From 393b6da1b24f5ce70e567630f5a82bbb260a72dc Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Wed, 7 Oct 2026 06:25:02 -0700
Subject: [PATCH] Bound degradation and competition evidence and diatom graph
scope
---
...dococcus_Chloronitrobenzene_Coculture.html | 105 +-
...us_RDK17_Terephthalic_Acid_Consortium.html | 82 +-
...thalene_Biochar_Engineered_Consortium.html | 122 +-
...donitzschia_Sulfitobacter_Association.html | 230 +---
.../2026-10-07T125451Z-codex-edc25d.yaml | 26 +
.../2026-10-07T130739Z-codex-a070e2.yaml | 26 +
.../2026-10-07T125451Z-codex-55758a.yaml | 27 +
.../2026-10-07T125451Z-codex-1ff079.yaml | 27 +
.../2026-10-07T130739Z-codex-d6881b.yaml | 26 +
.../2026-10-07T125452Z-codex-a42433.yaml | 26 +
...dococcus_Chloronitrobenzene_Coculture.yaml | 92 +-
...us_RDK17_Terephthalic_Acid_Consortium.yaml | 84 +-
...thalene_Biochar_Engineered_Consortium.yaml | 129 +-
...donitzschia_Sulfitobacter_Association.yaml | 170 +--
reports/causal_graph_review/README.md | 28 +
.../adversarial-review-20261007-batch90.yaml | 304 +++++
.../20261007-four-records-batch90.yaml | 671 ++++++++++
reports/causal_graph_review/inventory.tsv | 8 +-
reports/causal_graph_review/summary.json | 6 +-
.../validation-20261007-batch90.json | 1120 +++++++++++++++++
tests/test_causal_review_batch90.py | 165 +++
tests/test_participating_taxa.py | 2 +
22 files changed, 3076 insertions(+), 400 deletions(-)
create mode 100644 history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T125451Z-codex-edc25d.yaml
create mode 100644 history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T130739Z-codex-a070e2.yaml
create mode 100644 history/records/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium/2026-10-07T125451Z-codex-55758a.yaml
create mode 100644 history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T125451Z-codex-1ff079.yaml
create mode 100644 history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T130739Z-codex-d6881b.yaml
create mode 100644 history/records/Pseudonitzschia_Sulfitobacter_Association/2026-10-07T125452Z-codex-a42433.yaml
create mode 100644 reports/causal_graph_review/adversarial-review-20261007-batch90.yaml
create mode 100644 reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
create mode 100644 reports/causal_graph_review/validation-20261007-batch90.json
create mode 100644 tests/test_causal_review_batch90.py
diff --git a/docs/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.html b/docs/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.html
index dbf601876..f1fa87960 100644
--- a/docs/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.html
+++ b/docs/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.html
@@ -583,7 +583,7 @@ Ecological Interactions
Ecological interaction network for Pseudomonas-Rhodococcus Chloronitrobenzene Coculture
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, syntrophy).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding).
@@ -596,8 +596,8 @@
Ecological Interactions
@@ -608,7 +608,7 @@ Ecological Interactions
Pseudomonas Partial Chloronitrobenzene Transformation
CROSS_FEEDING
- P. putida HS12 converts 3- and 4-chloronitrobenzene to chlorohydroxyacetanilide intermediates through partial reduction and acetylation, supplying compounds that the Rhodococcus partner can further degrade.
+ The source reports chemically identified conversion of the substrates into intermediates subsequently degraded by the partner. PARTIAL: the sequential transformation supports the reported directed coupling, not reciprocal metabolite supply or directly traced assimilation by both partners.
Source Taxon: Pseudomonas putida HS12
@@ -651,8 +651,7 @@ Pseudomonas Partial Chloronitrobenzene Transformation
→ Rhodococcus Intermediate Degradation
-
P. putida HS12 partial reduction and acetylation generate chlorohydroxyacetanilide intermediates that Rhodococcus sp. strain HS51 further degrades in the sequential two-strain pathway.
-
+
The reported upstream transformation produces the intermediates that the downstream partner degrades, coupling the two steps. PARTIAL: the accessible abstract does not resolve every transfer or assimilation step.
@@ -695,16 +694,19 @@ Evidence
-
Rhodococcus sp. strain HS51 degrades the chlorohydroxyacetanilide intermediates generated by P. putida HS12, completing the sequential catabolic design.
