
+ target: SynCom3-induced leaf oxylipin responses
+ description: 'SynCom3 treatment intensified oxylipin responses in infected tomato leaves. PARTIAL for biofilm
+ formation as the mediator: the abstract links complementary community functions to protection but does not
+ isolate biofilm formation as the unique cause of leaf pathway activation.'
+ - &id004
+ source: SynCom3-induced leaf oxylipin responses
+ target: Divinyl Ether-Dependent Botrytis Protection
+ description: 'The host oxylipin branch supplies divinyl ethers implicated in protection: inhibiting their biosynthesis
+ abolished the community-induced resistance, while SlLOX5/SlDES1 overexpression with higher divinyl-ether levels
+ increased resistance. Retain this pathway-level perturbation evidence without claiming separate necessity
+ of each compound or bacterial-to-plant transfer.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: 'SynCom3 treatment intensified oxylipin responses in infected tomato leaves. PARTIAL for biofilm
+ formation as the mediator: the abstract links complementary community functions to protection but does not
+ isolate biofilm formation as the unique cause of leaf pathway activation.'
+ - before: *id003
+ after: *id004
+ rationale: 'The host oxylipin branch supplies divinyl ethers implicated in protection: inhibiting their biosynthesis
+ abolished the community-induced resistance, while SlLOX5/SlDES1 overexpression with higher divinyl-ether levels
+ increased resistance. Retain this pathway-level perturbation evidence without claiming separate necessity
+ of each compound or bacterial-to-plant transfer.'
+ removed_edge_decisions: []
+ references:
+ - PMID:37549573
+ issues:
+ - 1939
+ - 1943
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Tomato_Oxylipin_SynCom3/2026-10-08T150228Z-codex-b1572f.yaml
+- path: kb/communities/Wheat_Consortium_C1.yaml
+ id: CommunityMech:000076
+ original_sha256: 85d31a840c65d17f94c0682554165bfb33ac23168ca21cbcc45e8eb986e22dbe
+ record_sha256: 96fe252612fed33b257aed133760e929462f7021eef085750dfbb4469b1e6f26
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Keep measured whole-C1 fungal inhibition without a bilateral-competition interpretation.; Retain positive
+ greenhouse protection and root weight without claiming superiority or identified mediation.
+ node_decisions:
+ - node: C1 SynCom inhibition of R. solani AG8 radial growth
+ rationale: Keep measured whole-C1 fungal inhibition without a bilateral-competition interpretation.
+ - node: C1 SynCom protection of wheat under AG8 challenge
+ rationale: Retain positive greenhouse protection and root weight without claiming superiority or identified
+ mediation.
+ removed_node_decisions:
+ - node: Equal-Ratio Pseudomonas C1 Assembly
+ rationale: Equal-ratio mixing is inoculum preparation, not demonstrated colonization facilitation or an ecological
+ interaction. Composition, design and growth metadata remain unchanged; previously removed assay-workflow arrows
+ are not restored.
+ renamed_nodes: {}
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:36118206
+ issues:
+ - 1940
+ - 1944
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wheat_Consortium_C1/2026-10-08T150228Z-codex-ff737c.yaml
+- path: kb/communities/Wheat_Consortium_C6.yaml
+ id: CommunityMech:000077
+ original_sha256: 8a0747e8c630c65a8f0f56009905770543266386bb0c8f08e9a32e1426dcbfaa
+ record_sha256: e0fca5ba8eedf1676949159803aa46771fa28af92dab641d102f531d3adc2c87
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain whole-C6 plate inhibition without bilateral competition or automatic greenhouse benefit.; Bound
+ auxin production to the calibrated colorimetric assay without assigning reciprocal benefit or plant delivery.;
+ Preserve measured Arabidopsis root shortening without turning a correlation into a hormone-mediated growth benefit.;
+ Keep positive member supernatants and the negative whole-C6 supernatant outcome together.; Keep positive member
+ volatile assays distinct from the non-significant whole-C6 mixture result.
+ node_decisions:
+ - node: C6 Dual-Culture AG8 Radial Inhibition
+ rationale: Retain whole-C6 plate inhibition without bilateral competition or automatic greenhouse benefit.
+ - node: C6 Salkowski auxin-assay output
+ rationale: Bound auxin production to the calibrated colorimetric assay without assigning reciprocal benefit
+ or plant delivery.
+ - node: C6-associated Arabidopsis primary-root shortening
+ rationale: Preserve measured Arabidopsis root shortening without turning a correlation into a hormone-mediated
+ growth benefit.
+ - node: C6 cell-free contrast with inhibitory member cultures
+ rationale: Keep positive member supernatants and the negative whole-C6 supernatant outcome together.
