SynCom 3 inoculation increased Conejo maize root and shoot growth in gnotobiotic tubes and greenhouse pots after its constituent PGP activities were expressed in vitro.
-
SynCom 3 inoculation increased Conejo maize growth in gnotobiotic tubes and greenhouse pots. Gnotobiotic root and shoot sizes were 4.2 and 3.0 times the controls. In greenhouse comparisons, root/shoot lengths were 3.3/1.4 times controls and shoot/root dry weights were 2.3/3 times controls. These are positive whole-inoculant treatment effects in the Conejo landrace, not proof that its earlier in-vitro trait panel caused them or that those seedlings produced the separate hybrid field harvest. The four canonical participants are a subset of the reported six-strain SynCom 3, not a complete four-member inoculant; exact membership and the primary Pseudomonas strain inconsistency remain under #1521.
-
In open-field hybrid maize tests, SynCom 3 increased grain yield relative to the untreated control and significantly reduced fungal rust incidence.
-
+
In the reported one-site field experiment with CPL9105W hybrid maize, SynCom 3 treatment increased grain yield from 11 to 16 tons/ha relative to control. The abstract reports rust incidence falling from 12.5 to 8 percent, not a 12.5-percentage-point reduction. The treatment involved seed inoculation and subsequent applications; it is distinct from the Conejo seedling experiments. The whole-inoculant effects do not establish which traits or members mediated them, universal efficacy across sites/seasons, or a benefit for every tested SynCom. The four canonical participants are a subset of the reported six-strain SynCom 3, not a complete four-member inoculant; exact membership and the primary Pseudomonas strain inconsistency remain under #1521.
+
+
+
+
+
Participating Taxa:
+
+ Pseudomonas protegens,
+ Pantoea ananatis,
+ Klebsiella variicola,
+ Burkholderia sp.
+
+
@@ -1098,6 +1022,25 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which SynCom 3 members and activities mediate maize growth and field rust reduction?
+
+
Remove the compatibility-assembly node and its two arrows as experimental workflow; design metadata remains. Remove seedling-to-field selection as workflow, not a causal effect connecting different hosts and experiments. Preserve positive whole-inoculant outcomes and the two proposed trait/defense routes as PARTIAL. The six-strain formulation is not the four canonical taxa; missing members and E1BL2 versus E2HL9 inconsistency remain #1521. Full cached primary main text, Methods, Tables 1-2 and Figures 1-6 captions read; fresh Frontiers formulation/Discussion spot-checks, not a second full reading. No original images, external supplements, raw data or code audited. No new graph structure; all non-graph blocks remain unchanged and are not recertified.
+
+
Attaches to: ecological_interactions#SynCom 3 Multi-Trait PGP Activity, ecological_interactions#SynCom 3 Antifungal and PAL Induction, ecological_interactions#Conejo Maize Seedling Growth Promotion, ecological_interactions#Field Yield Increase and Rust Reduction
+
+
+
+
+
@@ -1320,35 +1263,7 @@
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 = 3;
-
- nodes.push({
- id: intId,
- label: "Compatibility-Constrained SynCom 3 Assembly",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1380,11 +1295,28 @@
Evidence
+ var participantKeys = [
+
+ "Pseudomonas protegens",
+
+ "Pantoea ananatis",
+
+ "Klebsiella variicola",
+
+ "Burkholderia sp."
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
- var intId = "interaction:2";
- var intType = "COMPETITION";
+ var intId = "interaction:1";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1408,11 +1340,28 @@
Evidence
+ var participantKeys = [
+
+ "Pseudomonas protegens",
+
+ "Pantoea ananatis",
+
+ "Klebsiella variicola",
+
+ "Burkholderia sp."
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
- var intId = "interaction:3";
- var intType = "MUTUALISM";
+ var intId = "interaction:2";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1436,11 +1385,28 @@
Evidence
+ var participantKeys = [
+
+ "Pseudomonas protegens",
+
+ "Pantoea ananatis",
+
+ "Klebsiella variicola",
+
+ "Burkholderia sp."
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
- var intId = "interaction:4";
- var intType = "MUTUALISM";
+ var intId = "interaction:3";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1466,6 +1432,23 @@
Evidence
+ var participantKeys = [
+
+ "Pseudomonas protegens",
+
+ "Pantoea ananatis",
+
+ "Klebsiella variicola",
+
+ "Burkholderia sp."
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
@@ -1487,7 +1470,7 @@
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 = 9;
+ var nodeCount = 8;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.html b/docs/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.html
index f3e8ab535..b56859516 100644
--- a/docs/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.html
+++ b/docs/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.html
@@ -599,59 +599,22 @@
Ecological Interactions
-
LAB isolates from traditional Jiangshui were screened down to Y-5-3, Y-6-2, and HN, then manually combined in 20 ratios to tune a defined Jiangshui SynCom.
+
The tested Y-5-3:Y-6-2:HN 2:3:1 formulation had the highest reported sensory score, 89.38 +/- 4.10, among the assayed three-strain fermentation schemes. This is a positive combined-inoculant fermentation result, not an isolated molecular mechanism or proof that the ratio alone explains its difference from natural fermentation. All three canonical strain names remain distinct despite their unresolved species-level identifiers.
+
Participating Taxa:
+ LAB strain Y-5-3,
+ LAB strain Y-6-2,
+ LAB strain HN
-
-
-
-
Downstream Effects:
-
-
-
→ Optimized 2:3:1 Jiangshui fermentation
-
The three selected LAB strains were assembled at empirically varied ratios before the optimized Y-5-3:Y-6-2:HN ratio was selected.
-
-
-
-
-
-
-
Evidence
-
-
- -
-
-
-
"On this basis, 3 high-performance strains (Y-5-3, Y-6-2, HN) were selected and manually combined in 20 ratios to construct SynComs"
-
-
-
-
-
-
-
-
-
-
A Y-5-3:Y-6-2:HN ratio of 2:3:1 was the optimal mixed-strain fermentation scheme among the assayed three-strain LAB SynCom ratios.
-
-
-
+
@@ -675,7 +638,7 @@
Optimized 2:3:1 Jiangshui fermentation
→ Jiangshui phenol and flavonoid increase
-
The optimized 2:3:1 strain ratio increased measured total phenols and flavonoids compared with natural Jiangshui.
+
The tested three-strain 2:3:1 fermentation treatment increased measured total phenol and flavonoid contents relative to natural Jiangshui. This positive formulation-level intervention does not isolate the ratio, a particular strain, release versus synthesis, or a molecular mediator as the cause.
@@ -719,11 +682,21 @@
Evidence
-
The optimized three-strain LAB scheme increased total phenols and flavonoids relative to natural Jiangshui while reducing off-odors and improving stability.
+
The tested three-strain formulation increased total phenols by 72.20 percent and total flavonoids by 61.13 percent relative to natural Jiangshui, with reported P < 0.01. The abstract also reports reduced off-odors and improved stability without the operational detail available in a full protocol. These are total-content endpoints, not identified compound flux, de-novo flavonoid synthesis or demonstrated benefits exchanged between individual strains.
+
Participating Taxa:
+
+ LAB strain Y-5-3,
+
+ LAB strain Y-6-2,
+
+ LAB strain HN
+
+
+
Metabolites:
@@ -777,7 +750,7 @@
Evidence
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -792,6 +765,21 @@
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which processes underlie the positive formulation-level fermentation endpoints?
+
+
Remove screening/ratio assembly and its arrow as researcher workflow; retain the biological fermentation treatment and positive content response. No isolated ratio effect or de-novo biosynthesis is demonstrated by the accessible abstract. Complete cached abstract and indexed publisher fragments read; direct publisher requests returned403 and no primary full body was inspected. Fragments do not map selected strain codes to species or give the fermentation protocol; preserve the existing taxonomy/growth-conditions knowledge gap and prior histories. In-vitro biosafety screens do not establish clinical safety. No original images, supplements, raw data or code audited and no new graph structure added.
+
+
Attaches to: ecological_interactions#Three-Strain 2:3:1 Jiangshui Fermentation, ecological_interactions#Jiangshui phenol and flavonoid increase
+
+
+
+
@@ -1054,11 +1042,15 @@
Evidence
var processes = [];
- var evidenceCount = 1;
+
+ processes.push("fermentation");
+
+
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Jiangshui LAB screening and ratio assembly",
+ label: "Three-Strain 2:3:1 Jiangshui Fermentation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1069,38 +1061,25 @@
Evidence
- })();
-
- (function() {
- var intId = "interaction:1";
- var intType = "UNKNOWN";
- var metabolites = [];
-
- var processes = [];
-
+ var participantKeys = [
- processes.push("fermentation");
+ "LAB strain Y-5-3",
+ "LAB strain Y-6-2",
- var evidenceCount = 2;
+ "LAB strain HN"
- nodes.push({
- id: intId,
- label: "Optimized 2:3:1 Jiangshui fermentation",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
});
-
-
-
})();
(function() {
- var intId = "interaction:2";
+ var intId = "interaction:1";
var intType = "UNKNOWN";
var metabolites = [];
@@ -1129,6 +1108,21 @@
Evidence
+ var participantKeys = [
+
+ "LAB strain Y-5-3",
+
+ "LAB strain Y-6-2",
+
+ "LAB strain HN"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
@@ -1150,7 +1144,7 @@
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 = 6;
+ var nodeCount = 5;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/history/records/Ion_Adsorption_REE_Indigenous_Community/2026-10-06T174553Z-codex-f8ce0e.yaml b/history/records/Ion_Adsorption_REE_Indigenous_Community/2026-10-06T174553Z-codex-f8ce0e.yaml
new file mode 100644
index 000000000..f7c34cb3f
--- /dev/null
+++ b/history/records/Ion_Adsorption_REE_Indigenous_Community/2026-10-06T174553Z-codex-f8ce0e.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml
+ slug: Ion_Adsorption_REE_Indigenous_Community
+session:
+ id: 2026-10-06T174553Z-codex-f8ce0e
+ timestamp: '2026-10-06T17:45:53Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1517
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Separate positive REE laboratory adsorption from proposed weathering and deposit-scale
+ mediation.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml
diff --git a/history/records/Jala_Maize_PGPB_SynCom/2026-10-06T174554Z-codex-56c270.yaml b/history/records/Jala_Maize_PGPB_SynCom/2026-10-06T174554Z-codex-56c270.yaml
new file mode 100644
index 000000000..ed73a3b33
--- /dev/null
+++ b/history/records/Jala_Maize_PGPB_SynCom/2026-10-06T174554Z-codex-56c270.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Jala_Maize_PGPB_SynCom.yaml
+ slug: Jala_Maize_PGPB_SynCom
+session:
+ id: 2026-10-06T174554Z-codex-56c270
+ timestamp: '2026-10-06T17:45:54Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1518
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain maize SynCom assay and plant outcomes without workflow causality or proven
+ trait mediation.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml
diff --git a/history/records/Jiangshui_LAB_Directed_Fermentation_SynCom/2026-10-06T174554Z-codex-394a99.yaml b/history/records/Jiangshui_LAB_Directed_Fermentation_SynCom/2026-10-06T174554Z-codex-394a99.yaml
new file mode 100644
index 000000000..03153a9a7
--- /dev/null
+++ b/history/records/Jiangshui_LAB_Directed_Fermentation_SynCom/2026-10-06T174554Z-codex-394a99.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml
+ slug: Jiangshui_LAB_Directed_Fermentation_SynCom
+session:
+ id: 2026-10-06T174554Z-codex-394a99
+ timestamp: '2026-10-06T17:45:54Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1519
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain the Jiangshui formulation effect and remove experimental screening from
+ the biological graph.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml
diff --git a/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml b/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml
index d08ae80cb..05084783c 100644
--- a/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml
+++ b/kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml
@@ -312,299 +312,245 @@ taxonomy:
explanation: Establishes fungal role in REE mineralization
ecological_interactions:
- name: Teichoic Acid-Mediated HREE Selective Biosorption
- description: 'Gram-positive bacteria (Bacillus, Micrococcus) selectively adsorb heavy rare earth elements
- (HREE) through teichoic acids in their cell walls, achieving 82-85% HREE uptake versus 70-78% LREE
- uptake. Teichoic acids are anionic polymers containing phosphate groups that serve as the primary
- binding sites for REE cations. The selectivity arises from lanthanide contraction—the progressive
- decrease in ionic radius from La³⁺ (1.16 Å) to Lu³⁺ (0.98 Å) across the lanthanide series. Smaller
- HREE cations form stronger coordination bonds with phosphate oxygen atoms due to higher charge density
- and better geometric fit. TEM/EDS spectroscopy confirmed co-localization of ytterbium (Yb, Z=70) with
- phosphorus along bacterial cell walls, demonstrating P-O-REE bonding. Removal of teichoic acids reduced
- REE adsorption from 65.5% to 17.8%, proving their essentiality. This natural HREE fractionation mechanism
- explains the commercial HREE enrichment in ion-adsorption deposits and offers a biological model for
- selective REE recovery technologies.
-
- '
- interaction_type: COMMENSALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Bacillus
- term:
- id: NCBITaxon:1386
- label: Bacillus
- target_taxon:
- preferred_term: Micrococcus
- term:
- id: NCBITaxon:1269
- label: Micrococcus
+ description: Isolated Bacillus and Micrococcus strains from the Renju profile preferentially adsorbed HREEs in
+ separate laboratory assays. In the Bacillus pumilus cell-wall comparison, removing teichoic acids reduced total
+ REE adsorption from 65.5 to 17.8 percent and removed HREE preference; residual binding remained. Freeze-dried
+ cells retained adsorption, consistent with passive surface binding rather than active metal transport. Ytterbium/phosphorus
+ colocalization and spectroscopy support wall binding groups, not a resolved bond geometry or proof that ionic
+ radius is the sole cause. The canonical genera represent separately tested isolates, not measured commensalism
+ between them or every strain in either genus.
+ scope: COMMUNITY_LEVEL
metabolites:
- - preferred_term: dysprosium(3+)
- term:
- id: CHEBI:33377
- label: dysprosium atom
- notes: Critical HREE for permanent magnets, selectively adsorbed by teichoic acids
- preferred_term: yttrium(3+)
term:
id: CHEBI:49962
label: yttrium(3+)
- notes: HREE analog, selectively adsorbed; enriched 56-184 ppm in B horizon
+ notes: Laboratory REE cation; the multi-element adsorption series and higher-concentration Yb microscopy are
+ distinct assays. No profile-wide ionic concentration is assigned.