+
Rhodococcus degrades the intermediates generated by Pseudomonas in the proposed two-member pathway. This is the downstream transformation step, not evidence of Rhodococcus supplying a metabolite back to Pseudomonas.
-
Source Taxon: Rhodococcus sp. strain HS51
+
Participating Taxa:
+
+ Pseudomonas putida HS12,
+
+ Rhodococcus sp. strain HS51
-
Target Taxon: Pseudomonas putida HS12
+
@@ -728,8 +730,7 @@
Rhodococcus Intermediate Degradation
→ Coculture Chloronitrobenzene Mineralization
-
Rhodococcus degradation of the Pseudomonas-derived chlorohydroxyacetanilide intermediates completes the sequential pathway needed for 3- and 4-chloronitrobenzene mineralization by the coculture.
-
+
The reported downstream intermediate degradation contributes to the proposed two-strain pathway and conditional coculture mineralization. PARTIAL: the full pathway and carbon-balance measurements were not independently inspected.
Evidence
-
The two-member coculture mineralizes 3- and 4-chloronitrobenzene in the presence of an additional carbon source.
+
The primary abstract reports coculture mineralization in the presence of an additional carbon source. Preserve that conditional result. The endpoint is not itself evidence that removal of a partner product makes the upstream metabolism favourable, and a complete carbon balance was not independently audited.
@@ -845,6 +845,60 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ What evidence resolves transfer direction and the conditional mineralization pathway?
+
+
The sequential transformations and reported mineralization are preserved. The reverse-feeding label on the intermediate-degradation node was removed without reversing either graph arrow. Only the primary abstract was retrieved: XML failed after bounded retries, the article page presented a browser challenge and the open-access metadata request returned404. Missing full methods are not evidence that controls were absent. SYNTROPHY does not require obligacy in the local schema; the endpoint label is removed because pathway completion alone does not demonstrate product-removal feedback on the upstream metabolism.
+
+
Attaches to: ecological_interactions#Pseudomonas Partial Chloronitrobenzene Transformation, ecological_interactions#Rhodococcus Intermediate Degradation, ecological_interactions#Coculture Chloronitrobenzene Mineralization
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
Rhodococcus sp. strain HS51, which degrades 4- and 5-chloro-2-hydroxyacetanilides
+
Supports HS51 as the organism degrading P. putida-derived intermediates.
+
+
+
This coculture was confirmed to mineralize 3- and 4-CNBs
+
Directly supports the community-level mineralization claim.
+
+
+
+
@@ -1293,7 +1347,7 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1315,23 +1369,26 @@
Evidence
});
- var srcKey = "Rhodococcus sp. strain HS51";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Pseudomonas putida HS12";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Pseudomonas putida HS12",
+
+ "Rhodococcus sp. strain HS51"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:2";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
diff --git a/docs/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html b/docs/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html
index 90602e9fe..cb97ce9a3 100644
--- a/docs/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html
+++ b/docs/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html
@@ -578,7 +578,7 @@
Ecological Interactions
Exploitative competition for terephthalic acid
COMPETITION
Both strains utilize TPA at comparable rates in monoculture, but they compete for TPA as the shared sole carbon and energy source in coculture; Pp-TE consistently outcompetes RDK17, partly through relative growth kinetics.
+ Both members use the shared substrate, and the source reports that abolishing its metabolism in Pp-TE removes dominance. This supports a metabolic contribution to competition; dominance alone does not identify that mechanism. PARTIAL: the abstract does not separately quantify resource competition and contact-inhibition contributions.
Source Taxon: Pseudomonas putida strain Pp-TE (engineered)
@@ -606,8 +606,7 @@ Exploitative competition for terephthalic acid
→ Pp-TE Dominance During TPA Coculture
-
Competition for terephthalic acid contributes to Pp-TE dominance in the two-member TPA coculture fermentations.
-
+
The source-reported metabolic perturbation supports a contribution of substrate use to dominance, alongside contact inhibition. PARTIAL: their separate effect sizes are not resolved by the accessible abstract.