+ - node: C6 volatile contrast with inhibitory member cultures
+ rationale: Keep positive member volatile assays distinct from the non-significant whole-C6 mixture result.
+ removed_node_decisions:
+ - node: Equal-Ratio Mixed-Genus C6 Assembly
+ rationale: Equal-ratio mixing is inoculum preparation, not demonstrated colonization facilitation or an ecological
+ interaction. Composition, design and growth metadata remain unchanged; previously removed assay-workflow arrows
+ are not restored.
+ renamed_nodes:
+ C6 Auxin Production: C6 Salkowski auxin-assay output
+ SynCom Arabidopsis Root-Length Response: C6-associated Arabidopsis primary-root shortening
+ C6-Member Cell-Free AG8 Antagonism: C6 cell-free contrast with inhibitory member cultures
+ C6-Member Volatile AG8 Antagonism: C6 volatile contrast with inhibitory member cultures
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:36118206
+ issues:
+ - 1941
+ - 1944
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wheat_Consortium_C6/2026-10-08T150229Z-codex-b61a7a.yaml
+- path: kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml
+ id: CommunityMech:000414
+ original_sha256: 2836c0fbd27593a8f35cbd3a676164300df8ae316681cd7c813f5708008977d6
+ record_sha256: cf2ae08aab3fed7a94f5a0068db6d108baf734b22152547241ebe258f52d15ce
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Preserve the positive SMC disease and grain outcomes without an unsupported bilateral-competition mechanism.;
+ Keep relative community-profile observations distinct from colonization facilitation and inferred ecological
+ functions.
+ node_decisions:
+ - node: Six-strain SMC suppression of Fusarium crown rot
+ rationale: Preserve the positive SMC disease and grain outcomes without an unsupported bilateral-competition
+ mechanism.
+ - node: SMC-associated wheat rhizosphere remodeling
+ rationale: Keep relative community-profile observations distinct from colonization facilitation and inferred
+ ecological functions.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:41504167
+ issues:
+ - 1942
+ - 1945
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Wheat_CrownRot_SixStrain_CrossKingdom_SMC/2026-10-08T150229Z-codex-fc0ee7.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index de6387842..6bc340f0c 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -429,7 +429,7 @@ kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml Co
kb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml CommunityMech:000239 0bf172f2ca5732c1c0ff0b2853f2685a65da950dface53edd4e00ba108a3c281 3 1 78.3 reports/causal_graph_review/decisions/20261008-three-records-batch115.yaml reviewed
kb/communities/Tinto_River_Iron_Cycling_Community.yaml CommunityMech:000074 0597ed078c3761a0c46d2d8590ce3c328bd9897730a232938f4f5709bba02d09 4 1 79.2 reports/causal_graph_review/decisions/20261008-three-records-batch115.yaml reviewed
kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml CommunityMech:000106 2d1851c88c385f813706b923eeb0754bf70bbac4dd94fb15369bf5e45317e371 3 2 86.7 reports/causal_graph_review/decisions/20261008-four-records-batch120.yaml reviewed
-kb/communities/Tomato_Oxylipin_SynCom3.yaml CommunityMech:000107 9c5917f46de396ed1c278b2cb65ff5d6d5a78be8aa470ce09e20a9e8550ccafe 3 2 100.0 pending
+kb/communities/Tomato_Oxylipin_SynCom3.yaml CommunityMech:000107 228468ac43630c33939dd4b0708476ef4006c9af7dbf1f108e7f88c36b0962c3 3 2 90.0 reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml reviewed
kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml CommunityMech:000112 1349b3976b1d7a34ce789447fa6b35e8659b80725ec6aa09694f2f8d5e1aa6a8 4 3 95.0 reports/causal_graph_review/decisions/20261008-four-records-batch117.yaml reviewed
kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml CommunityMech:000188 19be2baf6f39a410bce4ce119b4b192d16c49f03e57b39ba4d1a3bf59f8c1ff0 3 2 90.0 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
kb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml CommunityMech:000205 3fe13833fafecd516fd06ee844c2a33de7ce3b5e5e230654691a79fa21560461 3 2 93.3 reports/causal_graph_review/decisions/20261008-three-records-batch116.yaml reviewed
@@ -443,9 +443,9 @@ kb/communities/Viili_Fungus_Bacterium_EPS_SynCom.yaml CommunityMech:000408 b39ce
kb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml CommunityMech:000328 96790620c4f70dd5ca498af0636db53fc9fb7d6779a96851bb31385b71c6f329 4 2 92.5 reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml reviewed
kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml CommunityMech:000098 4eda48481991d8d22dad2d32ec24284d8580ba33e540377b8f5509bced74c31b 2 0 60.0 reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml reviewed
kb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml CommunityMech:000255 0703409d520c9c561d99c075761f37adff7ca856e14b3d438df2080e975e1e1a 3 0 68.3 reports/causal_graph_review/decisions/20261008-four-records-batch118.yaml reviewed
-kb/communities/Wheat_Consortium_C1.yaml CommunityMech:000076 85d31a840c65d17f94c0682554165bfb33ac23168ca21cbcc45e8eb986e22dbe 3 0 75.0 pending
-kb/communities/Wheat_Consortium_C6.yaml CommunityMech:000077 8a0747e8c630c65a8f0f56009905770543266386bb0c8f08e9a32e1426dcbfaa 6 0 75.0 pending
-kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml CommunityMech:000414 2836c0fbd27593a8f35cbd3a676164300df8ae316681cd7c813f5708008977d6 2 0 70.0 pending