- preferred_term: ytterbium(3+)
term:
id: CHEBI:49980
label: ytterbium(3+)
- notes: HREE used in EDS co-localization studies with phosphate
- - preferred_term: phosphate
- term:
- id: CHEBI:18367
- label: phosphate(3-)
- notes: Binding site in teichoic acids for REE coordination
- biological_processes:
- - preferred_term: metal ion transport
- term:
- id: GO:0030001
- label: metal ion transport
- - preferred_term: cellular response to metal ion
- term:
- id: GO:0071248
- label: cellular response to metal ion
- downstream:
- - target: HREE Enrichment in B Horizon
- description: Bacterial biosorption concentrates HREE in clay-rich weathering zones
+ notes: Laboratory REE cation; the multi-element adsorption series and higher-concentration Yb microscopy are
+ distinct assays. No profile-wide ionic concentration is assigned.
evidence:
- reference: PMID:35708325
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated
- with Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall
- served as the main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit
- explanation: Quantifies HREE selectivity
+ evidence_source: IN_VITRO
+ snippet: Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated with
+ Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall served as the
+ main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit
+ explanation: Supports laboratory isolate/cell-wall adsorption and its proposed binding groups, not universal
+ essentiality, active transport or quantified field mediation.
- reference: PMID:35708325
supports: SUPPORT
- evidence_source: IN_VIVO
+ evidence_source: IN_VITRO
snippet: teichoic acids in the cell walls of G+ bacteria lead to REE fractionation
- explanation: Proves teichoic acid essentiality for REE binding
+ explanation: Supports laboratory isolate/cell-wall adsorption and its proposed binding groups, not universal
+ essentiality, active transport or quantified field mediation.
- reference: PMID:35708325
supports: SUPPORT
- evidence_source: IN_VIVO
+ evidence_source: IN_VITRO
snippet: surface carboxyl and phosphate groups are active sites for REE adsorption
- explanation: Spectroscopic evidence for phosphate-HREE binding
-- name: Bioweathering and REE Mineral Dissolution
- description: 'Proteobacteria (Acinetobacter, Pseudomonas), Actinobacteria, and fungi (Ascomycota, Basidiomycota)
- accelerate weathering of granitic bedrock and dissolution of REE-bearing minerals through production
- of organic acids (citric, oxalic, gluconic), siderophores, and extracellular enzymes. Bacterial and
- fungal metabolites acidify the microenvironment, protonate silicate minerals, and complex REE cations,
- driving mineral dissolution rates orders of magnitude faster than abiotic weathering. Acinetobacter
- and Pseudomonas are known REE-mineral dissolvers that facilitate REE release from resistant phases
- like monazite, xenotime, and REE-enriched clays. Fungal hyphae physically penetrate grain boundaries
- and chemically attack mineral surfaces, creating high surface-area weathering zones. This bioweathering
- process transforms primary REE minerals into secondary clay-bound ion-adsorption forms that are economically
- extractable through simple ammonium sulfate leaching. The biogeochemical cascade (mineral dissolution
- → REE release → biosorption → HREE fractionation) drives formation of commercially valuable HREE-enriched
- ion-adsorption deposits.
-
- '
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Proteobacteria
+ explanation: Supports laboratory isolate/cell-wall adsorption and its proposed binding groups, not universal
+ essentiality, active transport or quantified field mediation.
+ - reference: PMID:35708325
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: decreased the REE adsorption from 65.5% to only 17.8%
+ explanation: Primary cell-wall perturbation retains positive teichoic-acid contribution with residual adsorption,
+ not abolition of all binding.
+ participating_taxa:
+ - preferred_term: Bacillus
term:
- id: NCBITaxon:1224
- label: Pseudomonadota
- target_taxon:
- preferred_term: Actinobacteria
+ id: NCBITaxon:1386
+ label: Bacillus
+ - preferred_term: Micrococcus
term:
- id: NCBITaxon:201174
- label: Actinomycetota
+ id: NCBITaxon:1269
+ label: Micrococcus
+ downstream:
+ - target: Observed B-Horizon HREE Enrichment
+ description: PARTIAL - preferential HREE binding by indigenous bacterial cell walls could contribute to retention
+ and fractionation in the B horizon. Laboratory adsorption and field community/geochemical associations support
+ this route, but do not isolate its deposit-scale magnitude from mineral adsorption and water transport.
+- name: Proposed Microbial REE Mineral Dissolution
+ description: HYPOTHESIZED - microbial organic acids and other ligands could weather minerals and release REEs
+ in the Renju profile. The primary discussion combines community/geochemical associations with weathering functions
+ known from prior literature; it does not measure these routes in every listed phylum or isolate direct Proteobacteria-to-Actinobacteria
+ transfer. The canonical bacterial and fungal phyla are contextual groups, not a demonstrated four-partner cross-feeding
+ unit. An orders-of-magnitude acceleration relative to abiotic weathering was not established in the inspected
+ study.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: citric acid
term:
id: CHEBI:30769
label: citric acid
- notes: Organic acid complexing agent for REE mobilization
+ notes: Contextual candidate weathering ligand from the proposed mechanism, not a measured product or traced
+ transfer by every listed taxon in the Renju profile.
- preferred_term: oxalic acid
term:
id: CHEBI:16995
label: oxalic acid
- notes: Strong chelator for REE and mineral cations
+ notes: Contextual candidate weathering ligand from the proposed mechanism, not a measured product or traced
+ transfer by every listed taxon in the Renju profile.
- preferred_term: organic molecular entity
term:
id: CHEBI:50860
label: organic molecular entity
- notes: Diverse organic metabolites driving bioweathering
- downstream:
- - target: Teichoic Acid-Mediated HREE Selective Biosorption
- description: Dissolved REE become available for selective bacterial biosorption
+ notes: Contextual candidate weathering ligand from the proposed mechanism, not a measured product or traced
+ transfer by every listed taxon in the Renju profile.
evidence:
- reference: PMID:35708325
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene
- REE mineralization but also provide insights into efficient utilization of mineral resources via
- a biological pathway
- explanation: Documents bacterial REE-mineral dissolution
+ snippet: These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene REE
+ mineralization but also provide insights into efficient utilization of mineral resources via a biological
+ pathway
+ explanation: Supports the authors' proposed microbial contribution in conjunction with profile associations;
+ it does not demonstrate this exact phylum-level dissolution mechanism or mutualism.
- reference: PMID:35708325
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
snippet: Both fungi and bacteria contributed to the accumulation of REEs
- explanation: Establishes synergistic microbial REE mobilization
-- name: HREE Enrichment in B Horizon
- description: 'The combined effects of bioweathering (REE release), selective bacterial biosorption (HREE
- preference), and downward percolation concentrate HREE in the B horizon (enrichment zone) of the weathering
- profile, creating the economic ion-adsorption deposit. The B horizon shows peak total REE content
- of 776 ppm at ~6m depth with HREE concentrations of 56-184 ppm. Gram-positive bacteria preferentially
- sequester HREE from percolating groundwater, while LREE are more mobile and leach downward or re-distribute.
- The teichoic acid fractionation mechanism results in HREE/LREE ratios higher than parent granite,
- creating the characteristic HREE enrichment that makes South China ion-adsorption deposits the world''s
- dominant source of critical heavy REE (Dy, Y, Tb, Eu, Er, Yb) for permanent magnets, phosphors, and
- advanced technologies. This natural biogeochemical concentration process operates over thousands of
- years in stable weathering profiles under subtropical monsoon conditions.
-
- '
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Bacillus
- term:
- id: NCBITaxon:1386
- label: Bacillus
- metabolites:
- - preferred_term: dysprosium(3+)
+ explanation: Supports the authors' proposed microbial contribution in conjunction with profile associations;
+ it does not demonstrate this exact phylum-level dissolution mechanism or mutualism.
+ participating_taxa:
+ - preferred_term: Proteobacteria
term:
- id: CHEBI:33377
- label: dysprosium atom
- notes: Critical HREE for permanent magnets
- - preferred_term: yttrium(3+)
+ id: NCBITaxon:1224
+ label: Pseudomonadota
+ - preferred_term: Actinobacteria
term:
- id: CHEBI:49962
- label: yttrium(3+)
- concentration: 56-184 ppm in B horizon
- - preferred_term: terbium(3+)
+ id: NCBITaxon:201174
+ label: Actinomycetota
+ - preferred_term: Ascomycota
term:
- id: CHEBI:49902
- label: terbium(3+)
- notes: Critical HREE for phosphors
- biological_processes:
- - preferred_term: metal ion transport
+ id: NCBITaxon:4890
+ label: Ascomycota
+ - preferred_term: Basidiomycota
term:
- id: GO:0030001
- label: metal ion transport
+ id: NCBITaxon:5204
+ label: Basidiomycota
+ downstream:
+ - target: Teichoic Acid-Mediated HREE Selective Biosorption
+ description: HYPOTHESIZED - microbial mineral dissolution could release REEs that become substrates for bacterial
+ surface adsorption. This substrate-availability route is proposed from profile associations and known weathering
+ functions, not traced from the listed phyla to the tested isolates in situ.
+- name: Observed B-Horizon HREE Enrichment
+ description: Field geochemistry shows HREE enrichment in the Renju B horizon, with total HREE concentrations of
+ 56-184 ppm and a total-REE maximum of 776 ppm near 6 m. These are elemental sums, not the concentration or speciation
+ of a single yttrium ion. The sampled profile extends to 45 m and uses A, B and P horizons. Microbial composition
+ correlations and isolate adsorption support a proposed biological contribution alongside clay/mineral binding
+ and hydrology; they do not quantify the microbial share of deposit formation. The canonical taxa are a sampled
+ community subset, not proven joint causes or reciprocal beneficiaries of enrichment.
+ scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:35708325
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated
- with Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall
- served as the main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit
- explanation: Quantifies HREE enrichment in B horizon
- - reference: PMID:35708325
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: teichoic acids in the cell wall served as the main sites for HREE adsorption
- explanation: Links bacterial selectivity to deposit-scale HREE enrichment.
-- name: Fungal Bioweathering and Mineral Dissolution
- description: 'Ascomycota and Basidiomycota fungi work synergistically to accelerate granite weathering
- and REE mineral dissolution through complementary enzymatic and chemical attack mechanisms. Together
- comprising over 88% of fungal sequences, these two dominant phyla produce diverse organic acids (citric,
- oxalic, gluconic), extracellular enzymes (laccases, peroxidases), and siderophores that chelate REE
- cations and dissolve silicate minerals. Ascomycete hyphae mechanically penetrate mineral grain boundaries
- while secreting organic acids that protonate and dissolve REE-bearing phases like monazite, xenotime,
- and REE-enriched clays. Basidiomycete enzymes further degrade silicate matrices and mobilize REE from
- resistant mineral structures. The fungal bioweathering creates high-surface-area weathering zones
- where primary REE minerals transform into secondary clay-bound ion-adsorption forms. This fungal-bacterial
- partnership drives the biogeochemical cascade: fungal mineral dissolution releases REE → bacterial
- biosorption concentrates HREE → deposit-scale HREE enrichment occurs. The synergistic action of Ascomycota
- and Basidiomycota accelerates REE mineralization orders of magnitude faster than abiotic weathering
- processes.
-
- '
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Ascomycota
+ snippet: the B horizon is rich in HREEs
+ explanation: Primary field geochemistry supports observed enrichment; the body supplies profile depth and elemental-sum
+ context, not a single-ion measurement.
+ participating_taxa:
+ - preferred_term: Proteobacteria
+ term:
+ id: NCBITaxon:1224
+ label: Pseudomonadota
+ - preferred_term: Acidobacteria
+ term:
+ id: NCBITaxon:57723
+ label: Acidobacteriota
+ - preferred_term: Actinobacteria
+ term:
+ id: NCBITaxon:201174
+ label: Actinomycetota
+ - preferred_term: Bacillus
+ term:
+ id: NCBITaxon:1386
+ label: Bacillus
+ - preferred_term: Micrococcus
+ term:
+ id: NCBITaxon:1269
+ label: Micrococcus
+ - preferred_term: Ascomycota
term:
id: NCBITaxon:4890
label: Ascomycota
- target_taxon:
- preferred_term: Basidiomycota
+ - preferred_term: Basidiomycota
term:
id: NCBITaxon:5204
label: Basidiomycota
+- name: Proposed Fungal REE Bioweathering
+ description: HYPOTHESIZED - fungal organic acids and mineral-surface interactions could contribute to REE mobilization.
+ Ascomycota/Basidiomycota profiles and selected fungal-genus correlations are positive community observations;
+ the exact weathering functions are discussed partly from prior literature. The study does not isolate mutual
+ benefit between these phyla, complementary enzyme action, direct fungal-to-bacterial transfer or an orders-of-magnitude
+ rate increase in this profile. The canonical phyla delimit the represented fungal groups, not a resolved two-member
+ consortium.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: citric acid
term:
id: CHEBI:30769
label: citric acid
- notes: Fungal organic acid for REE complexation
+ notes: Contextual candidate weathering ligand from the proposed mechanism, not a measured product or traced
+ transfer by every listed taxon in the Renju profile.
- preferred_term: oxalic acid
term:
id: CHEBI:16995
label: oxalic acid
- notes: Strong chelator for mineral dissolution
- downstream:
- - target: Teichoic Acid-Mediated HREE Selective Biosorption
- description: Fungal dissolution releases REE for bacterial biosorption
+ notes: Contextual candidate weathering ligand from the proposed mechanism, not a measured product or traced
+ transfer by every listed taxon in the Renju profile.
evidence:
- reference: PMID:35708325
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
snippet: Both fungi and bacteria contributed to the accumulation of REEs
- explanation: Documents synergistic fungal bioweathering
+ explanation: Supports the authors' proposed microbial contribution in conjunction with profile associations;
+ it does not demonstrate this exact phylum-level dissolution mechanism or mutualism.
- reference: PMID:35708325
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene
- REE mineralization but also provide insights into efficient utilization of mineral resources via
- a biological pathway
- explanation: Establishes fungal role in REE mobilization
-- name: Oligotrophic REE Mobilization and Deep Profile Colonization
- description: 'Acidobacteria employ oligotrophic K-strategist metabolic strategies to colonize nutrient-depleted
- deep weathering zones (up to 40m depth) and contribute to long-term REE mobilization and biogeochemical
- cycling. Representing 14.6% of the bacterial community, Acidobacteria thrive in low-organic-carbon
- regolith environments where r-strategist copiotrophs (like many Proteobacteria) cannot compete. Their
- slow-growing, stress-tolerant lifestyle enables sustained activity in the C horizon weathered bedrock
- where microbial biomass decreases to 23.6 ppm. Acidobacteria produce exopolysaccharides and organic
- ligands that bind REE cations and enhance mineral dissolution at depth, complementing the more abundant
- Proteobacteria in upper horizons. This vertical metabolic partitioning ensures continuous REE mobilization
- throughout the 40-meter weathering profile. The oligotrophic adaptations of Acidobacteria are critical
- for establishing stable indigenous microbial communities in the nutrient-scarce, low-productivity
- conditions of regolith-hosted REE deposits, enabling the thousand-year biogeochemical processes that
- create economically viable HREE enrichment.