@@ -630,6 +629,19 @@ Evidence
+
+
+
+ "when TPA metabolism was abolished in Pp-TE, it lost its dominance to RDK17"
+
+
+
@@ -639,7 +651,7 @@ Evidence
Interference competition via type VI secretion system
COMPETITION
- Pp-TE inhibits RDK17 through contact-dependent inhibition mediated by its type VI secretion system, which impairs RDK17 growth and reinforces Pp-TE dominance in coculture.
+ The authors report assays attributing the main competitive advantage to type-VI-secretion-associated contact inhibition, with a partial contribution from relative growth kinetics. Preserve this experimental attribution; the accessible abstract does not expose the full controls or separate effect sizes.
Source Taxon: Pseudomonas putida strain Pp-TE (engineered)
@@ -670,8 +682,7 @@ Interference competition via type VI secretion system
→ Pp-TE Dominance During TPA Coculture
-
Contact-dependent growth inhibition reinforces Pp-TE dominance over RDK17 in TPA-fed cocultures.
-
+
The source reports that contact-dependent impairment of the partner is the main contributor to dominance, alongside metabolic capability and relative kinetics. This preserves the reported causal attribution without independently certifying unreviewed methods.
@@ -703,8 +714,7 @@ Evidence
Pp-TE Dominance During TPA Coculture
COMPETITION
- P. putida Pp-TE consistently dominates Rhodococcus sp. RDK17 in batch and serial-transfer cocultures supplied with terephthalic acid as the sole carbon and energy source.
-
+ Pp-TE consistently outcompetes RDK17 in the reported batch and serial-transfer cocultures. This is the measured population outcome; its mechanistic attribution is represented by the two upstream nodes, not inferred from dominance alone.
Source Taxon: Pseudomonas putida strain Pp-TE (engineered)
@@ -765,6 +775,60 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How are the two competitive contributions distinguished from the dominance observation?
+
+
All three competition nodes and both existing directions remain. The primary abstract reports contact inhibition, relative kinetics and a metabolism-loss comparison; those positive findings are retained. Full methods and quantitative decomposition were unavailable, which does not imply absent controls. No new resistance-selection details, genetic designs or experimental protocols were added.
+
+
Attaches to: ecological_interactions#Exploitative competition for terephthalic acid, ecological_interactions#Interference competition via type VI secretion system, ecological_interactions#Pp-TE Dominance During TPA Coculture
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
Pp-TE consistently outcompeted RDK17 in batch and multitransfer coculture fermentations, even when RDK17 was inoculated at a significantly higher initial abundance
+
Supports the observed competitive outcome, not by itself the mechanism of resource competition.
+
+
+
the dominance of Pp-TE was primarily conferred by its type VI secretion system, which impaired the growth of RDK17 via contact-dependent inhibition
+
Contact-dependent inhibition through the Pp-TE T6SS is interference competition against RDK17.
+
+
+
+
@@ -933,7 +997,7 @@ Evidence
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
diff --git a/docs/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.html b/docs/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.html
index 90a122834..54be500a2 100644
--- a/docs/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.html
+++ b/docs/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.html
@@ -581,6 +581,11 @@ Ecological Interactions
aria-hidden="true" data-symbol="symbolTriangle"
data-color="#7f30cf"> Syntrophy
+
+
@@ -590,7 +595,7 @@ Ecological Interactions
Biochar-bridged direct interspecies electron transfer (DIET)
SYNTROPHY
- The conductive S-N-doped biochar matrix bridges the two strains, facilitating direct interspecies electron transfer (DIET) and extracellular electron transfer (EET). Pseudomonas stutzeri acts as an oxidative bio-anode releasing electrons that are harnessed by the Rhodococcus reductive bio-cathode.
+ PARTIAL: the authors interpret the conductive material as coupling donor electron release with recipient electron use in a syntrophic model. Retain this reported coupling type, which does not assert obligacy. Electrochemical and multi-omics support do not independently isolate the interspecies route from other material-associated effects in the accessible abstract.
Source Taxon: Pseudomonas stutzeri (overexpressing nahAc and nahB)
@@ -621,7 +626,7 @@ Biochar-bridged direct interspecies electron transfer (DIET)
→ Syntrophic naphthalene mineralization circuit
-
Conductive biochar-mediated electron transfer bridges the engineered Pseudomonas bio-anode and Rhodococcus bio-cathode that jointly mineralize naphthalene.
+
PARTIAL: the reported conductive interface is proposed to couple the partners within the authors degradation-circuit model; route-specific mediation is not independently resolved by the accessible abstract.