+kb/communities/Wheat_Consortium_C1.yaml CommunityMech:000076 96fe252612fed33b257aed133760e929462f7021eef085750dfbb4469b1e6f26 2 0 60.0 reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml reviewed
+kb/communities/Wheat_Consortium_C6.yaml CommunityMech:000077 e0fca5ba8eedf1676949159803aa46771fa28af92dab641d102f531d3adc2c87 5 0 65.0 reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml reviewed
+kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml CommunityMech:000414 cf2ae08aab3fed7a94f5a0068db6d108baf734b22152547241ebe258f52d15ce 2 0 57.5 reports/causal_graph_review/decisions/20261008-four-records-batch121.yaml reviewed
kb/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml CommunityMech:000391 9683a30be6276fa5ee8b726a80349b69e211633394d73127a6cde7c9b7131a37 2 0 70.0 pending
kb/communities/Wheat_DT_Rhizosphere_SynCom.yaml CommunityMech:000429 b68dea3c5b4af59f9ebf86a64ac55ab18c7a3ab42dbb60cd110ddf63b9238172 2 0 55.0 pending
kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml CommunityMech:000118 f2bb440b5a0d802fb677fb80f49caf5dc915f7fb34a7cad164bd5d91db2ccccb 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 649645b16..c49f2002f 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": 1375,
+ "nodes": 1373,
"edges": 530,
"records_without_nodes": 10,
"records_without_edges": 189,
"review_status_counts": {
"needs_research": 54,
- "pending": 18,
- "reviewed": 388
+ "pending": 14,
+ "reviewed": 392
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch121.json b/reports/causal_graph_review/validation-20261008-batch121.json
new file mode 100644
index 000000000..abfd33faf
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch121.json
@@ -0,0 +1,1293 @@
+{
+ "base_commit": "5afca28e40023b10e05db1c228ec70ecbaf5d7a9",
+ "scope": [
+ "kb/communities/Tomato_Oxylipin_SynCom3.yaml",
+ "kb/communities/Wheat_Consortium_C1.yaml",
+ "kb/communities/Wheat_Consortium_C6.yaml",
+ "kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml"
+ ],
+ "results": [
+ {
+ "check": "Tomato_Oxylipin_SynCom3-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Tomato_Oxylipin_SynCom3.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Tomato_Oxylipin_SynCom3-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Tomato_Oxylipin_SynCom3-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch121/Tomato_Oxylipin_SynCom3-strict.tsv",
+ "kb/communities/Tomato_Oxylipin_SynCom3.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Tomato_Oxylipin_SynCom3-strict.log",
+ "log_sha256": "dabcbc4cb6d7b0bf7752263a7ddde3fcc2c7fbe2f91b1e6de6725d7f7baaf92c",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch121/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-batch121/Tomato_Oxylipin_SynCom3-strict.tsv\n"
+ },
+ {
+ "check": "Tomato_Oxylipin_SynCom3-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Tomato_Oxylipin_SynCom3.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Tomato_Oxylipin_SynCom3-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Tomato_Oxylipin_SynCom3-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Tomato_Oxylipin_SynCom3.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Tomato_Oxylipin_SynCom3-references.log",
+ "log_sha256": "ecf0ef0d5f94468a1e01ea448f778d3310f55a497fa2bea3fdd98cd8133960c0",
+ "output_tail": "Validating kb/communities/Tomato_Oxylipin_SynCom3.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/Tomato_Oxylipin_SynCom3.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": "Tomato_Oxylipin_SynCom3-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Tomato_Oxylipin_SynCom3.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Tomato_Oxylipin_SynCom3-snippets.log",
+ "log_sha256": "872637a69e95b3997368edea80eba5db2a2155e0ac9344b758394dcf97491410",
+ "output_tail": "# 14 evidence snippets scanned across 1 files\n MATCH 14\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": "Tomato_Oxylipin_SynCom3-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Tomato_Oxylipin_SynCom3.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Tomato_Oxylipin_SynCom3-rank.log",
+ "log_sha256": "0c671ee9ead14f127ba0f94a856eae4dc18b7635a3b76168978051f7fd7bc713",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000107\",\n \"name\": \"Tomato Oxylipin-Protective SynCom3\",\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\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Tomato_Oxylipin_SynCom3.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Tomato_Oxylipin_SynCom3-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Tomato_Oxylipin_SynCom3/2026-10-08T150228Z-codex-b1572f.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Tomato_Oxylipin_SynCom3-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_Consortium_C1-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
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+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C1-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_Consortium_C1-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
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+ "--out",
+ "/private/tmp/communitymech-batch121/Wheat_Consortium_C1-strict.tsv",
+ "kb/communities/Wheat_Consortium_C1.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ },
+ {
+ "check": "Wheat_Consortium_C1-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wheat_Consortium_C1.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C1-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wheat_Consortium_C1-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