-
- '
- interaction_type: COMMENSALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Acidobacteria
- term:
- id: NCBITaxon:57723
- label: Acidobacteriota
- target_taxon:
- preferred_term: Proteobacteria
+ snippet: These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene REE
+ mineralization but also provide insights into efficient utilization of mineral resources via a biological
+ pathway
+ explanation: Supports the authors' proposed microbial contribution in conjunction with profile associations;
+ it does not demonstrate this exact phylum-level dissolution mechanism or mutualism.
+ participating_taxa:
+ - preferred_term: Ascomycota
term:
- id: NCBITaxon:1224
- label: Pseudomonadota
- metabolites:
- - preferred_term: organic molecular entity
+ id: NCBITaxon:4890
+ label: Ascomycota
+ - preferred_term: Basidiomycota
term:
- id: CHEBI:50860
- label: organic molecular entity
- notes: Exopolysaccharides and organic ligands for REE binding
+ id: NCBITaxon:5204
+ label: Basidiomycota
+ downstream:
+ - target: Teichoic Acid-Mediated HREE Selective Biosorption
+ description: HYPOTHESIZED - fungal weathering could release REEs for bacterial cell-wall binding. The fungal
+ associations and separate adsorption assays support a candidate route, not selectively demonstrated fungal
+ dissolution, partner transfer or its necessity for field enrichment.
+- name: Acidobacteria Profile Distribution and Oligotrophic Interpretation
+ description: Acidobacteria averaged 14.6 percent of bacterial sequences and generally decreased with depth to
+ 40 m before a slight increase at 45 m. The primary discussion invokes an oligotrophic K-strategist interpretation,
+ not increasing deep-profile dominance. Neither taxonomic abundance nor that ecological interpretation demonstrates
+ Acidobacteria ligand production, measured REE mobilization, exclusion of Proteobacteria or a benefit supplied
+ to them. Preserve the observed distribution without assigning a phylum-wide biochemical pathway.
+ scope: COMMUNITY_LEVEL
evidence:
- - reference: PMID:35708325
- supports: PARTIAL
- evidence_source: IN_VIVO
- snippet: regolith-hosted REE deposits
- explanation: The abstract supports the regolith-hosted REE-deposit setting but
- does not name Acidobacteria; the oligotrophic K-strategist lifestyle described
- in the full text is not present in the abstract, so this evidence is downgraded
- to PARTIAL.
- reference: PMID:35708325
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: However, little is known about the roles of microorganisms in the formation of exogenic deposits
- such as regolith-hosted REE deposits that are of HREE enrichment and provide over 90% of global
- HREE demand
- explanation: Establishes Acidobacteria contribution to REE mobilization
+ snippet: tends to decrease with increasing depth
+ explanation: Primary Acidobacteria distribution result; the surrounding body supplies mean abundance and the
+ deepest-sample exception, not measured ligand-mediated REE transfer.
+ participating_taxa:
+ - preferred_term: Acidobacteria
+ term:
+ id: NCBITaxon:57723
+ label: Acidobacteriota
environmental_factors:
- name: Weathering Profile Depth
value: 0-40
@@ -785,3 +731,30 @@ growth_media:
snippet: R2A was used as the separation culture medium.
explanation: R2A was the isolation medium used to recover community members from
the weathering profile.
+discussions:
+- discussion_id: ree_lab_to_profile_mediation
+ prompt: How much do specific microbial weathering and adsorption processes contribute to field enrichment?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Teichoic Acid-Mediated HREE Selective Biosorption
+ - ecological_interactions#Proposed Microbial REE Mineral Dissolution
+ - ecological_interactions#Observed B-Horizon HREE Enrichment
+ - ecological_interactions#Proposed Fungal REE Bioweathering
+ - ecological_interactions#Acidobacteria Profile Distribution and Oligotrophic Interpretation
+ rationale: 'Retain the positive isolated-cell/cell-wall experiments and field elemental distributions without
+ treating laboratory adsorption as a quantified deposit-scale cause. Teichoic-acid removal is not a genetic knockout
+ or purified rescue, and residual adsorption remains. Phylum-level weathering assignments, fungal synergy and
+ Acidobacteria ligand transfer are unresolved, not demonstrated pairwise benefits. Full cached primary main text,
+ Methods and Figures 1-7 captions read; selected claims independently verified in fresh NCBI XML. No original
+ images, external supplements, raw data or code inspected. Non-graph profile, function, economic and cultivation
+ claims remain unresolved under #1520 and are preserved, not recertified.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T17:45:53Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Separate positive REE laboratory adsorption from proposed weathering and deposit-scale mediation. Issue
+ #1517; reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Jala_Maize_PGPB_SynCom.yaml b/kb/communities/Jala_Maize_PGPB_SynCom.yaml
index bc156e100..0291abed2 100644
--- a/kb/communities/Jala_Maize_PGPB_SynCom.yaml
+++ b/kb/communities/Jala_Maize_PGPB_SynCom.yaml
@@ -108,175 +108,190 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: Compatibility-Constrained SynCom 3 Assembly
- description: >
- Jala maize PGPB isolates were screened for mutual antagonism and then
- assembled as SynCom 3 by combining compatible strains with complementary
- nitrogen-fixation, phosphate-solubilization, metallophore, IAA, ACC
- deaminase, and antifungal traits.
- 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
- downstream:
- - target: SynCom 3 Multi-Trait PGP Activity
- description: >
- Compatibility filtering retained a SynCom that could be assayed for
- complementary nutrient-mobilization and hormone-related plant-growth
- promoting activities.
- - target: SynCom 3 Antifungal and PAL Induction
- description: >
- The compatible SynCom 3 formulation also carried candidate antifungal and
- induced systemic resistance traits.
- evidence:
- - *id001
- - reference: PMID:37275168
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: The SynCom design included bacterial strains with partially redundant and
- complementary PGP features, but antagonistic strains were not included
- explanation: >
- Supports the compatibility criterion used when the Jala isolates were
- assembled into SynComs.
- - reference: PMID:37275168
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: 'SynCom 3: A. xylosoxidans Z2K8, Burkholderia sp. Z1AL11, K. variicola R3J3HD7'
- explanation: >
- Anchors SynCom 3 as one of the final compatible formulations.
- name: SynCom 3 Multi-Trait PGP Activity
- description: >
- The SynCom 3 mixed inoculant expressed the plant-growth promoting trait set
- prioritized by design, including soluble orthophosphate accumulation, IAA
- production, ACC deaminase activity, metallophore production, and biological
- nitrogen fixation.
+ description: 'The mixed SynCom 3 inoculant produced positive phosphate-solubilization, indole-reactive colorimetric,
+ ACC-growth, metal-chelation and acetylene-reduction assay results. Salkowski chemistry is not specific identification
+ of IAA; growth with ACC as sole nitrogen source is an indirect deaminase screen. Acetylene reduction is a nitrogenase
+ proxy, not measured nitrogen transfer to maize, and the CAS assay does not identify a particular metallophore.
+ These positive in-vitro traits were not selectively perturbed as mediators of plant growth. The four canonical
+ participants are a subset of the reported six-strain SynCom 3, not a complete four-member inoculant; exact membership
+ and the primary Pseudomonas strain inconsistency remain under #1521.'
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
metabolites:
- preferred_term: phosphate ion
term:
id: CHEBI:35780
label: phosphate ion
+ notes: Measured soluble phosphate output in the in-vitro assay, not quantified uptake by maize.
- preferred_term: indole-3-acetic acid
term:
id: CHEBI:16411
label: indole-3-acetic acid
+ notes: IAA-associated colorimetric readout; Salkowski also responds to related indole compounds, so exact molecular
+ identity is not established by this assay.
- preferred_term: 1-aminocyclopropanecarboxylic acid
term:
id: CHEBI:18053
label: 1-aminocyclopropanecarboxylic acid
+ notes: Assay substrate in the indirect ACC-growth screen, not a measured community product or demonstrated plant
+ ethylene decrease.
biological_processes:
- preferred_term: nitrogen fixation
term:
id: GO:0009399
label: nitrogen fixation
- downstream:
- - target: Conejo Maize Seedling Growth Promotion
- description: >
- SynCom 3's measured nutrient and hormone traits preceded gnotobiotic and
- greenhouse maize growth-promotion assays.
+ notes: Inferred from acetylene reduction and growth under assay conditions; not direct plant nitrogen incorporation
+ or identified member-level flux.
evidence:
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Phosphate solubilization, IAA, BNF, metallophores, biocontrol against Fusarium oxysporum,
- Pestalotia sp., Curvularia sp.
- explanation: Names phosphate solubilization, IAA production, and biological
- nitrogen fixation among the screened plant-growth-promoting traits of the
- Jala-derived SynCom members.
+ snippet: Phosphate solubilization, IAA, BNF, metallophores, biocontrol against Fusarium oxysporum, Pestalotia
+ sp., Curvularia sp.
+ explanation: Supports the positive screened trait or assay result within the mixed inoculant; the primary Methods
+ bound specificity and do not isolate plant-growth mediation.
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VITRO
snippet: SynCom 3 accumulated more soluble orthophosphate
- explanation: >
- Supports high soluble-orthophosphate accumulation by the mixed SynCom 3
- inoculant.
+ explanation: Supports the positive screened trait or assay result within the mixed inoculant; the primary Methods
+ bound specificity and do not isolate plant-growth mediation.
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VITRO
snippet: Aminocyclopropane-1-carboxylate (ACC) deaminase production
- explanation: Names ACC deaminase, acting on the ethylene precursor ACC, as a
- screened plant-growth-promoting trait.
+ explanation: Supports the positive screened trait or assay result within the mixed inoculant; the primary Methods
+ bound specificity and do not isolate plant-growth mediation.
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VITRO
snippet: only SynCom 3 exhibited evident growth in the BMGM media and reduced acetylene
- explanation: >
- Supports the biological nitrogen fixation phenotype measured in the
- SynCom-level acetylene reduction assay.
+ explanation: Supports the positive screened trait or assay result within the mixed inoculant; the primary Methods
+ bound specificity and do not isolate plant-growth mediation.
+ participating_taxa:
+ - preferred_term: Pseudomonas protegens
+ term:
+ id: NCBITaxon:380021
+ label: Pseudomonas protegens
+ - preferred_term: Pantoea ananatis
+ term:
+ id: NCBITaxon:553
+ label: Pantoea ananatis
+ - preferred_term: Klebsiella variicola
+ term:
+ id: NCBITaxon:244366
+ label: Klebsiella variicola
+ - preferred_term: Burkholderia sp.
+ term:
+ id: NCBITaxon:32008
+ label: Burkholderia
+ downstream:
+ - target: Conejo Maize Seedling Growth Promotion
+ description: PARTIAL - nutrient mobilization and hormone-related activities could improve nutrient availability
+ or plant signaling and thereby support Conejo seedling growth. Positive in-vitro assays and inoculation responses
+ support these candidate mechanisms, but no selective trait perturbation establishes mediation or their individual
+ contributions.
- name: SynCom 3 Antifungal and PAL Induction
- description: >
- SynCom 3 inhibited phytopathogenic fungi in vitro and significantly
- increased maize-root phenylalanine ammonia-lyase activity, connecting
- antagonistic isolates with induced systemic resistance in the plant host.
+ description: 'SynCom 3 inhibited several tested fungi in vitro, reaching up to 80 percent in the reported comparisons,
+ but Helminthosporium was hardly inhibited by SynCom 3. It also tripled maize-root phenylalanine ammonia-lyase
+ activity. These are positive but distinct assays: the authors did not test induced systemic resistance with
+ a fungal challenge. PAL induction and inhibition of these cultured fungi do not by themselves demonstrate the
+ mechanism of rust reduction in the field. The four canonical participants are a subset of the reported six-strain
+ SynCom 3, not a complete four-member inoculant; exact membership and the primary Pseudomonas strain inconsistency
+ remain under #1521.'
scope: COMMUNITY_LEVEL
- interaction_type: COMPETITION
biological_processes:
- preferred_term: biological process involved in interspecies interaction between organisms
term:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Field Yield Increase and Rust Reduction
- description: >
- In vitro fungal inhibition and the PAL response were candidate mechanisms
- for reduced fungal rust incidence in the open-field SynCom 3 treatment.
evidence:
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VITRO
snippet: SynCom 3 exhibited the highest inhibition percentages reaching 80% of inhibition
- explanation: >
- Supports SynCom 3 as a high-performing inhibitor of fungal
- phytopathogens.
+ explanation: Supports high inhibition in some tested comparisons, not 80 percent for every fungus or direct
+ suppression of field rust.
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: only the effect of SynCom 3 was statistically significant as it tripled the
- activity of the enzyme
- explanation: >
- Supports significant induction of maize-root PAL activity by SynCom 3.
+ snippet: only the effect of SynCom 3 was statistically significant as it tripled the activity of the enzyme
+ explanation: Supports positive root PAL induction, not a fungal-challenge demonstration of systemic resistance
+ or selective mediation.
+ participating_taxa:
+ - preferred_term: Pseudomonas protegens
+ term:
+ id: NCBITaxon:380021
+ label: Pseudomonas protegens
+ - preferred_term: Pantoea ananatis
+ term:
+ id: NCBITaxon:553
+ label: Pantoea ananatis
+ - preferred_term: Klebsiella variicola
+ term:
+ id: NCBITaxon:244366
+ label: Klebsiella variicola
+ - preferred_term: Burkholderia sp.
+ term:
+ id: NCBITaxon:32008
+ label: Burkholderia
+ downstream:
+ - target: Field Yield Increase and Rust Reduction
+ description: PARTIAL - antifungal activity or host defense responses could contribute to the rust-reduction
+ component of the field outcome. Separate inhibition and PAL assays support candidate routes, but no fungal-challenge
+ ISR test or selective PAL/antifungal perturbation establishes this mediation or explains the yield increase.
- name: Conejo Maize Seedling Growth Promotion
- description: >
- SynCom 3 inoculation increased Conejo maize root and shoot growth in
- gnotobiotic tubes and greenhouse pots after its constituent PGP activities
- were expressed in vitro.
+ description: 'SynCom 3 inoculation increased Conejo maize growth in gnotobiotic tubes and greenhouse pots. Gnotobiotic
+ root and shoot sizes were 4.2 and 3.0 times the controls. In greenhouse comparisons, root/shoot lengths were
+ 3.3/1.4 times controls and shoot/root dry weights were 2.3/3 times controls. These are positive whole-inoculant
+ treatment effects in the Conejo landrace, not proof that its earlier in-vitro trait panel caused them or that
+ those seedlings produced the separate hybrid field harvest. The four canonical participants are a subset of
+ the reported six-strain SynCom 3, not a complete four-member inoculant; exact membership and the primary Pseudomonas
+ strain inconsistency remain under #1521.'