@@ -653,14 +658,18 @@ Evidence
Syntrophic naphthalene mineralization circuit
SYNTROPHY
- Pseudomonas stutzeri initiates naphthalene degradation and releases electrons; the directed electron flux is harnessed by Rhodococcus to drive oxygenolytic ring-cleavage catalysis, establishing a syntrophic circuit that mineralizes naphthalene while minimizing intermediate accumulation.
+ PARTIAL: the authors interpret coordinated electron flux and catabolic responses as a syntrophic degradation circuit. Retain that reported model with canonical participants. The local interaction type does not assert obligacy, and the accessible abstract does not independently isolate every mediator.
- Source Taxon: Pseudomonas stutzeri (overexpressing nahAc and nahB)
+ Participating Taxa:
-
Target Taxon: Rhodococcus rhodococcus (overexpressing nahH and catA)
+ Pseudomonas stutzeri (overexpressing nahAc and nahB),
+
+ Rhodococcus rhodococcus (overexpressing nahH and catA)
+
+
@@ -681,8 +690,7 @@ Syntrophic naphthalene mineralization circuit
→ Enhanced Naphthalene Removal and Mineralization
-
Biochar-mediated electron flux feeds the Pseudomonas-Rhodococcus syntrophic circuit that removes and mineralizes naphthalene.
-
+
PARTIAL: the proposed coordinated circuit is offered as an explanation for the reported removal and mineralization endpoints. The abstract does not isolate each mediator from concurrent treatment effects.
@@ -712,13 +720,19 @@ Evidence
-
The biochar-bridged engineered circuit achieved more than 98.3% naphthalene removal and 89.5% mineralization by coordinating electron flux between Pseudomonas and Rhodococcus and limiting intermediate accumulation.
-
+
The source reports more than 98.3% naphthalene removal and 89.5% mineralization. Preserve these separate positive endpoints without treating the measured outcome itself as an electron-transfer interaction or independently auditing a complete carbon balance.
+
+
Participating Taxa:
+
+ Pseudomonas stutzeri (overexpressing nahAc and nahB),
+
+ Rhodococcus rhodococcus (overexpressing nahH and catA)
+
+
@@ -761,6 +775,60 @@
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ What distinguishes the reported electron-transfer model from the treatment endpoints?
+
+
All three nodes and both existing directions remain. The authors electron-transfer model retains its SYNTROPHY classification with PARTIAL evidence bounds: the local enum does not require obligacy. The community removal/mineralization endpoint is distinct from the coupling mechanism. Only the fresh primary abstract was retrieved; unavailable methods are not proof that route-specific controls were absent. Canonical source labels are preserved, not newly certified strain identities. No new genetic designs, optimization details or experimental procedures were added.
+
+
Attaches to: ecological_interactions#Biochar-bridged direct interspecies electron transfer (DIET), ecological_interactions#Syntrophic naphthalene mineralization circuit, ecological_interactions#Enhanced Naphthalene Removal and Mineralization
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
facilitating direct interspecies electron transfer (DIET) and enhancing extracellular electron transfer (EET)
+
Supports the authors DIET/EET interpretation, not independent resolution of the electron-transfer route or obligatory mutual dependence.
+
+
+
The resulting bioelectrochemical synergy achieved exceptional naphthalene removal (>98.3%) and mineralization efficiency (89.5%)
+
Supports the measured removal and mineralization endpoint of the engineered consortium.
+
+
+
+
@@ -917,23 +985,26 @@
Evidence
});
- var srcKey = "Pseudomonas stutzeri (overexpressing nahAc and nahB)";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Rhodococcus rhodococcus (overexpressing nahH and catA)";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Pseudomonas stutzeri (overexpressing nahAc and nahB)",
+
+ "Rhodococcus rhodococcus (overexpressing nahH and catA)"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:2";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -957,6 +1028,19 @@
Evidence
+ var participantKeys = [
+
+ "Pseudomonas stutzeri (overexpressing nahAc and nahB)",
+
+ "Rhodococcus rhodococcus (overexpressing nahH and catA)"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/docs/communities/Pseudonitzschia_Sulfitobacter_Association.html b/docs/communities/Pseudonitzschia_Sulfitobacter_Association.html
index a6f3b2eda..2ffc1d803 100644
--- a/docs/communities/Pseudonitzschia_Sulfitobacter_Association.html
+++ b/docs/communities/Pseudonitzschia_Sulfitobacter_Association.html
@@ -559,7 +559,7 @@
Ecological Interactions
Ecological interaction network for Pseudo-nitzschia-Sulfitobacter Marine Association
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (mutualism, niche partitioning).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -567,76 +567,18 @@
Ecological Interactions
-
-
-
-
The Pseudo-nitzschia study decomposed a diatom-associated bacterial consortium to identify a Sulfitobacter species that participates in a nutrient and signaling exchange with the phytoplankton host.