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+ "kb/communities/Wheat_Consortium_C1.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C1-references.log",
+ "log_sha256": "f0a3ee6f7b43628b9470451f04f5e4d1bfb63f1bfbd10717c5ff5bbee10f9e9a",
+ "output_tail": "Validating kb/communities/Wheat_Consortium_C1.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/Wheat_Consortium_C1.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": "Wheat_Consortium_C1-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
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+ "expected_exit_codes": [
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+ },
+ {
+ "check": "Wheat_Consortium_C1-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wheat_Consortium_C1.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C1-rank.log",
+ "log_sha256": "69a810cb13b62440bcb2cce87f58398c3041f0c5849c6cbf02053f0d3cc6f943",
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+ },
+ {
+ "check": "Wheat_Consortium_C1-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wheat_Consortium_C1/2026-10-08T150228Z-codex-ff737c.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C1-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_Consortium_C6-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C6-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_Consortium_C6-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
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+ "--out",
+ "/private/tmp/communitymech-batch121/Wheat_Consortium_C6-strict.tsv",
+ "kb/communities/Wheat_Consortium_C6.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C6-strict.log",
+ "log_sha256": "98a9a701159ca9ddf1272ede04a8c9951766f7efab9b4f73ccbbb79dc96a5ba5",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch121/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-batch121/Wheat_Consortium_C6-strict.tsv\n"
+ },
+ {
+ "check": "Wheat_Consortium_C6-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wheat_Consortium_C6.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C6-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wheat_Consortium_C6-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wheat_Consortium_C6.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C6-references.log",
+ "log_sha256": "6de43f5e0e514e02462dd7a2608838c14e11b35400d7079a4644848fc6adf155",
+ "output_tail": "Validating kb/communities/Wheat_Consortium_C6.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/Wheat_Consortium_C6.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": "Wheat_Consortium_C6-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wheat_Consortium_C6.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C6-snippets.log",
+ "log_sha256": "084ae27007699db0121de3de19b35f22b279fa80b76f47de2b781d3ae6d70cdc",
+ "output_tail": "# 21 evidence snippets scanned across 1 files\n MATCH 19\n RENDERING 2\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 2 kb/communities/Wheat_Consortium_C6.yaml\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": "Wheat_Consortium_C6-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wheat_Consortium_C6.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C6-rank.log",
+ "log_sha256": "a39483ba0dd1f4aaae05793416521ea68b0c11faab4320a786d1052498823a61",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000077\",\n \"name\": \"Wheat Synthetic Consortium C6\",\n \"score\": 65.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 5,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 11,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Wheat_Consortium_C6.yaml\"\n }\n]\n"
+ },
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+ "check": "Wheat_Consortium_C6-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wheat_Consortium_C6/2026-10-08T150229Z-codex-b61a7a.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_Consortium_C6-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_CrownRot_SixStrain_CrossKingdom_SMC-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_CrownRot_SixStrain_CrossKingdom_SMC-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Wheat_CrownRot_SixStrain_CrossKingdom_SMC-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch121/Wheat_CrownRot_SixStrain_CrossKingdom_SMC-strict.tsv",
+ "kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_CrownRot_SixStrain_CrossKingdom_SMC-strict.log",
+ "log_sha256": "128af60b561cb5a0bc0ffd6c1e051032c2cbf63ea29bd7de907031322761389b",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch121/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-batch121/Wheat_CrownRot_SixStrain_CrossKingdom_SMC-strict.tsv\n"
+ },
+ {
+ "check": "Wheat_CrownRot_SixStrain_CrossKingdom_SMC-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_CrownRot_SixStrain_CrossKingdom_SMC-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Wheat_CrownRot_SixStrain_CrossKingdom_SMC-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_CrownRot_SixStrain_CrossKingdom_SMC-references.log",
+ "log_sha256": "cfaba4ea8ce733614bfdcbc8633fdbb8ddad41c9418c9be38fcb505c74628d5e",
+ "output_tail": "Validating kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.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/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.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": "Wheat_CrownRot_SixStrain_CrossKingdom_SMC-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_CrownRot_SixStrain_CrossKingdom_SMC-snippets.log",