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
biological_processes:
- preferred_term: growth
term:
id: GO:0040007
label: growth
- downstream:
- - target: Field Yield Increase and Rust Reduction
- description: >
- Seedling growth promotion in controlled systems supported the choice to
- test SynCom 3 on hybrid maize in the field.
evidence:
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VIVO
snippet: promoted the growth of the roots and shoots to sizes 4.2 and 3.0 times greater
- explanation: >
- Supports SynCom 3-mediated maize root and shoot growth promotion in the
- gnotobiotic assay.
+ explanation: Supports positive gnotobiotic Conejo growth effects, not selective trait mediation.
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: increases of 3.3 and 1.4 times the roots and shoot length and 2.3 and 3 times
- the dry weights
- explanation: >
- Supports the SynCom 3 growth phenotype in the greenhouse assay.
+ snippet: increases of 3.3 and 1.4 times the roots and shoot length and 2.3 and 3 times the dry weights
+ explanation: Supports positive greenhouse growth; the primary Results assign dry-weight folds to shoots 2.3
+ and roots 3, distinct from the root/shoot length ordering.
+ participating_taxa:
+ - preferred_term: Pseudomonas protegens
+ term:
+ id: NCBITaxon:380021
+ label: Pseudomonas protegens
+ - preferred_term: Pantoea ananatis
+ term:
+ id: NCBITaxon:553
+ label: Pantoea ananatis
+ - preferred_term: Klebsiella variicola
+ term:
+ id: NCBITaxon:244366
+ label: Klebsiella variicola
+ - preferred_term: Burkholderia sp.
+ term:
+ id: NCBITaxon:32008
+ label: Burkholderia
- name: Field Yield Increase and Rust Reduction
- description: >
- In open-field hybrid maize tests, SynCom 3 increased grain yield relative
- to the untreated control and significantly reduced fungal rust incidence.
+ description: 'In the reported one-site field experiment with CPL9105W hybrid maize, SynCom 3 treatment increased
+ grain yield from 11 to 16 tons/ha relative to control. The abstract reports rust incidence falling from 12.5
+ to 8 percent, not a 12.5-percentage-point reduction. The treatment involved seed inoculation and subsequent
+ applications; it is distinct from the Conejo seedling experiments. The whole-inoculant effects do not establish
+ which traits or members mediated them, universal efficacy across sites/seasons, or a benefit for every tested
+ SynCom. The four canonical participants are a subset of the reported six-strain SynCom 3, not a complete four-member
+ inoculant; exact membership and the primary Pseudomonas strain inconsistency remain under #1521.'
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
biological_processes:
- preferred_term: growth
term:
@@ -290,19 +305,33 @@ ecological_interactions:
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: the yield increased from 11 tons/ha for the control to 16 tons/ha inoculated
- with SynCom 3
- explanation: >
- Supports the open-field grain-yield increase observed after SynCom 3
- inoculation.
+ snippet: the yield increased from 11 tons/ha for the control to 16 tons/ha inoculated with SynCom 3
+ explanation: Supports the positive SynCom 3 field yield effect in this trial; not universal multi-site or all-SynCom
+ performance.
- reference: PMID:37275168
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: incidence of rust fungal infections decreased significantly from 12.5% in the
- control to 8% in the treatment with SynCom 3
- explanation: >
- Supports the field-level reduction in maize fungal rust incidence after
- SynCom 3 treatment.
+ snippet: incidence of rust fungal infections decreased significantly from 12.5% in the control to 8% in the
+ treatment with SynCom 3
+ explanation: Supports the explicit abstract rust-incidence comparison; original figure pixels and raw plot data
+ were not inspected.
+ participating_taxa:
+ - preferred_term: Pseudomonas protegens
+ term:
+ id: NCBITaxon:380021
+ label: Pseudomonas protegens
+ - preferred_term: Pantoea ananatis
+ term:
+ id: NCBITaxon:553
+ label: Pantoea ananatis
+ - preferred_term: Klebsiella variicola
+ term:
+ id: NCBITaxon:244366
+ label: Klebsiella variicola
+ - preferred_term: Burkholderia sp.
+ term:
+ id: NCBITaxon:32008
+ label: Burkholderia
environmental_factors:
- name: defined synthetic community design
value: Multiple SynComs were assembled from PGPB with growth promotion, biocontrol, and induced systemic
@@ -408,3 +437,29 @@ cultivation_setup:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: The bottles were sealed and incubated for 48 h at 28°C
+discussions:
+- discussion_id: jala_trait_and_defense_mediation
+ prompt: Which SynCom 3 members and activities mediate maize growth and field rust reduction?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#SynCom 3 Multi-Trait PGP Activity
+ - ecological_interactions#SynCom 3 Antifungal and PAL Induction
+ - ecological_interactions#Conejo Maize Seedling Growth Promotion
+ - ecological_interactions#Field Yield Increase and Rust Reduction
+ rationale: 'Remove the compatibility-assembly node and its two arrows as experimental workflow; design metadata
+ remains. Remove seedling-to-field selection as workflow, not a causal effect connecting different hosts and
+ experiments. Preserve positive whole-inoculant outcomes and the two proposed trait/defense routes as PARTIAL.
+ The six-strain formulation is not the four canonical taxa; missing members and E1BL2 versus E2HL9 inconsistency
+ remain #1521. Full cached primary main text, Methods, Tables 1-2 and Figures 1-6 captions read; fresh Frontiers
+ formulation/Discussion spot-checks, not a second full reading. No original images, external supplements, raw
+ data or code audited. No new graph structure; all non-graph blocks remain unchanged and are not recertified.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T17:45:53Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain maize SynCom assay and plant outcomes without workflow causality or proven trait mediation. Issue
+ #1518; reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml b/kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml
index 1c7f81998..0e6816b25 100644
--- a/kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml
+++ b/kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml
@@ -124,44 +124,53 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: Jiangshui LAB screening and ratio assembly
- description: LAB isolates from traditional Jiangshui were screened down to Y-5-3, Y-6-2, and HN, then manually combined
- in 20 ratios to tune a defined Jiangshui SynCom.
- scope: COMMUNITY_LEVEL
- downstream:
- - target: Optimized 2:3:1 Jiangshui fermentation
- description: The three selected LAB strains were assembled at empirically varied ratios before the optimized Y-5-3:Y-6-2:HN
- ratio was selected.
- evidence:
- - reference: PMID:42425667
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: On this basis, 3 high-performance strains (Y-5-3, Y-6-2, HN) were selected and manually combined in 20 ratios
- to construct SynComs
- explanation: Supports the selection of strains Y-5-3, Y-6-2, and HN and their assembly into multiple synthetic-community
- ratios.
-- name: Optimized 2:3:1 Jiangshui fermentation
- description: A Y-5-3:Y-6-2:HN ratio of 2:3:1 was the optimal mixed-strain fermentation scheme among the assayed three-strain
- LAB SynCom ratios.
+- name: Three-Strain 2:3:1 Jiangshui Fermentation
+ description: The tested Y-5-3:Y-6-2:HN 2:3:1 formulation had the highest reported sensory score, 89.38 +/- 4.10,
+ among the assayed three-strain fermentation schemes. This is a positive combined-inoculant fermentation result,
+ not an isolated molecular mechanism or proof that the ratio alone explains its difference from natural fermentation.
+ All three canonical strain names remain distinct despite their unresolved species-level identifiers.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: fermentation
term:
id: GO:0006113
label: fermentation
- downstream:
- - target: Jiangshui phenol and flavonoid increase
- description: The optimized 2:3:1 strain ratio increased measured total phenols and flavonoids compared with natural Jiangshui.
evidence:
- - *id002
+ - reference: PMID:42425667
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 'The optimal fermentation scheme was Y-5-3: Y-6-2: HN = 2:3:1'
+ explanation: Supports the Y-5-3:Y-6-2:HN 2:3:1 ratio as the optimized three-strain fermentation scheme.
- reference: PMID:42425667
supports: SUPPORT
evidence_source: IN_VITRO
snippet: achieving the highest sensory score (89.38 ± 4.10 points)
- explanation: Supports the optimized SynCom's superior sensory score among the assessed Jiangshui fermentation outcomes.
+ explanation: Supports the optimized SynCom's superior sensory score among the assessed Jiangshui fermentation
+ outcomes.
+ participating_taxa:
+ - preferred_term: LAB strain Y-5-3
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+ - preferred_term: LAB strain Y-6-2
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+ - preferred_term: LAB strain HN
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+ downstream:
+ - target: Jiangshui phenol and flavonoid increase
+ description: The tested three-strain 2:3:1 fermentation treatment increased measured total phenol and flavonoid
+ contents relative to natural Jiangshui. This positive formulation-level intervention does not isolate the
+ ratio, a particular strain, release versus synthesis, or a molecular mediator as the cause.
- name: Jiangshui phenol and flavonoid increase
- description: The optimized three-strain LAB scheme increased total phenols and flavonoids relative to natural Jiangshui
- while reducing off-odors and improving stability.
+ description: The tested three-strain formulation increased total phenols by 72.20 percent and total flavonoids
+ by 61.13 percent relative to natural Jiangshui, with reported P < 0.01. The abstract also reports reduced off-odors
+ and improved stability without the operational detail available in a full protocol. These are total-content
+ endpoints, not identified compound flux, de-novo flavonoid synthesis or demonstrated benefits exchanged between
+ individual strains.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: fermentation
@@ -173,14 +182,29 @@ ecological_interactions:
term:
id: CHEBI:47916
label: flavonoid
+ notes: Contextual class for a reported total-flavonoid endpoint; not a specific molecule, biosynthetic pathway
+ or demonstrated direct interstrain transfer.
evidence:
- reference: PMID:42425667
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: significantly increasing total phenols (72.20% higher, P < 0.01) and flavonoids (61.13% higher, P < 0.01) compared
- with natural Jiangshui, while reducing off-odors and improving stability.
- explanation: Supports the optimized SynCom's elevated phenol and flavonoid contents and improved sensory stability relative
- to natural Jiangshui.
+ snippet: significantly increasing total phenols (72.20% higher, P < 0.01) and flavonoids (61.13% higher, P < 0.01)
+ compared with natural Jiangshui, while reducing off-odors and improving stability.
+ explanation: Supports the optimized SynCom's elevated phenol and flavonoid contents and improved sensory stability
+ relative to natural Jiangshui.
+ participating_taxa:
+ - preferred_term: LAB strain Y-5-3
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+ - preferred_term: LAB strain Y-6-2
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+ - preferred_term: LAB strain HN
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
related_ingredients:
- preferred_term: flavonoid
chebi_term:
@@ -237,8 +261,8 @@ external_resources:
explanation: Lists the DOI-bearing article for the Jiangshui LAB synthetic community.
discussions:
- discussion_id: jiangshui_lab_species_and_conditions
- prompt: Which species identities, isolate accessions, Jiangshui recipe, inoculation units, and fermentation conditions were
- used for the Y-5-3/Y-6-2/HN 2:3:1 SynCom?
+ prompt: Which species identities, isolate accessions, Jiangshui recipe, inoculation units, and fermentation conditions
+ were used for the Y-5-3/Y-6-2/HN 2:3:1 SynCom?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
@@ -246,10 +270,26 @@ discussions:
- taxonomy#LAB strain Y-6-2
- taxonomy#LAB strain HN
- growth_media#Jiangshui vegetable fermentation
- rationale: The PubMed abstract names the selected strain codes and the optimized 2:3:1 ratio, but does not expose species-level
- identifications or a reproducible Jiangshui fermentation recipe.
+ rationale: The PubMed abstract names the selected strain codes and the optimized 2:3:1 ratio, but does not expose
+ species-level identifications or a reproducible Jiangshui fermentation recipe.
posed_by: codex
posed_date: '2026-09-13'
+- discussion_id: jiangshui_formulation_endpoint_scope
+ prompt: Which processes underlie the positive formulation-level fermentation endpoints?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Three-Strain 2:3:1 Jiangshui Fermentation
+ - ecological_interactions#Jiangshui phenol and flavonoid increase
+ rationale: Remove screening/ratio assembly and its arrow as researcher workflow; retain the biological fermentation
+ treatment and positive content response. No isolated ratio effect or de-novo biosynthesis is demonstrated by
+ the accessible abstract. Complete cached abstract and indexed publisher fragments read; direct publisher requests
+ returned403 and no primary full body was inspected. Fragments do not map selected strain codes to species or
+ give the fermentation protocol; preserve the existing taxonomy/growth-conditions knowledge gap and prior histories.
+ In-vitro biosafety screens do not establish clinical safety. No original images, supplements, raw data or code
+ audited and no new graph structure added.
+ posed_by: codex
+ posed_date: '2026-10-06'
metals_present: []
rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
@@ -259,13 +299,19 @@ curation_history:
- timestamp: '2026-09-13T05:08:17Z'
curator: codex
action: CREATE_COMMUNITY_RECORD
- changes: Created CommunityMech:000356 for the Jiangshui Y-5-3/Y-6-2/HN LAB SynCom with abstract-backed membership, fermentation
- interactions, growth context, external resources, flavonoid linkage, and open knowledge gaps for unresolved strain identities
- and recipe details.
+ changes: Created CommunityMech:000356 for the Jiangshui Y-5-3/Y-6-2/HN LAB SynCom with abstract-backed membership,
+ fermentation interactions, growth context, external resources, flavonoid linkage, and open knowledge gaps for
+ unresolved strain identities and recipe details.
llm_assisted: true
- timestamp: '2026-09-13T05:14:31Z'
curator: codex
action: FIX_JIANGSHUI_THREE_STRAIN_WORDING
- changes: 'Resolved issue #824 by changing the Jiangshui three-strain SynCom description from two-member pairing language
- to three-member combining language.'
+ changes: 'Resolved issue #824 by changing the Jiangshui three-strain SynCom description from two-member pairing
+ language to three-member combining language.'
+ llm_assisted: true
+- timestamp: '2026-10-06T17:45:54Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain the Jiangshui formulation effect and remove experimental screening from the biological graph.
+ Issue #1519; reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml'
llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 35a12c9ad..c9c32b361 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,25 @@ 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`.
+## Batch55: REE, Maize And Jiangshui
+
+[Decisions](decisions/20261006-three-records-batch55.yaml),
+[validation](validation-20261006-batch55.json) and
+[self-adversarial review](adversarial-review-20261006-batch55.yaml) retain eleven
+biological nodes and six arrows. Two screening/assembly nodes and four workflow
+arrows are removed. Positive cell-wall adsorption, maize inoculation effects and
+fermentation endpoints remain; proposed weathering and trait/defense mediation
+are explicitly qualified.
+
+Complete cached primary main texts and Methods were read for REE and Jala, with
+main captions and Jala tables. Jiangshui review is limited to its abstract and
+indexed publisher fragments; direct full-text access failed. No original figures,
+external supplements, raw data or code were audited. All 920 caches are unchanged.