-
-
-
-
-
-
-
-
-
-
Biological Processes:
-
-
-
- interspecies interaction
- (GO:0044419 )
-
-
-
-
-
-
-
-
-
Evidence
-
-
-
-
Sulfitobacter synthesizes indole-3-acetic acid using tryptophan supplied both by Pseudo-nitzschia and by endogenous bacterial metabolism.
-
+
The primary abstract reports bacterial IAA production using both diatom-derived and endogenous precursor pools. Preserve this biochemical attribution without treating the individual synthesis process as proof of reciprocal fitness benefits.
Source Taxon: Sulfitobacter sp. SA11
@@ -723,10 +665,8 @@
Evidence
-
Sulfitobacter-secreted indole-3-acetic acid promoted Pseudo-nitzschia cell division, establishing auxin as a growth-promoting bacterial signal in this diatom association.
-
+
The source reports that bacterial IAA promotes diatom cell division. Preserve the existing positive signaling finding and its direction, without making the individual response node a claim of reciprocal partner benefit.
Source Taxon: Sulfitobacter sp. SA11
@@ -786,13 +726,19 @@
Evidence
-
Indole-3-acetic acid and tryptophan functioned as signaling molecules within a nutrient exchange that included diatom organosulfur compounds and bacterial-excreted ammonia.
-
+
The source describes signaling within a broader nutrient exchange between the partners. PARTIAL: the accessible abstract does not independently establish complete exchange fluxes or the necessity of every component for reciprocal fitness.
+
+
Participating Taxa:
+
+ Pseudo-nitzschia multiseries,
+
+ Sulfitobacter sp. SA11
+
+
@@ -850,71 +796,70 @@
Evidence
-
-
-
Metabolite and metatranscriptome analyses detected widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, especially in coastal environments.
-
+
+
+
+ Knowledge gaps & discussions (1)
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which observations belong to the exact pair and which describe the broader environment?
+
+
The consortium-resolution workflow and broad coastal-prevalence nodes were removed from the pair-specific interaction graph; the environmental observation remains in environmental_factors. The three biological signal/exchange nodes and existing causal direction are retained. The fresh primary abstract and public publisher preview were read, not the full main methods or supplements. No new growth mechanism, toxin-production guidance, cultivation optimization or experimental design was added. Non-graph citation, culture and metal metadata remain #1742.
+
Attaches to: ecological_interactions#Tryptophan-Supported Sulfitobacter IAA Synthesis, ecological_interactions#Auxin-Mediated Diatom Cell Division, ecological_interactions#Infochemical Nutrient Exchange
-
Metabolites:
- indole-3-acetic acid
- (CHEBI:16411 )
-
+
+ 2 evidence item(s)
+
+
+
IN_VITRO
+
SUPPORT
-
Biological Processes:
-
-
- indole-3-acetic acid biosynthetic process
- (GO:0009684 )
-
-
-
+
PMID:26017307
+
+
Indole-3-acetic acid and tryptophan serve as signalling molecules that are part of a complex exchange of nutrients, including diatom-excreted organosulfur molecules and bacterial-excreted ammonia
+
+
Supports IAA and tryptophan signaling inside a broader nutrient exchange.
+
+
+
+
OTHER
+
SUPPORT
-
Evidence
-
-
-
+ widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, particularly in coastal environments
+
+ Supports environmental prevalence of Sulfitobacter-related bacterial IAA production.