+ "log_sha256": "6f2de9fb4d8c177ffbcd0ad88a37a36fb65a242f256bee6a97070647234944fe",
+ "output_tail": "# 33 evidence snippets scanned across 1 files\n MATCH 33\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Wheat_CrownRot_SixStrain_CrossKingdom_SMC-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_CrownRot_SixStrain_CrossKingdom_SMC-rank.log",
+ "log_sha256": "7bd9055ac43ff9d34734e4142a030d12fc83ca11dce20a5d364ff28052269924",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000414\",\n \"name\": \"Wheat Crown-Rot Six-Strain Cross-Kingdom SMC\",\n \"score\": 57.5,\n \"taxonomy\": 6,\n \"connected_taxa\": 6,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Wheat_CrownRot_SixStrain_CrossKingdom_SMC-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Wheat_CrownRot_SixStrain_CrossKingdom_SMC/2026-10-08T150229Z-codex-fc0ee7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/Wheat_CrownRot_SixStrain_CrossKingdom_SMC-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-batch121/verification/inventory.log",
+ "log_sha256": "6b4a4bb06880c11cf6364b7daea50992c44d4472ff6985c7315b09315421f87e",
+ "output_tail": "{\n \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n \"records\": 460,\n \"nodes\": 1373,\n \"edges\": 530,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 189,\n \"review_status_counts\": {\n \"needs_research\": 54,\n \"pending\": 14,\n \"reviewed\": 392\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-batch121/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-batch121/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-batch121/verification/rank-all.log",
+ "log_sha256": "8084657da95074bb9bb07e0ae16e9cd243302301d6f23768983197735c3efe76",
+ "output_tail": ":000174\tClostridium cellulovorans-Methanosarcina barkeri Cellulose Methane Coculture\t2\t2\t0\t3\t2\t8\tinteraction_type\t0\t0\n405\t96.7\tkb/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.yaml\tCommunityMech:000206\tClostridium-Saccharomyces Cellulose Ethanol Coculture\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n406\t96.7\tkb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml\tCommunityMech:000297\tDIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n407\t96.7\tkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml\tCommunityMech:000023\tDesulfovibrio-Methanococcus Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n408\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\n409\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\n410\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\n411\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\n412\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\n413\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\n414\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\n415\t96.7\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t9\tinteraction_type\t0\t0\n416\t96.7\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\tinteraction_type\t0\t0\n417\t96.7\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n418\t96.7\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n419\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\n420\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\n421\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\n422\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\n423\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\n424\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\n425\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\n426\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\n427\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\n428\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\n429\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\n430\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\n431\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\n432\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\n433\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\n434\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\n435\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\n436\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\n437\t100.0\tkb/communities/DVM_Triculture.yaml\tCommunityMech:000021\tDVM Tri-culture\t3\t3\t0\t4\t2\t7\t\t0\t0\n438\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\n439\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\n440\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\n441\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\n442\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\n443\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\n444\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\n445\t100.0\tkb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml\tCommunityMech:000156\tNeocallimastix-Methanobrevibacter Xylanolytic Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\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\n447\t100.0\tkb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\tCommunityMech:000052\tPelotomaculum-Methanothermobacter Syntrophic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n448\t100.0\tkb/communities/Phenol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n449\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\n450\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\n451\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\n452\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\n453\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\n454\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\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": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/render.log",