+Non-graph REE claims (#1520), the exact Jala roster/strain discrepancy (#1521),
+and the existing Jiangshui taxonomy/protocol gap remain unresolved. No new graph
+structure or paid provider call. Linked validation records report actual gates,
+not independent approval or a claim that these follow-ups are resolved.
+
## Batch54: Infant Gut Persistence And Prebiotic Responses
[Decisions](decisions/20261006-infant-gut-batch54.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch55.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch55.yaml
new file mode 100644
index 000000000..c2dad2ba3
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch55.yaml
@@ -0,0 +1,189 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: e2dacf7f7d0069c9ed46a91a18f91a5743a7fc09
+scope:
+- kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml
+- kb/communities/Jala_Maize_PGPB_SynCom.yaml
+- kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch55.json
+findings:
+- issue: 1517
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate positive REE laboratory adsorption from proposed weathering and deposit-scale mediation.
+ disposition: Close only after protected main merge.
+- issue: 1518
+ severity: P2
+ status: addressed_in_this_change
+ finding: Retain maize SynCom assay and plant outcomes without workflow causality or proven trait mediation.
+ disposition: Close only after protected main merge.
+- issue: 1519
+ severity: P2
+ status: addressed_in_this_change
+ finding: Retain the Jiangshui formulation effect and remove experimental screening from the biological
+ graph.
+ disposition: Close only after protected main merge.
+- issue: 1520
+ severity: P2
+ status: unresolved_non_graph
+ finding: Non-graph REE profile/function/economic/cultivation claims remain unreviewed.
+ disposition: Keep open after graph repair merges.
+- issue: 1521
+ severity: P2
+ status: unresolved_non_graph
+ finding: Exact six-strain Jala membership and primary Pseudomonas strain inconsistency remain unresolved.
+ disposition: Keep open after graph repair merges.
+adversarial_checks:
+- Whole787-line REE,410-line Jala and271-line Jiangshui records read, all13 nodes/10 arrows. Full cached
+ primary main text and Methods for REE/Jala, Figures1-7/1-6 captions and Jala Tables1-2. Jiangshui abstract/indexed
+ publisher fragments only, direct403; no primary full body. No original images, external supplements,
+ raw data or code audited.
+- REE fresh NCBI XML selected-claim spot-check, not a full second reading. Jala fresh Frontiers formulation/Discussion
+ spot-checks only; duplicate pmc_full cache not independently read. Source scope is not inferred from
+ misleading abstract-only cache headers. All920 caches unchanged;22 already-cached source words independently
+ verified against XML with digest.
+- REE Bacillus/Micrococcus isolate assays are separate cultures, not reciprocal commensalism. Teichoic-acid
+ removal lowers total wall adsorption65.5to17.8percent and removes HREE preference but residual binding
+ remains. Positive intervention preserved as SUPPORT/IN_VITRO, not downgraded merely because deposit
+ mediation is unresolved.
+- Freeze-dried binding is consistent with passive adsorption, not active metal-ion transport. Yb/P colocalization
+ supports surface groups, not uniquely resolved geometry or exclusive ionic-radius cause. Multi-element
+ adsorption and higher-doseYb imaging differ. Graph removes dysprosium atom mislabeled ion and free phosphate
+ as bound wall groups; no guessed replacement CURIE.
+- Field HREE56-184ppm is an elemental sum, not a single Y-ion concentration. TotalREE776ppm near6m and45mA/B/P
+ profile retained. Profile microbial/geochemical correlations and laboratory fractionation support a
+ PARTIAL contribution, not isolated deposit-scale magnitude. Non-graph40m/C-horizon and other inherited
+ claims remain1520, not silently certified.
+- Microbial/fungal weathering routes remain HYPOTHESIZED because the primary discussion uses prior-literature
+ functions and community associations. No measured phylum-level complementarity, orders-of-magnitude
+ acceleration or direct donor-recipient flux. Acidobacteria generally decrease with depth before the45m
+ exception; neither abundance nor oligotrophic interpretation establishes ligand transfer to Proteobacteria.
+- Jala actual SynCom3 has six strains. All four canonical entries are explicit subsets; no four-member
+ experiment invented. Missing Achromobacter/Phytobacter, exact strain identity and E1BL2-versus-E2HL9
+ primary-source inconsistency remain unresolved1521. Canonical IDs/labels unchanged.
+- Positive maize assays remain SUPPORT, with Salkowski indole-reactivity, ACC-growth proxy, acetylene-reduction
+ rather than plantN transfer, and CAS identity limits. These are not selective mediator perturbations.
+ Up-to80percent inhibition is not every fungus; Helminthosporium hardly inhibited by3. PAL triples but
+ fungal-challenge ISR test was not conducted.
+- Conejo gnotobiotic/greenhouse growth and CPL9105W field effects are distinct experiments. Greenhouse
+ shoot/root dry weights2.3/3 differ from root/shoot length ordering3.3/1.4. Field16vs11tons/ha and abstractrust12.5to8percent
+ retained within one-site scope, not12.5percentagepoints or all-SynCom generality.
+- Remove maize compatibility-assembly node and two workflow arrows, and the seedling-to-field selection
+ arrow. Keep four biological nodes/two PARTIAL proposed routes with explicit mediating ideas and missing
+ tests. Field defense arrow is scoped to rust component, not a demonstrated explanation of yield.
+- Jiangshui screening/ratio design node and arrow removed, not the positive fermentation effect. Retain
+ formulation-to-content intervention:2:3:1,phenols+72.20percent,flavonoids+61.13percent versus natural
+ fermentation. Do not assert isolated ratio causation, specific compound flux or de-novo synthesis. Three
+ differently named NCBITaxon2 strains stay distinct; existing taxonomy/protocol discussion and both histories
+ preserved.
+- Full record diffs, eight focused tests, ledger partitions and participant registry inspected. All11
+ remaining nodes have explicit canonical participants. Two nodes/four arrows removed; two HYPOTHESIZED,
+ three PARTIAL and one direct formulation-level arrow retained. Only graph/discussion/curation-history
+ record fields change;457 other records and raw non-graph blocks unchanged.
+- Actual focused schema/strict/term/reference/snippet/history/rank gates passed. All34 baseline network
+ findings unchanged with zero structural errors. Repeat renders deterministic and descriptions parser-checked
+ across456 pages, not browser screenshots. Measured both-root participant census is recorded, no production
+ matching or census-bound change.
+- Dedup searched822 all-state issue titles/bodies and14 ignored/hidden local matches; relevant contexts
+ inspected, not every historical comment/review. Closed824 is prior wording fix.1517-1519 addressed but
+ open until protected-main merge;1520-1521 unresolved. No Edison dry run, paid call or new graph structure.
+ Self-review is not independent approval.
+verification:
+ combined_regressions: 519 passed in 179.14s (0:02:59)
+ new_regression_tests: 8
+ schema_strict_terms_history: Passed with actual output digests
+ references: CLI Total checks counts reported issues, not executed checks. Exit0 means no issues reported,
+ not independent source verification. SupportingReference coverage476, Linux DOI-cache lookup1091 and
+ selected-cache provenance1362 remain limitations.
+ snippet_counts_by_record:
+ kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml:
+ MATCH: 31
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Jala_Maize_PGPB_SynCom.yaml:
+ MATCH: 23
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml:
+ MATCH: 14
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ network:
+ existing_findings_preserved: 34
+ added_findings: {}
+ removed_findings: {}
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml: d248e12db1ffcb8e4f473578cee8c0f047e9820cdd0b4b5a3313beb7d11463a6
+ tests/test_causal_review_batch55.py: e66bf27a6a0e0991b974002fea204517a75fc64638ae3ce3e7c0ec2dc35be952
+ tests/test_participating_taxa.py: 75c95befbd04131db8ce5dd1a400b3f4a77b69cf4ee7506fcf3a510e6e50f1dc
+ kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml: 09de6c3346c0253626f8175162e663538a44860465124483cf12f75ba655c0bd
+ kb/communities/Jala_Maize_PGPB_SynCom.yaml: f1f84af4838a5c066a06690f4e5ab55130ac29dcd6bf28db302b5ce116627652
+ kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml: 2a203d55521c6c2f51365d762a7294e4daa222232e808468239c89b2405d8456
+ reports/causal_graph_review/README.md: 33a18f2e25bb47cce9546e338420c2eaf0fb21c3f99d524d9f4bc0213a194644
+ post_commit_docs_current: Separate publication gate; not asserted before commit.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 389
+ mixed: 125
+ community_level_only: 264
+ taxa: 1498
+ credited_solely_by_the_rule: 1226
+ current:
+ records: 460
+ with_community_level: 390
+ mixed: 125
+ community_level_only: 265
+ taxa: 1505
+ credited_solely_by_the_rule: 1233
+ interpretation: 'REE pairwise-benefit assignments become explicitly scoped community/laboratory observations.
+ The survey counts taxa only in records with community-level nodes: its denominator adds the seven
+ existing REE taxa,1498to1505, and solely credited count1226to1233. No taxonomy additions. All11 nodes
+ use canonical participants; three registry entries added. No production matching or census-bound changes.'
+corpus:
+ records: 460
+ nodes: 1463
+ edges: 660
+ review_status_counts:
+ needs_research: 18
+ pending: 255
+ reviewed: 187
+limitations:
+- Whole three records, all13 original nodes and10 arrows reviewed;11 nodes and6 arrows remain. Two procedural
+ nodes and four workflow arrows removed; no new graph structure.
+- Full cached primary main texts/Methods/captions read for REE and Jala, including Jala main tables. Fresh
+ primary spot-checks only. Jiangshui accessible abstract/indexed publisher fragments only; direct publisher403,
+ no full body.
+- No original figure pixels, external supplements, raw data or code audited. Duplicate Jala pmc_full cache
+ not independently read. All920 caches remain byte-identical; source matching is not universal provenance
+ certification.
+- Positive isolate/wall adsorption, field REE observations, maize assay/inoculation effects and Jiangshui
+ formulation endpoints retained. Lab-to-field, trait and defense mediation remain bounded; hypothesized
+ weathering is not exact phylum-level flux.
+- Canonical taxon IDs/labels and raw non-graph blocks preserved, not recertified. REE broader claims remain1520
+ and Jala exact six-strain roster/source inconsistency remains1521. Existing Jiangshui taxonomy/protocol
+ knowledge gap remains open.
+- No Edison dry run, paid provider request/report, credit spend or new graph structure in this batch.
+ Future extensions require the separate one-community research and specific payload/spend authorization
+ workflow.
+- Dedup searched822 all-state issue titles/bodies and14 ignored/hidden local matches. Closed824 was a
+ prior wording repair, not a duplicate of this scientific finding. Relevant contexts read, not every
+ historical comment/review.
+- 1517-1519 stay open until protected-main merge;1520-1521 remain unresolved afterward. Existing graph
+ review is complete within stated scope, not resolution of non-graph followups. Self-adversarial review
+ is not independent approval.
+- SupportingReference coverage476, Linux DOI-cache lookup1091, selected-cache provenance1362 and writer
+ artifact1095 remain limitations. Reference CLI Total checks counts reported issues, not executed checks.
diff --git a/reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml b/reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml
new file mode 100644
index 000000000..8d4cd27ea
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml
@@ -0,0 +1,352 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: e2dacf7f7d0069c9ed46a91a18f91a5743a7fc09
+baseline_commit: e2dacf7f7d0069c9ed46a91a18f91a5743a7fc09
+base_tree: 734a4ea137b8f273578794858d8ca9cd34e08ba1
+pre_source_baseline_sha256: 7debb30f3dbc7f18af7580224acc3e5efd7cf0c08e805bc2cb5fa045f67fd4cc
+issues:
+- 1517
+- 1518
+- 1519
+unresolved_non_graph_issues:
+- 1520
+- 1521
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 822
+ ignored_hidden_local_search: true
+ matching_issues:
+ - 824
+ matching_local_files: 14
+ disposition: Closed824 is prior wording repair; relevant local contexts concern inventory/scouting/validation
+ or that repair.
+ limitations: Not every historical comment/review inspected.
+reference_cache_original_hashes:
+ references_cache/PMID_35708325.md: da09acb3f66302e8e61e26ea0b3ea82f00abebdee99bb7d01628f4d888a67ceb
+ references_cache/PMID_37275168.txt: fb504515a61888e87dbcba28915cbfdc7fb8766bc925231c099b7aade2e03971
+ references_cache/PMID_42425667.txt: 5ff70e3b348de06b82b5e5d837815d9c6349d7660e0fe836c416bf890a2210ac
+primary_artifacts:
+ PMC9275249-efetch.xml: 5c44d21a88083ee77672d8cd7669b3563e226a102e7636d84bf018c57aa096ff
+ source-progress.md: 2fc71b2528df4ba51129d44911cb2e6c44104e533b6963aa67ae83c70fbf4b10
+primary_spot_check:
+ xml_sha256: 5c44d21a88083ee77672d8cd7669b3563e226a102e7636d84bf018c57aa096ff
+ url: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=9275249
+ verified_excerpts:
+ - decreased the REE adsorption from 65.5% to only 17.8%
+ - the B horizon is rich in HREEs
+ - tends to decrease with increasing depth
+ quoted_words: 22
+ cache_changed: false
+ scope: Selected critical quotes verified, not a complete second primary reading.
+limitations:
+- Whole three records, all13 original nodes and10 arrows reviewed;11 nodes and6 arrows remain. Two procedural nodes
+ and four workflow arrows removed; no new graph structure.
+- Full cached primary main texts/Methods/captions read for REE and Jala, including Jala main tables. Fresh primary
+ spot-checks only. Jiangshui accessible abstract/indexed publisher fragments only; direct publisher403, no full
+ body.
+- No original figure pixels, external supplements, raw data or code audited. Duplicate Jala pmc_full cache not independently
+ read. All920 caches remain byte-identical; source matching is not universal provenance certification.
+- Positive isolate/wall adsorption, field REE observations, maize assay/inoculation effects and Jiangshui formulation
+ endpoints retained. Lab-to-field, trait and defense mediation remain bounded; hypothesized weathering is not exact
+ phylum-level flux.
+- Canonical taxon IDs/labels and raw non-graph blocks preserved, not recertified. REE broader claims remain1520
+ and Jala exact six-strain roster/source inconsistency remains1521. Existing Jiangshui taxonomy/protocol knowledge
+ gap remains open.
+- No Edison dry run, paid provider request/report, credit spend or new graph structure in this batch. Future extensions
+ require the separate one-community research and specific payload/spend authorization workflow.
+- Dedup searched822 all-state issue titles/bodies and14 ignored/hidden local matches. Closed824 was a prior wording
+ repair, not a duplicate of this scientific finding. Relevant contexts read, not every historical comment/review.