+
+
-
"widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, particularly in coastal environments
-"
-
-
+
-
Evidence
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("interspecies interaction");
-
-
- var evidenceCount = 1;
-
- nodes.push({
- id: intId,
- label: "Diatom-Associated Bacterial Consortium Resolution",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
- })();
-
- (function() {
- var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1443,8 +1360,8 @@ Evidence
})();
(function() {
- var intId = "interaction:2";
- var intType = "MUTUALISM";
+ var intId = "interaction:1";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1485,8 +1402,8 @@ Evidence
})();
(function() {
- var intId = "interaction:3";
- var intType = "MUTUALISM";
+ var intId = "interaction:2";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1518,38 +1435,19 @@ Evidence
- })();
-
- (function() {
- var intId = "interaction:4";
- var intType = "NICHE_PARTITIONING";
- var metabolites = [];
-
-
- metabolites.push("indole-3-acetic acid");
-
-
- var processes = [];
-
-
- processes.push("indole-3-acetic acid biosynthetic process");
+ var participantKeys = [
+ "Pseudo-nitzschia multiseries",
- var evidenceCount = 1;
+ "Sulfitobacter sp. SA11"
- nodes.push({
- id: intId,
- label: "Coastal Sulfitobacter IAA Prevalence",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
});
-
-
-
})();
@@ -1571,7 +1469,7 @@ Evidence
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
- var nodeCount = 7;
+ var nodeCount = 5;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T125451Z-codex-edc25d.yaml b/history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T125451Z-codex-edc25d.yaml
new file mode 100644
index 000000000..e86d25ef9
--- /dev/null
+++ b/history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T125451Z-codex-edc25d.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
+ slug: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+session:
+ id: 2026-10-07T125451Z-codex-edc25d
+ timestamp: '2026-10-07T12:54:51Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1738
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve chemically supported upstream transformation with transfer limits.; Remove
+ the reverse-feeding implication while retaining downstream degradation.; Preserve conditional
+ reported mineralization without an obligatory-syntrophy label.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
diff --git a/history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T130739Z-codex-a070e2.yaml b/history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T130739Z-codex-a070e2.yaml
new file mode 100644
index 000000000..335cc460c
--- /dev/null
+++ b/history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T130739Z-codex-a070e2.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
+ slug: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+session:
+ id: 2026-10-07T130739Z-codex-a070e2
+ timestamp: '2026-10-07T13:07:39Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1738
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: 'Correct the precommit syntrophy rationale: the local enum does not require obligacy;
+ an endpoint alone does not establish product-removal feedback.'
+ details: Adversarial precommit correction after reading InteractionTypeEnum.SYNTROPHY. Initial
+ local results are retained as superseded; full validation will be rerun.
diff --git a/history/records/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium/2026-10-07T125451Z-codex-55758a.yaml b/history/records/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium/2026-10-07T125451Z-codex-55758a.yaml
new file mode 100644
index 000000000..ca21b33cc
--- /dev/null
+++ b/history/records/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium/2026-10-07T125451Z-codex-55758a.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml
+ slug: Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium
+session:
+ id: 2026-10-07T125451Z-codex-55758a
+ timestamp: '2026-10-07T12:54:51Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1739
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Add reported metabolic-perturbation evidence rather than treating dominance alone
+ as mechanism.; Preserve reported contact inhibition and relative-kinetics attribution
+ with source-access limits.; Preserve the measured dominance outcome separately from its
+ explanatory mechanisms.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
diff --git a/history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T125451Z-codex-1ff079.yaml b/history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T125451Z-codex-1ff079.yaml
new file mode 100644
index 000000000..d52f5fbc3
--- /dev/null
+++ b/history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T125451Z-codex-1ff079.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
+ slug: Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium
+session:
+ id: 2026-10-07T125451Z-codex-1ff079
+ timestamp: '2026-10-07T12:54:51Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1740
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Qualify the authors electron-transfer model without asserting obligatory syntrophy.;
+ Represent the composite circuit collectively with explicit canonical participants.; Preserve
+ reported removal and mineralization without conflating endpoints with a specific interaction
+ type.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
diff --git a/history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T130739Z-codex-d6881b.yaml b/history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T130739Z-codex-d6881b.yaml
new file mode 100644
index 000000000..6530b2f4f
--- /dev/null
+++ b/history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T130739Z-codex-d6881b.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
+ slug: Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium
+session:
+ id: 2026-10-07T130739Z-codex-d6881b
+ timestamp: '2026-10-07T13:07:39Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1740
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Restore the authors qualified SYNTROPHY model on the transfer and circuit nodes;
+ the local enum explicitly does not assert obligacy. Keep the measurement endpoint distinct.