+ "log_sha256": "ef9df36ebdcf8c956cac6474c7751a3a47aba5f4875d235fc33268c8f7d87aec",
+ "output_tail": "unitymech-causal-batch121/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch121/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch121/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch121/docs/index.html\n"
+ },
+ {
+ "check": "render-repeat",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/render-repeat.log",
+ "log_sha256": "ef9df36ebdcf8c956cac6474c7751a3a47aba5f4875d235fc33268c8f7d87aec",
+ "output_tail": "unitymech-causal-batch121/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch121/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch121/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch121/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch121/docs/index.html\n"
+ },
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+ "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']()))"
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+ },
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "output_tail": "............... [100%]\n15 passed in 3.78s\n"
+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "tests/test_causal_review_batch42.py",
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+ "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"
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+ "output_tail": "........................................................................ [ 6%]\n........................................................................ [ 12%]\n........................................................................ [ 18%]\n........................................................................ [ 25%]\n........................................................................ [ 31%]\n........................................................................ [ 37%]\n........................................................................ [ 43%]\n........................................................................ [ 50%]\n........................................................................ [ 56%]\n........................................................................ [ 62%]\n........................................................................ [ 69%]\n........................................................................ [ 75%]\n........................................................................ [ 81%]\n........................................................................ [ 87%]\n........................................................................ [ 94%]\n.................................................................. [100%]\n1146 passed in 406.93s (0:06:46)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
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+ "log_sha256": "7ae3d908f4fe72dfd165bbe8a81a58257715a1d115d15864227a361e3182e5ad",
+ "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\n374 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\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-batch121/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-batch121/verification/audit-snippets-all.log",
+ "log_sha256": "279b5a4a022a502c4880b9e422754c6a12912bc8349045127d13f86ba8b23593",
+ "output_tail": "# 9073 evidence snippets scanned across 460 files\n MATCH 8925\n RENDERING 31\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch121/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Both-root baseline precedes primary research:460records,923caches,57existing warnings,zero structural defects. All four whole records and14existing nodes/two arrows reviewed. Retain12nodes/two arrows,remove two inoculum-assembly nodes,rename six nodes,no new topology.",
+ "Four fresh EuropePMC abstract/metadata and Crossref retrievals cover three unique primary studies. Complete wheat C1/C6 and crown-rot main bodies read including methods,results,discussion,tables and captions. C1/C6 XML/body hashes are identical. No original figure pixels,separate supplementary files,raw data or analysis code audited.",
+ "Tomato changes are abstract-bounded. EuropePMC has no PMC identifier and lists subscription-required DOI access; DOI open was unavailable and ScienceDirect PII S0981942823004527 returned403. No exhaustive full-text absence claim,access bypass or author contact. No full article-body import.",
+ "Tomato retains positive complementary community functions,leaf oxylipin activation,biosynthesis-inhibition loss of protection,and SlLOX5/SlDES1 overexpression benefit. This supports pathway-level causality,not reciprocal bacterial fitness,unique biofilm mediation or independent necessity of each divinyl ether. Exact member/role metadata remains1943.",
+ "Wheat C1/C6 primary is CC BY4.0. Equal-ratio assembly is preparation,not ecological colonization; prior workflow-arrow removals remain intact. C1 retains significant greenhouse benefits but no demonstrated superiority over the best single strain. C6 retains positive dual-plate inhibition and Salkowski output but Arabidopsis root shortening is not growth promotion. Positive individual-member secretion/volatile assays do not override whole-mixture nulls. Persistence explicitly was not assessed. Negative r-squared notation is not silently repaired. Non-graph abundance/metal scope remains1944.",