+- 1517-1519 stay open until protected-main merge;1520-1521 remain unresolved afterward. Existing graph review is
+ complete within stated scope, not resolution of non-graph followups. Self-adversarial review is not independent
+ approval.
+- SupportingReference coverage476, Linux DOI-cache lookup1091, selected-cache provenance1362 and writer artifact1095
+ remain limitations. Reference CLI Total checks counts reported issues, not executed checks.
+records:
+- path: kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml
+ id: CommunityMech:000036
+ original_sha256: 1ff9a8dfbeb6fc987d41baa44a6022aa9df027634214684722c01b141873bc21
+ record_sha256: 09de6c3346c0253626f8175162e663538a44860465124483cf12f75ba655c0bd
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml
+ scope: Whole record and every original node/arrow; primary-source-bounded existing structure repair.
+ summary: Separate positive REE laboratory adsorption from proposed weathering and deposit-scale mediation.
+ renamed_nodes:
+ Bioweathering and REE Mineral Dissolution: Proposed Microbial REE Mineral Dissolution
+ HREE Enrichment in B Horizon: Observed B-Horizon HREE Enrichment
+ Fungal Bioweathering and Mineral Dissolution: Proposed Fungal REE Bioweathering
+ Oligotrophic REE Mobilization and Deep Profile Colonization: Acidobacteria Profile Distribution and Oligotrophic
+ Interpretation
+ node_decisions:
+ - node: Teichoic Acid-Mediated HREE Selective Biosorption
+ rationale: Preserve positive separate-isolate and cell-wall interventions without active transport or reciprocal
+ benefit.
+ - node: Proposed Microbial REE Mineral Dissolution
+ rationale: Bound literature-informed weathering as a proposed community contribution, not traced cross-feeding.
+ - node: Observed B-Horizon HREE Enrichment
+ rationale: Preserve observed elemental enrichment separately from unquantified biological mediation.
+ - node: Proposed Fungal REE Bioweathering
+ rationale: Bound fungal weathering as a hypothesis without phylum-level mutualism or measured acceleration.
+ - node: Acidobacteria Profile Distribution and Oligotrophic Interpretation
+ rationale: Replace unsupported deep mobilization with the measured Acidobacteria distribution and bounded ecological
+ interpretation.
+ removed_node_decisions: []
+ edges_before:
+ - source: Teichoic Acid-Mediated HREE Selective Biosorption
+ target: HREE Enrichment in B Horizon
+ description: Bacterial biosorption concentrates HREE in clay-rich weathering zones
+ - source: Bioweathering and REE Mineral Dissolution
+ target: Teichoic Acid-Mediated HREE Selective Biosorption
+ description: Dissolved REE become available for selective bacterial biosorption
+ - source: Fungal Bioweathering and Mineral Dissolution
+ target: Teichoic Acid-Mediated HREE Selective Biosorption
+ description: Fungal dissolution releases REE for bacterial biosorption
+ edges_after:
+ - source: Teichoic Acid-Mediated HREE Selective Biosorption
+ target: Observed B-Horizon HREE Enrichment
+ description: PARTIAL - preferential HREE binding by indigenous bacterial cell walls could contribute to retention
+ and fractionation in the B horizon. Laboratory adsorption and field community/geochemical associations support
+ this route, but do not isolate its deposit-scale magnitude from mineral adsorption and water transport.
+ - source: Proposed Microbial REE Mineral Dissolution
+ target: Teichoic Acid-Mediated HREE Selective Biosorption
+ description: HYPOTHESIZED - microbial mineral dissolution could release REEs that become substrates for bacterial
+ surface adsorption. This substrate-availability route is proposed from profile associations and known weathering
+ functions, not traced from the listed phyla to the tested isolates in situ.
+ - source: Proposed Fungal REE Bioweathering
+ target: Teichoic Acid-Mediated HREE Selective Biosorption
+ description: HYPOTHESIZED - fungal weathering could release REEs for bacterial cell-wall binding. The fungal
+ associations and separate adsorption assays support a candidate route, not selectively demonstrated fungal
+ dissolution, partner transfer or its necessity for field enrichment.
+ retained_edge_decisions:
+ - source: Teichoic Acid-Mediated HREE Selective Biosorption
+ target: Observed B-Horizon HREE Enrichment
+ description: PARTIAL - preferential HREE binding by indigenous bacterial cell walls could contribute to retention
+ and fractionation in the B horizon. Laboratory adsorption and field community/geochemical associations support
+ this route, but do not isolate its deposit-scale magnitude from mineral adsorption and water transport.
+ rationale: Retain the proposed biological route with explicit evidence limits.
+ - source: Proposed Microbial REE Mineral Dissolution
+ target: Teichoic Acid-Mediated HREE Selective Biosorption
+ description: HYPOTHESIZED - microbial mineral dissolution could release REEs that become substrates for bacterial
+ surface adsorption. This substrate-availability route is proposed from profile associations and known weathering
+ functions, not traced from the listed phyla to the tested isolates in situ.
+ rationale: Retain the proposed biological route with explicit evidence limits.
+ - source: Proposed Fungal REE Bioweathering
+ target: Teichoic Acid-Mediated HREE Selective Biosorption
+ description: HYPOTHESIZED - fungal weathering could release REEs for bacterial cell-wall binding. The fungal
+ associations and separate adsorption assays support a candidate route, not selectively demonstrated fungal
+ dissolution, partner transfer or its necessity for field enrichment.
+ rationale: Retain the proposed biological route with explicit evidence limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:35708325
+ issues:
+ - 1517
+ - 1520
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Ion_Adsorption_REE_Indigenous_Community/2026-10-06T174553Z-codex-f8ce0e.yaml
+ source_review:
+ PMID:35708325:
+ cache: references_cache/PMID_35708325.md
+ sha256: da09acb3f66302e8e61e26ea0b3ea82f00abebdee99bb7d01628f4d888a67ceb
+ original_sha256: da09acb3f66302e8e61e26ea0b3ea82f00abebdee99bb7d01628f4d888a67ceb
+ url: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=9275249
+ scope: Complete cached primary main text, Methods and Figures1-7 captions read; fresh NCBI XML selected-claim
+ spot-check only.
+- path: kb/communities/Jala_Maize_PGPB_SynCom.yaml
+ id: CommunityMech:000099
+ original_sha256: df8ec76afd60a1db220eb761731b8ac9f694681b0804b754f08ee1e04a3a1862
+ record_sha256: f1f84af4838a5c066a06690f4e5ab55130ac29dcd6bf28db302b5ce116627652
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml
+ scope: Whole record and every original node/arrow; primary-source-bounded existing structure repair.
+ summary: Retain maize SynCom assay and plant outcomes without workflow causality or proven trait mediation.
+ renamed_nodes: {}
+ node_decisions:
+ - node: SynCom 3 Multi-Trait PGP Activity
+ rationale: Preserve positive assay results with their specificity limits and explicit incomplete canonical roster.
+ - node: SynCom 3 Antifungal and PAL Induction
+ rationale: Preserve fungal inhibition and PAL activity without an unperformed challenge experiment.
+ - node: Conejo Maize Seedling Growth Promotion
+ rationale: Preserve controlled Conejo growth with correct dry-weight assignments and no workflow arrow.
+ - node: Field Yield Increase and Rust Reduction
+ rationale: Preserve the hybrid field treatment response within one trial, not universal efficacy or proven mediation.
+ removed_node_decisions:
+ - node: Compatibility-Constrained SynCom 3 Assembly
+ rationale: Researcher screening and assembly are workflow, not a biological interaction; non-graph design metadata
+ is preserved.
+ edges_before:
+ - source: Compatibility-Constrained SynCom 3 Assembly
+ target: SynCom 3 Multi-Trait PGP Activity
+ description: 'Compatibility filtering retained a SynCom that could be assayed for complementary nutrient-mobilization
+ and hormone-related plant-growth promoting activities.
+
+ '
+ - source: Compatibility-Constrained SynCom 3 Assembly
+ target: SynCom 3 Antifungal and PAL Induction
+ description: 'The compatible SynCom 3 formulation also carried candidate antifungal and induced systemic resistance
+ traits.
+
+ '
+ - source: SynCom 3 Multi-Trait PGP Activity
+ target: Conejo Maize Seedling Growth Promotion
+ description: 'SynCom 3''s measured nutrient and hormone traits preceded gnotobiotic and greenhouse maize growth-promotion
+ assays.
+
+ '
+ - source: SynCom 3 Antifungal and PAL Induction
+ target: Field Yield Increase and Rust Reduction
+ description: 'In vitro fungal inhibition and the PAL response were candidate mechanisms for reduced fungal rust
+ incidence in the open-field SynCom 3 treatment.
+
+ '
+ - source: Conejo Maize Seedling Growth Promotion
+ target: Field Yield Increase and Rust Reduction
+ description: 'Seedling growth promotion in controlled systems supported the choice to test SynCom 3 on hybrid
+ maize in the field.
+
+ '
+ edges_after:
+ - source: SynCom 3 Multi-Trait PGP Activity
+ target: Conejo Maize Seedling Growth Promotion
+ description: PARTIAL - nutrient mobilization and hormone-related activities could improve nutrient availability
+ or plant signaling and thereby support Conejo seedling growth. Positive in-vitro assays and inoculation responses
+ support these candidate mechanisms, but no selective trait perturbation establishes mediation or their individual
+ contributions.
+ - source: SynCom 3 Antifungal and PAL Induction
+ target: Field Yield Increase and Rust Reduction
+ description: PARTIAL - antifungal activity or host defense responses could contribute to the rust-reduction
+ component of the field outcome. Separate inhibition and PAL assays support candidate routes, but no fungal-challenge
+ ISR test or selective PAL/antifungal perturbation establishes this mediation or explains the yield increase.
+ retained_edge_decisions:
+ - source: SynCom 3 Multi-Trait PGP Activity
+ target: Conejo Maize Seedling Growth Promotion
+ description: PARTIAL - nutrient mobilization and hormone-related activities could improve nutrient availability
+ or plant signaling and thereby support Conejo seedling growth. Positive in-vitro assays and inoculation responses
+ support these candidate mechanisms, but no selective trait perturbation establishes mediation or their individual
+ contributions.
+ rationale: Retain the proposed biological route with explicit evidence limits.
+ - source: SynCom 3 Antifungal and PAL Induction
+ target: Field Yield Increase and Rust Reduction
+ description: PARTIAL - antifungal activity or host defense responses could contribute to the rust-reduction
+ component of the field outcome. Separate inhibition and PAL assays support candidate routes, but no fungal-challenge
+ ISR test or selective PAL/antifungal perturbation establishes this mediation or explains the yield increase.
+ rationale: Retain the proposed biological route with explicit evidence limits.
+ removed_edge_decisions:
+ - source: Compatibility-Constrained SynCom 3 Assembly
+ target: SynCom 3 Multi-Trait PGP Activity
+ description: 'Compatibility filtering retained a SynCom that could be assayed for complementary nutrient-mobilization
+ and hormone-related plant-growth promoting activities.
+
+ '
+ rationale: Experimental assembly, screening or selection does not establish a biological cause between these
+ nodes.
+ - source: Compatibility-Constrained SynCom 3 Assembly
+ target: SynCom 3 Antifungal and PAL Induction
+ description: 'The compatible SynCom 3 formulation also carried candidate antifungal and induced systemic resistance
+ traits.
+
+ '
+ rationale: Experimental assembly, screening or selection does not establish a biological cause between these
+ nodes.
+ - source: Conejo Maize Seedling Growth Promotion
+ target: Field Yield Increase and Rust Reduction
+ description: 'Seedling growth promotion in controlled systems supported the choice to test SynCom 3 on hybrid
+ maize in the field.
+
+ '
+ rationale: Experimental assembly, screening or selection does not establish a biological cause between these
+ nodes.
+ references:
+ - PMID:37275168
+ issues:
+ - 1518
+ - 1521
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Jala_Maize_PGPB_SynCom/2026-10-06T174554Z-codex-56c270.yaml
+ source_review:
+ PMID:37275168:
+ cache: references_cache/PMID_37275168.txt
+ sha256: fb504515a61888e87dbcba28915cbfdc7fb8766bc925231c099b7aade2e03971
+ original_sha256: fb504515a61888e87dbcba28915cbfdc7fb8766bc925231c099b7aade2e03971
+ url: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1167839/full
+ scope: Complete cached primary main text, Methods, Tables1-2 and Figures1-6 captions read; fresh Frontiers
+ formulation/Discussion spot-checks only. Duplicate pmc_full cache not independently read.
+- path: kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml
+ id: CommunityMech:000356
+ original_sha256: ac47988e722840fd5a4e813bfa7d35c1b9b1e75d101732954cc4866a0c1907b2
+ record_sha256: 2a203d55521c6c2f51365d762a7294e4daa222232e808468239c89b2405d8456
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml
+ scope: Whole record and every original node/arrow; primary-source-bounded existing structure repair.
+ summary: Retain the Jiangshui formulation effect and remove experimental screening from the biological graph.
+ renamed_nodes:
+ Optimized 2:3:1 Jiangshui fermentation: Three-Strain 2:3:1 Jiangshui Fermentation
+ node_decisions:
+ - node: Three-Strain 2:3:1 Jiangshui Fermentation
+ rationale: Preserve the assayed three-strain formulation as fermentation, not experimental optimization workflow.
+ - node: Jiangshui phenol and flavonoid increase
+ rationale: Preserve positive total-content endpoints without inferring molecular synthesis or exact strain mediation.
+ removed_node_decisions:
+ - node: Jiangshui LAB screening and ratio assembly
+ rationale: Researcher screening and assembly are workflow, not a biological interaction; non-graph design metadata
+ is preserved.
+ edges_before:
+ - source: Jiangshui LAB screening and ratio assembly
+ target: Optimized 2:3:1 Jiangshui fermentation
+ description: The three selected LAB strains were assembled at empirically varied ratios before the optimized
+ Y-5-3:Y-6-2:HN ratio was selected.
+ - source: Optimized 2:3:1 Jiangshui fermentation
+ target: Jiangshui phenol and flavonoid increase
+ description: The optimized 2:3:1 strain ratio increased measured total phenols and flavonoids compared with
+ natural Jiangshui.
+ edges_after:
+ - source: Three-Strain 2:3:1 Jiangshui Fermentation
+ target: Jiangshui phenol and flavonoid increase
+ description: The tested three-strain 2:3:1 fermentation treatment increased measured total phenol and flavonoid
+ contents relative to natural Jiangshui. This positive formulation-level intervention does not isolate the
+ ratio, a particular strain, release versus synthesis, or a molecular mediator as the cause.