+ details: Adversarial precommit correction after reading InteractionTypeEnum.SYNTROPHY. Initial
+ local results are retained as superseded; full validation will be rerun.
diff --git a/history/records/Pseudonitzschia_Sulfitobacter_Association/2026-10-07T125452Z-codex-a42433.yaml b/history/records/Pseudonitzschia_Sulfitobacter_Association/2026-10-07T125452Z-codex-a42433.yaml
new file mode 100644
index 000000000..c3a576b91
--- /dev/null
+++ b/history/records/Pseudonitzschia_Sulfitobacter_Association/2026-10-07T125452Z-codex-a42433.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml
+ slug: Pseudonitzschia_Sulfitobacter_Association
+session:
+ id: 2026-10-07T125452Z-codex-a42433
+ timestamp: '2026-10-07T12:54:52Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1741
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve reported bacterial synthesis without claiming individual-process mutualism.;
+ Preserve the reported signaling response and existing causal direction.; Preserve nutrient-exchange
+ interpretation with exact-pair and flux limits.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
diff --git a/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml b/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
index 193ffb764..a27bc54a8 100644
--- a/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
+++ b/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
@@ -121,9 +121,9 @@ taxonomy:
explanation: Supports inclusion of HS51 in the defined coculture with P. putida HS12.
ecological_interactions:
- name: Pseudomonas Partial Chloronitrobenzene Transformation
- description: P. putida HS12 converts 3- and 4-chloronitrobenzene to chlorohydroxyacetanilide
- intermediates through partial reduction and acetylation, supplying compounds that the
- Rhodococcus partner can further degrade.
+ description: 'The source reports chemically identified conversion of the substrates into intermediates subsequently
+ degraded by the partner. PARTIAL: the sequential transformation supports the reported directed coupling, not
+ reciprocal metabolite supply or directly traced assimilation by both partners.'
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -152,10 +152,8 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Rhodococcus Intermediate Degradation
- description: >
- P. putida HS12 partial reduction and acetylation generate
- chlorohydroxyacetanilide intermediates that Rhodococcus sp. strain HS51
- further degrades in the sequential two-strain pathway.
+ description: 'The reported upstream transformation produces the intermediates that the downstream partner degrades,
+ coupling the two steps. PARTIAL: the accessible abstract does not resolve every transfer or assimilation step.'
evidence:
- reference: PMID:10049867
supports: SUPPORT
@@ -168,20 +166,9 @@ ecological_interactions:
snippet: by partial reduction and subsequent acetylation
explanation: Supports the curated partial-reduction and acetylation mechanism.
- name: Rhodococcus Intermediate Degradation
- description: Rhodococcus sp. strain HS51 degrades the chlorohydroxyacetanilide intermediates generated
- by P. putida HS12, completing the sequential catabolic design.
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Rhodococcus sp. strain HS51
- term:
- id: NCBITaxon:1827
- label: Rhodococcus
- target_taxon:
- preferred_term: Pseudomonas putida HS12
- term:
- id: NCBITaxon:303
- label: Pseudomonas putida
+ description: Rhodococcus degrades the intermediates generated by Pseudomonas in the proposed two-member pathway.
+ This is the downstream transformation step, not evidence of Rhodococcus supplying a metabolite back to Pseudomonas.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
@@ -189,10 +176,9 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Coculture Chloronitrobenzene Mineralization
- description: >
- Rhodococcus degradation of the Pseudomonas-derived
- chlorohydroxyacetanilide intermediates completes the sequential pathway
- needed for 3- and 4-chloronitrobenzene mineralization by the coculture.
+ description: 'The reported downstream intermediate degradation contributes to the proposed two-strain pathway
+ and conditional coculture mineralization. PARTIAL: the full pathway and carbon-balance measurements were not
+ independently inspected.'
evidence:
- reference: PMID:10049867
supports: SUPPORT
@@ -204,10 +190,19 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: A degradation pathway for 3- and 4-CNBs by the two isolated strains was also proposed
explanation: Supports the sequential two-strain pathway interpretation.