+ "Crown-rot primary is CC BY-NC-ND4.0,not unrestricted CC BY. Preserve measured pot disease and grain benefits. Relative DNA profiles are not viable-cell colonization or functional flux; correlation networks do not establish cooperation or ecological necessity. Added allantoin/dihydrodaidzein have positive plant outcomes and negative direct fungal assays; do not erase these positives or infer intact-SMC necessity. Old cache wording differs from fresh abstract and bacterial-treatment assignments; timing and provenance remain1945.",
+ "Exactly three short crown-rot discussion excerpts,21quoted words,are appended with source/license attribution. Old cache bytes remain an unchanged prefix. No protocol addition or full-body import. All24graph and10discussion quotes independently matched to fresh primary and authoritative local caches; literal matches are not entailment proof. Existing selected caches and primary text read; no claim to manual whole-reading of the very long C1 markdown cache.",
+ "Initial and fresh pre-creation all-state1175issue titles/bodies searched,seven matching bodies read,161matching local paths found including ignored/hidden files except.git,docs,site,references_cache,.env.1035/1037 address crown-rot participants/CI;615 host-cultivation schema;1521,1378,1375,981 other records. Not a historical PR-comment audit.",
+ "Four guarded writes preserve456otherrecords,922unchangedcaches,unrelated raw YAML blocks and all prior histories/decisions. Four append-only histories and curation events. Taxon identities,participant lists and scopes unchanged; evidence aliases detached. No experimental optimization.",
+ "Existing-graph repair with no new nodes/directions: no Edison run,provider submission or spend. Prior authorized Ruegeria1883 authentication blocker not retried unchanged; no credential inspected. Source-based 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/Tomato_Oxylipin_SynCom3.yaml": {
+ "MATCH": 14,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wheat_Consortium_C1.yaml": {
+ "MATCH": 14,
+ "RENDERING": 1,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wheat_Consortium_C6.yaml": {
+ "MATCH": 19,
+ "RENDERING": 2,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml": {
+ "MATCH": 33,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 922,
+ "unchanged_raw_blocks": 54,
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+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch121/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-batch121/baseline-downstream.log",
+ "sha256": "cbe1386c04b624eed80061da4dce9c8f2a90bcc590a79a41f2c407a25e9e0c62"
+ }
+ ],
+ "baseline_sha256": "e92b45d03d6c465de8302b503b81336144391a7179c1c56de54b1b0e64245493"
+ },
+ "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_batch121.py b/tests/test_causal_review_batch121.py
new file mode 100644
index 000000000..eba2204ed
--- /dev/null
+++ b/tests/test_causal_review_batch121.py
@@ -0,0 +1,199 @@
+"""Guard measured plant outcomes and mixture-versus-member assay contrasts."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-four-records-batch121.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_tomato_complementarity_is_not_reciprocal_mutualism():
+ _, _, docs = records()
+ nodes = docs[0]["ecological_interactions"]
+ assert all("interaction_type" not in n for n in nodes)
+ assert "biofilm and host defense" in nodes[0]["name"]
+ assert "similar protective effects" in nodes[0]["evidence"][1]["snippet"]
+ assert "do not measure reciprocal bacterial fitness" in nodes[0]["description"]
+
+
+def test_tomato_biofilm_mediation_remains_partial():
+ _, _, docs = records()
+ a, b, c = docs[0]["ecological_interactions"]
+ assert len(a["downstream"]) == len(b["downstream"]) == 1
+ assert a["downstream"][0]["target"] == b["name"]
+ assert b["downstream"][0]["target"] == c["name"]
+ assert "PARTIAL for biofilm formation as the mediator" in a["downstream"][0]["description"]
+ assert "not microbial mutualism" in b["description"]
+
+
+def test_tomato_retains_positive_biosynthesis_perturbation():
+ _, _, docs = records()
+ nodes = docs[0]["ecological_interactions"]
+ evidence = nodes[2]["evidence"][0]
+ assert "fully abolished" in evidence["snippet"]
+ assert evidence["supports"] == "SUPPORT"
+ assert "biosynthesis perturbation" in nodes[1]["description"]
+ assert "inhibiting their biosynthesis abolished" in nodes[1]["downstream"][0]["description"]
+ assert "independently indispensable" in nodes[2]["description"]
+
+
+def test_tomato_retains_complementary_overexpression_evidence():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][2]
+ assert "overexpressing SlLOX5 and SlDES1" in node["evidence"][1]["snippet"]
+ assert "stronger resistance" in node["evidence"][1]["snippet"]
+ assert all(e["evidence_source"] == "IN_VIVO" for e in node["evidence"])
+ assert len(docs[0]["discussions"][-1]["evidence"]) == 1
+
+
+def test_wheat_c1_assembly_is_metadata_not_an_ecological_node():
+ _, rows, docs = records()
+ nodes = docs[1]["ecological_interactions"]
+ assert len(nodes) == 2 and len(rows[1]["removed_node_decisions"]) == 1
+ assert all("interaction_type" not in n for n in nodes)
+ assert not any(n.get("downstream") for n in nodes)
+ assert "persistence" in docs[1]["discussions"][-1]["evidence"][2]["snippet"]