+ retained_edge_decisions:
+ - source: Three-Strain 2:3:1 Jiangshui Fermentation
+ target: Jiangshui phenol and flavonoid increase
+ description: The tested three-strain 2:3:1 fermentation treatment increased measured total phenol and flavonoid
+ contents relative to natural Jiangshui. This positive formulation-level intervention does not isolate the
+ ratio, a particular strain, release versus synthesis, or a molecular mediator as the cause.
+ rationale: Retain positive tested formulation-to-content effect without claiming an isolated molecular mediator.
+ removed_edge_decisions:
+ - source: Jiangshui LAB screening and ratio assembly
+ target: Optimized 2:3:1 Jiangshui fermentation
+ description: The three selected LAB strains were assembled at empirically varied ratios before the optimized
+ Y-5-3:Y-6-2:HN ratio was selected.
+ rationale: Experimental assembly, screening or selection does not establish a biological cause between these
+ nodes.
+ references:
+ - PMID:42425667
+ issues:
+ - 1519
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Jiangshui_LAB_Directed_Fermentation_SynCom/2026-10-06T174554Z-codex-394a99.yaml
+ source_review:
+ PMID:42425667:
+ cache: references_cache/PMID_42425667.txt
+ sha256: 5ff70e3b348de06b82b5e5d837815d9c6349d7660e0fe836c416bf890a2210ac
+ original_sha256: 5ff70e3b348de06b82b5e5d837815d9c6349d7660e0fe836c416bf890a2210ac
+ url: https://www.sciencedirect.com/science/article/abs/pii/S0740002026001607
+ scope: Complete cached abstract and indexed primary publisher fragments read. Direct publisher403; no full-body
+ access.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 2568af9c3..5844aa4c4 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -203,9 +203,9 @@ kb/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.yaml CommunityMech
kb/communities/Infant_Gut_DNA_Phage_Succession_Community.yaml CommunityMech:000223 21f96693bd3c7fd376824ef7fff9897a3d8fbf3843395bb32abd9965c0b50bcf 4 2 88.8 reports/causal_graph_review/decisions/20261006-infant-gut-batch54.yaml reviewed
kb/communities/Infant_Gut_Prebiotic_Response_SynCom.yaml CommunityMech:000281 65a7283c698b0a9f7b3644df944199c1f9349c5675c58b84e2d76f746a6a43ac 3 1 80.0 reports/causal_graph_review/decisions/20261006-infant-gut-batch54.yaml needs_research
kb/communities/Infant_Gut_Strain_Persistence_Maternal_Community.yaml CommunityMech:000240 628d4ae9504b000f14951fa6179843051f2fad9f0a56b8f5ee89aae6a48e5e00 3 2 86.7 reports/causal_graph_review/decisions/20261006-infant-gut-batch54.yaml needs_research
-kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml CommunityMech:000036 1ff9a8dfbeb6fc987d41baa44a6022aa9df027634214684722c01b141873bc21 5 3 100.0 pending
-kb/communities/Jala_Maize_PGPB_SynCom.yaml CommunityMech:000099 df8ec76afd60a1db220eb761731b8ac9f694681b0804b754f08ee1e04a3a1862 5 5 100.0 pending
-kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml CommunityMech:000356 ac47988e722840fd5a4e813bfa7d35c1b9b1e75d101732954cc4866a0c1907b2 3 2 88.3 pending
+kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml CommunityMech:000036 09de6c3346c0253626f8175162e663538a44860465124483cf12f75ba655c0bd 5 3 88.0 reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml reviewed
+kb/communities/Jala_Maize_PGPB_SynCom.yaml CommunityMech:000099 f1f84af4838a5c066a06690f4e5ab55130ac29dcd6bf28db302b5ce116627652 4 2 90.0 reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml reviewed
+kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml CommunityMech:000356 2a203d55521c6c2f51365d762a7294e4daa222232e808468239c89b2405d8456 2 1 75.0 reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml reviewed
kb/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.yaml CommunityMech:000132 9f951642ed74d82ba8e0581acef30a3b4367e04c786c8065d658c8a5990ea217 3 2 100.0 pending
kb/communities/KBase_Models_for_Zahmeeth_Original_PLOS.yaml CommunityMech:000037 9363499efd03e336a153ea8d17d0e7e05a9a9ca6fb417160b59bc2099d2783a9 5 5 100.0 pending
kb/communities/KBase_ORT_Workflow_Community_Model.yaml CommunityMech:000038 850826c4759b18be1a87bcc88d948cd064fdfbe911c22a4bccb227bdc86d9ab0 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 7b26ee95b..40aa8e637 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": 1465,
- "edges": 664,
+ "nodes": 1463,
+ "edges": 660,
"records_without_nodes": 8,
"records_without_edges": 154,
"review_status_counts": {
"needs_research": 18,
- "pending": 258,
- "reviewed": 184
+ "pending": 255,
+ "reviewed": 187
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261006-batch55.json b/reports/causal_graph_review/validation-20261006-batch55.json
new file mode 100644
index 000000000..0c25d7c9f
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch55.json
@@ -0,0 +1,790 @@
+{
+ "base_commit": "e2dacf7f7d0069c9ed46a91a18f91a5743a7fc09",
+ "scope": [
+ "kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml",
+ "kb/communities/Jala_Maize_PGPB_SynCom.yaml",
+ "kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Ion_Adsorption_REE_Indigenous_Community-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Ion_Adsorption_REE_Indigenous_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Ion_Adsorption_REE_Indigenous_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch55/Ion_Adsorption_REE_Indigenous_Community-strict.tsv",
+ "kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Ion_Adsorption_REE_Indigenous_Community-strict.log",
+ "log_sha256": "658cd0ad9fc3b714108c7980d3ae367c4e5c6b6245818f3da2b933608839a021",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch55/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-batch55/Ion_Adsorption_REE_Indigenous_Community-strict.tsv\n"
+ },
+ {
+ "check": "Ion_Adsorption_REE_Indigenous_Community-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Ion_Adsorption_REE_Indigenous_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Ion_Adsorption_REE_Indigenous_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Ion_Adsorption_REE_Indigenous_Community-references.log",
+ "log_sha256": "75559967e2461d2bdfe04ebda0b88ff93c2a9805afa2a720fc3755351816195a",
+ "output_tail": "Validating kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Ion_Adsorption_REE_Indigenous_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Ion_Adsorption_REE_Indigenous_Community-snippets.log",
+ "log_sha256": "7cb30458f959a4a7649fd96c05ca0aecb145f69b34e2ebea471b4c38e6956f10",
+ "output_tail": "# 31 evidence snippets scanned across 1 files\n MATCH 31\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Ion_Adsorption_REE_Indigenous_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Ion_Adsorption_REE_Indigenous_Community-rank.log",
+ "log_sha256": "e237746645c554d3f96c243d7547e6181f340e597c761ec9c3bc1a1b53f1a420",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000036\",\n \"name\": \"Ion-Adsorption REE Indigenous Community\",\n \"score\": 88.0,\n \"taxonomy\": 7,\n \"connected_taxa\": 7,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 5,\n \"downstream_edges\": 3,\n \"interaction_evidence\": 10,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Ion_Adsorption_REE_Indigenous_Community-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Ion_Adsorption_REE_Indigenous_Community/2026-10-06T174553Z-codex-f8ce0e.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Ion_Adsorption_REE_Indigenous_Community-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Jala_Maize_PGPB_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Jala_Maize_PGPB_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jala_Maize_PGPB_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Jala_Maize_PGPB_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch55/Jala_Maize_PGPB_SynCom-strict.tsv",
+ "kb/communities/Jala_Maize_PGPB_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jala_Maize_PGPB_SynCom-strict.log",
+ "log_sha256": "32c7f76f4eaa729b857e6be25ef3bb9554a4993bd67954d36e97db08bfcc4e10",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch55/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-batch55/Jala_Maize_PGPB_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Jala_Maize_PGPB_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Jala_Maize_PGPB_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jala_Maize_PGPB_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Jala_Maize_PGPB_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Jala_Maize_PGPB_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jala_Maize_PGPB_SynCom-references.log",
+ "log_sha256": "9c5c15c4a602e46dfb65fa79db4b7fb1e1bc0609a111c138e4ee6e5b763b299c",
+ "output_tail": "Validating kb/communities/Jala_Maize_PGPB_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Jala_Maize_PGPB_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Jala_Maize_PGPB_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Jala_Maize_PGPB_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jala_Maize_PGPB_SynCom-snippets.log",
+ "log_sha256": "06a536479395cd60c7eab504952fd1ebaea7cd4609924c29d687dbc4183c3686",
+ "output_tail": "# 23 evidence snippets scanned across 1 files\n MATCH 23\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": "Jala_Maize_PGPB_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Jala_Maize_PGPB_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jala_Maize_PGPB_SynCom-rank.log",
+ "log_sha256": "49798488f6f749f606de1101f96f4e70ad7a7d2c58f71656c89643b7dffa2fe2",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000099\",\n \"name\": \"Jala Maize PGPB SynCom\",\n \"score\": 90.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 10,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Jala_Maize_PGPB_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Jala_Maize_PGPB_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Jala_Maize_PGPB_SynCom/2026-10-06T174554Z-codex-56c270.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jala_Maize_PGPB_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Jiangshui_LAB_Directed_Fermentation_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jiangshui_LAB_Directed_Fermentation_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Jiangshui_LAB_Directed_Fermentation_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch55/Jiangshui_LAB_Directed_Fermentation_SynCom-strict.tsv",
+ "kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jiangshui_LAB_Directed_Fermentation_SynCom-strict.log",
+ "log_sha256": "c284aa066e13baa6a1649a035f8888d5e33b5fd879de54093079c83a38d99818",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch55/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-batch55/Jiangshui_LAB_Directed_Fermentation_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Jiangshui_LAB_Directed_Fermentation_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jiangshui_LAB_Directed_Fermentation_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Jiangshui_LAB_Directed_Fermentation_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jiangshui_LAB_Directed_Fermentation_SynCom-references.log",
+ "log_sha256": "93db9b088585909ba974ff2a7da8a661ceb1b6aa3b14c242407c43f3be27acdf",
+ "output_tail": "Validating kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Jiangshui_LAB_Directed_Fermentation_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jiangshui_LAB_Directed_Fermentation_SynCom-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": "Jiangshui_LAB_Directed_Fermentation_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jiangshui_LAB_Directed_Fermentation_SynCom-rank.log",
+ "log_sha256": "5c9d2ed52ce5d221b76d88208ac081c933f7ac01bc6a65c940eafd62c913094a",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000356\",\n \"name\": \"Jiangshui LAB Directed Fermentation SynCom\",\n \"score\": 75.0,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"additional_downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Jiangshui_LAB_Directed_Fermentation_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Jiangshui_LAB_Directed_Fermentation_SynCom/2026-10-06T174554Z-codex-394a99.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/Jiangshui_LAB_Directed_Fermentation_SynCom-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-batch55/inventory.log",
+ "log_sha256": "7aa736402b5fa9fa463a35bc62b06079eea2bb22befeefc09a1d8f970dfa33aa",
+ "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\": 1463,\n \"edges\": 660,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 154,\n \"review_status_counts\": {\n \"needs_research\": 18,\n \"pending\": 255,\n \"reviewed\": 187\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-batch55/network.log",
+ "log_sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "output_tail": "{\n \"preferred_term\": \"Legionella MAGs\",\n \"term\": {\n \"id\": \"NCBITaxon:445\",\n \"label\": \"Legionella\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n },\n \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n \"evidence\": [\n {\n \"reference\": \"PMID:41457319\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"COMPUTATIONAL\",\n \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n }\n ]\n },\n \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/rank-all.log",
+ "log_sha256": "ced9f8fea391d04515d476080b62fdcc346daeca017d369dab1307dc378f4c95",
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Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch55/render.log",
+ "log_sha256": "014a8f11493eafff94f4a42200f37d18b85817db34358941dc5da67b31dbdb7f",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch55/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch55/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch55/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": [
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+ ],
+ "log": "/private/tmp/communitymech-batch55/render-repeat.log",
+ "log_sha256": "014a8f11493eafff94f4a42200f37d18b85817db34358941dc5da67b31dbdb7f",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch55/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch55/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch55/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch55/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json, pathlib, runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch54')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda: paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/connectivity-survey.log",
+ "log_sha256": "89c6437d76912927cdaa421e7904383ca0c73cf009335f5c92b32e9af5b522e9",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 389, \"mixed\": 125, \"community_level_only\": 264, \"taxa\": 1498, \"credited_solely_by_the_rule\": 1226}, \"current\": {\"records\": 460, \"with_community_level\": 390, \"mixed\": 125, \"community_level_only\": 265, \"taxa\": 1505, \"credited_solely_by_the_rule\": 1233}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/regressions.log",
+ "log_sha256": "797bdd963530f5f972b7e39b12836c083b0e5e85cecb80eee72a9f448571e341",
+ "output_tail": "........................................................................ [ 13%]\n........................................................................ [ 27%]\n........................................................................ [ 41%]\n........................................................................ [ 55%]\n........................................................................ [ 69%]\n........................................................................ [ 83%]\n........................................................................ [ 97%]\n............... [100%]\n519 passed in 179.14s (0:02:59)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/black.log",
+ "log_sha256": "b9cf511501d306d2bd8355ccb165c8ddc0a6fdd62d7c72c4a7b1795cf8934c8c",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n2 files would be left unchanged.\n"
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch55/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Whole three records, all13 original nodes and10 arrows reviewed;11 nodes and6 arrows remain. Two procedural nodes and four workflow arrows removed; no new graph structure.",
+ "Full cached primary main texts/Methods/captions read for REE and Jala, including Jala main tables. Fresh primary spot-checks only. Jiangshui accessible abstract/indexed publisher fragments only; direct publisher403, no full body.",
+ "No original figure pixels, external supplements, raw data or code audited. Duplicate Jala pmc_full cache not independently read. All920 caches remain byte-identical; source matching is not universal provenance certification.",
+ "Positive isolate/wall adsorption, field REE observations, maize assay/inoculation effects and Jiangshui formulation endpoints retained. Lab-to-field, trait and defense mediation remain bounded; hypothesized weathering is not exact phylum-level flux.",
+ "Canonical taxon IDs/labels and raw non-graph blocks preserved, not recertified. REE broader claims remain1520 and Jala exact six-strain roster/source inconsistency remains1521. Existing Jiangshui taxonomy/protocol knowledge gap remains open.",
+ "No Edison dry run, paid provider request/report, credit spend or new graph structure in this batch. Future extensions require the separate one-community research and specific payload/spend authorization workflow.",
+ "Dedup searched822 all-state issue titles/bodies and14 ignored/hidden local matches. Closed824 was a prior wording repair, not a duplicate of this scientific finding. Relevant contexts read, not every historical comment/review.",
+ "1517-1519 stay open until protected-main merge;1520-1521 remain unresolved afterward. Existing graph review is complete within stated scope, not resolution of non-graph followups. Self-adversarial review is not independent approval.",
+ "SupportingReference coverage476, Linux DOI-cache lookup1091, selected-cache provenance1362 and writer artifact1095 remain limitations. Reference CLI Total checks counts reported issues, not executed checks.",
+ "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate.",
+ "CLI Total checks counts reported issues, not executed checks. Exit0 means no issues reported, not independent source verification. SupportingReference coverage476, Linux DOI-cache lookup1091 and selected-cache provenance1362 remain limitations."