+
+
+def test_wheat_c1_retains_whole_mixture_plate_inhibition():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][0]
+ assert "37.00%" in node["description"]
+ assert "37.00" in node["evidence"][1]["snippet"]
+ assert "not evidence that both bacterial and fungal fitness declined" in node["description"]
+
+
+def test_wheat_c1_host_benefit_is_not_best_strain_superiority():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][1]
+ assert "reduced root-rot scores and increased fresh root weight" in node["description"]
+ assert (
+ node["evidence"][1]["snippet"]
+ == "None of them was significantly better than a single strain"
+ )
+ assert "Only B5" in node["description"]
+ assert "no antifungal activity from any SynCom" in docs[1]["discussions"][-1]["rationale"]
+
+
+def test_wheat_c6_preserves_direct_plate_inhibition_without_workflow_arrows():
+ _, rows, docs = records()
+ nodes = docs[2]["ecological_interactions"]
+ assert len(nodes) == 5 and len(rows[2]["removed_node_decisions"]) == 1
+ assert not any(n.get("downstream") for n in nodes)
+ assert "34.48%" in nodes[0]["description"]
+ assert "34.48" in nodes[0]["evidence"][1]["snippet"]
+
+
+def test_wheat_c6_salkowski_is_not_resolved_delivery_or_mutualism():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][1]
+ assert "interaction_type" not in node and "biological_processes" not in node
+ assert "Salkowski" in node["name"]
+ assert "11.76" in node["evidence"][1]["snippet"]
+ assert "not structural identification" in node["description"]
+ assert (
+ "not independently resolved molecular identity or plant delivery"
+ in node["metabolites"][0]["notes"]
+ )
+
+
+def test_wheat_c6_primary_root_shortening_is_not_growth_promotion():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][2]
+ assert "primary-root shortening" in node["name"]
+ assert "not demonstrated growth promotion" in node["description"]
+ assert "does not establish IAA as the necessary mediator" in node["description"]
+ assert node["evidence"][0]["evidence_source"] == "IN_VIVO"
+ assert "except C5" in node["evidence"][0]["snippet"]
+
+
+def test_wheat_c6_cell_free_member_positives_do_not_erase_mixture_null():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][3]
+ assert "interaction_type" not in node and len(node["participating_taxa"]) == 4
+ assert "significantly inhibited" in node["evidence"][1]["snippet"]
+ assert "10 SynComs did not show any antifungal activities" in node["evidence"][2]["snippet"]
+ assert (
+ "individual secretion-associated inhibition cannot be assigned to the mixed culture"
+ in node["description"]
+ )
+
+
+def test_wheat_c6_volatile_positive_list_is_not_a_mixture_benefit():
+ _, _, docs = records()
+ node = docs[2]["ecological_interactions"][4]
+ assert "interaction_type" not in node and len(node["participating_taxa"]) == 4
+ assert "SynComs C2-4, C7" in node["evidence"][2]["snippet"]
+ assert "C6 was not one of the four significantly inhibitory mixtures" in node["description"]
+ assert "Each of the four C6 member strains inhibited AG8" in node["description"]
+ assert "does not identify C6" in node["evidence"][0]["explanation"]
+
+
+def test_crown_rot_retains_positive_disease_and_grain_outcomes():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][0]
+ assert "interaction_type" not in node
+ assert "86.45%" in node["description"] and "25.93%" in node["description"]
+ assert node["evidence"][1]["snippet"] == "SMC+Fp increased TKW by 10.39% relative to Fp"
+ assert "not multilocation field validation" in node["description"]
+
+
+def test_crown_rot_profiles_and_compound_assays_do_not_prove_necessity():
+ ledger, _, docs = records()
+ node = docs[3]["ecological_interactions"][1]
+ assert "interaction_type" not in node and "biological_processes" not in node
+ assert "not absolute viable abundance" in node["description"]
+ assert "Total DNA was extracted" in node["evidence"][1]["snippet"]
+ discussion = docs[3]["discussions"][-1]
+ assert (
+ discussion["evidence"][1]["snippet"]
+ == "showed no direct antifungal activity of either compound"
+ )
+ assert discussion["evidence"][2]["snippet"] == "significantly reduced DSI"
+ assert "not their necessity in the intact SMC" in discussion["rationale"]
+ assert ledger["cache_changes"][0]["license"] == "CC BY-NC-ND 4.0"
+
+
+def test_review_accounts_for_nodes_arrows_and_append_only_cache():
+ ledger, rows, docs = records()
+ counts = ledger["reviewed_counts"]
+ assert (counts["original_nodes"], counts["retained_nodes"], counts["removed_nodes"]) == (
+ 14,
+ 12,
+ 2,
+ )
+ assert counts["renamed_nodes"] == 6
+ assert (counts["original_arrows"], counts["retained_arrows"], counts["removed_arrows"]) == (
+ 2,
+ 2,
+ 0,
+ )
+ assert (counts["graph_quotations"], counts["discussion_quotations"]) == (24, 10)
+ assert not ledger["independent_approval"] and ledger["edison"]["new_nodes_or_directions"] == 0
+ (change,) = ledger["cache_changes"]
+ assert change["old_prefix_preserved"] and change["added_quotation_words"] == 21
+ assert (
+ hashlib.sha256((ROOT / change["path"]).read_bytes()).hexdigest() == change["after_sha256"]
+ )
+ assert ledger["unresolved_non_graph_issues"] == [1943, 1944, 1945]
+ 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"]
+ assert len(doc["discussions"]) == 1
+ assert all(
+ a.removeprefix("ecological_interactions#") in names
+ for a in doc["discussions"][0]["attaches_to"]
+ )
+ 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", []))