+ ],
+ "superseded_checks": [],
+ "resume_note": "Existing receipts reused only after command identity, exit status, log hash, record hashes and unchanged caches verified. No unexecuted check counted as passed.",
+ "snippet_counts_by_record": {
+ "kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml": {
+ "MATCH": 31,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Jala_Maize_PGPB_SynCom.yaml": {
+ "MATCH": 23,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml": {
+ "MATCH": 14,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 44,
+ "unchanged_record_files": 457,
+ "unchanged_cache_files": 920,
+ "primary_spot_check": {
+ "xml_sha256": "5c44d21a88083ee77672d8cd7669b3563e226a102e7636d84bf018c57aa096ff",
+ "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=9275249",
+ "verified_excerpts": [
+ "decreased the REE adsorption from 65.5% to only 17.8%",
+ "the B horizon is rich in HREEs",
+ "tends to decrease with increasing depth"
+ ],
+ "quoted_words": 22,
+ "cache_changed": false,
+ "scope": "Selected critical quotes verified, not a complete second primary reading."
+ },
+ "network_delta": {
+ "existing_findings_preserved": 34,
+ "added_findings": {},
+ "removed_findings": {}
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1449,
+ "arrows": 652
+ },
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 389,
+ "mixed": 125,
+ "community_level_only": 264,
+ "taxa": 1498,
+ "credited_solely_by_the_rule": 1226
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 390,
+ "mixed": 125,
+ "community_level_only": 265,
+ "taxa": 1505,
+ "credited_solely_by_the_rule": 1233
+ }
+ },
+ "interpretation": "REE pairwise-benefit assignments become explicitly scoped community/laboratory observations. The survey counts taxa only in records with community-level nodes: its denominator adds the seven existing REE taxa,1498to1505, and solely credited count1226to1233. No taxonomy additions. All11 nodes use canonical participants; three registry entries added. No production matching or census-bound changes."
+ },
+ "verification_resume_reason": "Initial harness incorrectly expected the community-level survey denominator to remain1498. Actual survey exited0 and yielded1505; inspected _survey confirms it excludes records without community-level nodes. Corrected only the temporary harness expectation and interpretation; no record, production code, committed test or survey-bound change. Earlier real command logs remain unchanged and hash-verified.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1463,
+ "edges": 660,
+ "records_without_nodes": 8,
+ "records_without_edges": 154,
+ "review_status_counts": {
+ "needs_research": 18,
+ "pending": 255,
+ "reviewed": 187
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml": "d248e12db1ffcb8e4f473578cee8c0f047e9820cdd0b4b5a3313beb7d11463a6",
+ "tests/test_causal_review_batch55.py": "e66bf27a6a0e0991b974002fea204517a75fc64638ae3ce3e7c0ec2dc35be952",
+ "tests/test_participating_taxa.py": "75c95befbd04131db8ce5dd1a400b3f4a77b69cf4ee7506fcf3a510e6e50f1dc",
+ "kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml": "09de6c3346c0253626f8175162e663538a44860465124483cf12f75ba655c0bd",
+ "kb/communities/Jala_Maize_PGPB_SynCom.yaml": "f1f84af4838a5c066a06690f4e5ab55130ac29dcd6bf28db302b5ce116627652",
+ "kb/communities/Jiangshui_LAB_Directed_Fermentation_SynCom.yaml": "2a203d55521c6c2f51365d762a7294e4daa222232e808468239c89b2405d8456",
+ "reports/causal_graph_review/README.md": "33a18f2e25bb47cce9546e338420c2eaf0fb21c3f99d524d9f4bc0213a194644"
+ },
+ "status": "verified_ree_maize_jiangshui_graph_repair",
+ "reference_validator_caveat": "CLI Total checks counts reported issues, not executed checks. Exit0 means no issues reported, not independent source verification. SupportingReference coverage476, Linux DOI-cache lookup1091 and selected-cache provenance1362 remain limitations.",
+ "pre_research_baseline": {
+ "base_commit": "e2dacf7f7d0069c9ed46a91a18f91a5743a7fc09",
+ "base_tree": "734a4ea137b8f273578794858d8ca9cd34e08ba1",
+ "research_worktree": "/private/tmp/communitymech-causal-batch54",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch55/baseline-rank.log",
+ "sha256": "c36f562245132145f1bacfc96a0de9fb25f07e1d1fb44b492e00c1c0601d5f32",
+ "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch55/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch55/baseline-network.log",
+ "sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "output_tail": " \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch55/baseline-downstream.log",
+ "sha256": "a265f424a2a8d94dfeb1ce70c51ef0dcaed4caf82798205aa333c8ed89d09c27",
+ "output_tail": "ial_Consortia_Core_Microbiome.yaml:178: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:207: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\nkb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml:167: downstream:\nkb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml:198: downstream:\nkb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml:251: downstream:\nkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml:105: downstream:\nkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml:141: downstream:\nkb/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.yaml:140: downstream:\nkb/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.yaml:221: downstream:\nkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml:151: downstream:\nkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml:192: downstream:\nkb/communities/KBase_ORT_Workflow_Community_Model.yaml:170: downstream:\nkb/communities/KBase_ORT_Workflow_Community_Model.yaml:261: downstream:\nkb/communities/Infant_Gut_DNA_Phage_Succession_Community.yaml:93: downstream:\nkb/communities/Infant_Gut_DNA_Phage_Succession_Community.yaml:128: downstream:\nkb/communities/Grassland_Soil_WetUp_Virus_Host_Community.yaml:83: downstream:\nkb/communities/Grassland_Soil_WetUp_Virus_Host_Community.yaml:135: downstream:\nkb/communities/Dangl_SynComm_35.yaml:244: downstream:\nkb/communities/Dangl_SynComm_35.yaml:322: downstream:\nkb/communities/Sichuan_Shai_Vinegar_Yeast_Flavor_SynCom.yaml:160: downstream:\nkb/communities/Sichuan_Shai_Vinegar_Yeast_Flavor_SynCom.yaml:195: downstream:\nkb/communities/Sichuan_Shai_Vinegar_Yeast_Flavor_SynCom.yaml:233: downstream:\nkb/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.yaml:119: downstream:\nkb/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.yaml:189: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "7debb30f3dbc7f18af7580224acc3e5efd7cf0c08e805bc2cb5fa045f67fd4cc"
+ }
+}
diff --git a/tests/test_causal_review_batch55.py b/tests/test_causal_review_batch55.py
new file mode 100644
index 000000000..6087b2e3b
--- /dev/null
+++ b/tests/test_causal_review_batch55.py
@@ -0,0 +1,160 @@
+"""Pin positive results, experimental scope and every original graph decision."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-three-records-batch55.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ return ledger, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in ledger["records"]]
+
+
+def test_explicit_participants_preserve_canonical_subsets_and_strain_names():
+ _, docs = records()
+ scopes = [
+ [[3, 4], [0, 2, 5, 6], list(range(7)), [5, 6], [1]],
+ [list(range(4))] * 4,
+ [list(range(3))] * 2,
+ ]
+ for doc, indexes_by_node in zip(docs, scopes, strict=True):
+ for node, indexes in zip(doc["ecological_interactions"], indexes_by_node, strict=True):
+ assert node["scope"] == "COMMUNITY_LEVEL"
+ assert not {"interaction_type", "source_taxon", "target_taxon"} & node.keys()
+ assert node["participating_taxa"] == [
+ {
+ "preferred_term": doc["taxonomy"][i]["taxon_term"]["preferred_term"],
+ "term": doc["taxonomy"][i]["taxon_term"]["term"],
+ }
+ for i in indexes
+ ]
+ strains = docs[2]["ecological_interactions"][0]["participating_taxa"]
+ assert len({p["preferred_term"] for p in strains}) == 3
+ assert {p["term"]["id"] for p in strains} == {"NCBITaxon:2"}
+
+
+def test_ree_retains_positive_wall_perturbation_without_active_transport():
+ _, (doc, _, _) = records()
+ binding, _, field, _, acido = doc["ecological_interactions"]
+ assert "65.5 to 17.8 percent" in binding["description"]
+ assert "residual binding remained" in binding["description"]
+ assert "passive surface binding" in binding["description"]
+ assert "biological_processes" not in binding
+ assert all(e["evidence_source"] == "IN_VITRO" for e in binding["evidence"])
+ assert all(e["supports"] == "SUPPORT" for e in binding["evidence"])
+ assert {m["term"]["id"] for m in binding["metabolites"]} == {"CHEBI:49962", "CHEBI:49980"}
+ assert "elemental sums" in field["description"] and "45 m" in field["description"]
+ assert "metabolites" not in field and "biological_processes" not in field
+ assert "generally decreased with depth" in acido["description"]
+ assert "metabolites" not in acido and "downstream" not in acido
+
+
+def test_ree_proposed_weathering_and_field_mediation_remain_qualified():
+ _, (doc, _, _) = records()
+ binding, weather, field, fungi, _ = doc["ecological_interactions"]
+ assert binding["downstream"][0]["target"] == field["name"]
+ assert binding["downstream"][0]["description"].startswith("PARTIAL - ")
+ for node in [weather, fungi]:
+ assert node["description"].startswith("HYPOTHESIZED - ")
+ assert all(e["supports"] == "PARTIAL" for e in node["evidence"])
+ assert node["downstream"][0]["target"] == binding["name"]
+ assert node["downstream"][0]["description"].startswith("HYPOTHESIZED - ")
+ assert "#1520" in doc["discussions"][-1]["rationale"]
+
+
+def test_maize_assay_specificity_and_unperformed_challenge_are_explicit():
+ _, (_, doc, _) = records()
+ traits, defense, seedling, field = doc["ecological_interactions"]
+ assert "Salkowski chemistry is not specific identification" in traits["description"]
+ assert "nitrogenase proxy" in traits["description"]
+ assert "Helminthosporium was hardly inhibited" in defense["description"]
+ assert (
+ "did not test induced systemic resistance with a fungal challenge" in defense["description"]
+ )
+ assert "shoot/root dry weights were 2.3/3" in seedling["description"]
+ assert "Conejo" in seedling["description"] and "CPL9105W" in field["description"]
+ assert (
+ "11 to 16 tons/ha" in field["description"] and "12.5 to 8 percent" in field["description"]
+ )
+ assert all(
+ "subset of the reported six-strain" in n["description"]
+ for n in doc["ecological_interactions"]
+ )
+ assert all(
+ e["supports"] == "SUPPORT" for n in doc["ecological_interactions"] for e in n["evidence"]
+ )
+
+
+def test_maize_workflow_removed_but_candidate_mediation_retained():
+ ledger, (_, doc, _) = records()
+ traits, defense, seedling, field = doc["ecological_interactions"]
+ assert "downstream" not in seedling and "downstream" not in field
+ assert traits["downstream"][0]["target"] == seedling["name"]
+ assert defense["downstream"][0]["target"] == field["name"]
+ assert all(
+ n["downstream"][0]["description"].startswith("PARTIAL - ") for n in [traits, defense]
+ )
+ assert len(ledger["records"][1]["removed_edge_decisions"]) == 3
+ assert "#1521" in doc["discussions"][-1]["rationale"]
+
+
+def test_jiangshui_positive_formulation_effect_and_access_limits():
+ _, (_, _, doc) = records()
+ fermentation, products = doc["ecological_interactions"]
+ assert fermentation["name"] == "Three-Strain 2:3:1 Jiangshui Fermentation"
+ arrow = fermentation["downstream"][0]
+ assert arrow["target"] == products["name"]
+ assert "positive formulation-level intervention" in arrow["description"]
+ assert not arrow["description"].startswith("PARTIAL")
+ assert "72.20 percent" in products["description"] and "61.13 percent" in products["description"]
+ assert "not identified compound flux" in products["description"]
+ assert len(doc["curation_history"]) == 3
+ assert "no primary full body was inspected" in doc["discussions"][-1]["rationale"]
+ assert len(doc["discussions"]) >= 2
+
+
+def test_all_original_nodes_and_arrows_are_partitioned_into_decisions():
+ ledger, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1517, 1518, 1519]
+ assert ledger["unresolved_non_graph_issues"] == [1520, 1521]
+ assert ledger["issue_deduplication"]["ignored_hidden_local_search"] is True
+ for i, (row, doc) in enumerate(zip(ledger["records"], docs, strict=True)):
+ assert row["status"] == "reviewed"
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert len(row["node_decisions"]) + len(row["removed_node_decisions"]) == [5, 5, 3][i]
+ assert {d["node"] for d in row["node_decisions"]} == {
+ n["name"] for n in doc["ecological_interactions"]
+ }
+ rename = row["renamed_nodes"]
+ old_edges = {
+ (rename.get(e["source"], e["source"]), rename.get(e["target"], e["target"]))
+ for e in row["edges_before"]
+ }
+ retained = {(e["source"], e["target"]) for e in row["retained_edge_decisions"]}
+ removed = {
+ (rename.get(e["source"], e["source"]), rename.get(e["target"], e["target"]))
+ for e in row["removed_edge_decisions"]
+ }
+ assert old_edges == retained | removed and not retained & removed
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ for d in doc.get("discussions", []):
+ assert all(
+ a.split("#", 1)[1] in names
+ for a in d.get("attaches_to", [])
+ if a.startswith("ecological_interactions#")
+ )
+
+
+def test_caches_unchanged_and_spot_check_does_not_claim_full_second_reading():
+ ledger, _ = records()
+ for path, digest in ledger["reference_cache_original_hashes"].items():
+ assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == digest
+ check = ledger["primary_spot_check"]
+ assert not check["cache_changed"]
+ assert sum(len(q.split()) for q in check["verified_excerpts"]) == check["quoted_words"] == 22
+ assert "not a complete second" in check["scope"]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index a00489388..2895c1c44 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -297,6 +297,9 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Infant_Gut_DNA_Phage_Succession_Community.yaml",
"Infant_Gut_Prebiotic_Response_SynCom.yaml",
"Infant_Gut_Strain_Persistence_Maternal_Community.yaml",
+ "Ion_Adsorption_REE_Indigenous_Community.yaml",
+ "Jala_Maize_PGPB_SynCom.yaml",
+ "Jiangshui_LAB_Directed_Fermentation_SynCom.yaml",
"Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml",
"Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml",
"MSC1_Dominant_Core.yaml",