+ participating_taxa:
+ - preferred_term: Pseudomonas putida HS12
+ term:
+ id: NCBITaxon:303
+ label: Pseudomonas putida
+ - preferred_term: Rhodococcus sp. strain HS51
+ term:
+ id: NCBITaxon:1827
+ label: Rhodococcus
- name: Coculture Chloronitrobenzene Mineralization
- description: The two-member coculture mineralizes 3- and 4-chloronitrobenzene in the presence
- of an additional carbon source.
- interaction_type: SYNTROPHY
+ description: The primary abstract reports coculture mineralization in the presence of an additional carbon source.
+ Preserve that conditional result. The endpoint is not itself evidence that removal of a partner product makes
+ the upstream metabolism favourable, and a complete carbon balance was not independently audited.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Pseudomonas putida HS12
@@ -329,3 +324,44 @@ metal_relevance: NOT_APPLICABLE
metal_notes: >
No metal or rare earth element processing role is curated for this chloronitrobenzene
bioremediation coculture.
+discussions:
+- discussion_id: chloronitro-direction-and-mineralization
+ prompt: What evidence resolves transfer direction and the conditional mineralization pathway?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ rationale: 'The sequential transformations and reported mineralization are preserved. The reverse-feeding label
+ on the intermediate-degradation node was removed without reversing either graph arrow. Only the primary abstract
+ was retrieved: XML failed after bounded retries, the article page presented a browser challenge and the open-access
+ metadata request returned404. Missing full methods are not evidence that controls were absent. SYNTROPHY does
+ not require obligacy in the local schema; the endpoint label is removed because pathway completion alone does
+ not demonstrate product-removal feedback on the upstream metabolism.'
+ attaches_to:
+ - ecological_interactions#Pseudomonas Partial Chloronitrobenzene Transformation
+ - ecological_interactions#Rhodococcus Intermediate Degradation
+ - ecological_interactions#Coculture Chloronitrobenzene Mineralization
+ evidence:
+ - reference: PMID:10049867
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Rhodococcus sp. strain HS51, which degrades 4- and 5-chloro-2-hydroxyacetanilides
+ explanation: Supports HS51 as the organism degrading P. putida-derived intermediates.
+ - reference: PMID:10049867
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: This coculture was confirmed to mineralize 3- and 4-CNBs
+ explanation: Directly supports the community-level mineralization claim.
+curation_history:
+- timestamp: '2026-10-07T12:54:49Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve chemically supported upstream transformation with transfer limits.; Remove the reverse-feeding
+ implication while retaining downstream degradation.; Preserve conditional reported mineralization without an
+ obligatory-syntrophy label. Issue #1738; reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml'
+ llm_assisted: true
+- timestamp: '2026-10-07T13:07:38Z'
+ curator: codex
+ action: CORRECT_PRECOMMIT_SYNTROPHY_REVIEW
+ changes: 'Correct the precommit syntrophy rationale: the local enum does not require obligacy; an endpoint alone
+ does not establish product-removal feedback. Issue #1738; reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml b/kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml
index 3c5b8c55e..91970bd03 100644
--- a/kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml
+++ b/kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml
@@ -90,9 +90,10 @@ taxonomy:
explanation: Identifies Rhodococcus sp. strain RDK17 as the native member of the coculture.
ecological_interactions:
- name: Exploitative competition for terephthalic acid
- description: Both strains utilize TPA at comparable rates in monoculture, but they compete for TPA
- as the shared sole carbon and energy source in coculture; Pp-TE consistently outcompetes RDK17,
- partly through relative growth kinetics.
+ description: 'Both members use the shared substrate, and the source reports that abolishing its metabolism in
+ Pp-TE removes dominance. This supports a metabolic contribution to competition; dominance alone does not identify
+ that mechanism. PARTIAL: the abstract does not separately quantify resource competition and contact-inhibition
+ contributions.'
interaction_type: COMPETITION
scope: PAIRWISE
source_taxon:
@@ -112,19 +113,25 @@ ecological_interactions:
label: terephthalic acid
downstream:
- target: Pp-TE Dominance During TPA Coculture
- description: >
- Competition for terephthalic acid contributes to Pp-TE dominance in the
- two-member TPA coculture fermentations.
+ description: 'The source-reported metabolic perturbation supports a contribution of substrate use to dominance,
+ alongside contact inhibition. PARTIAL: their separate effect sizes are not resolved by the accessible abstract.'
evidence:
- reference: PMID:42324694
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Pp-TE consistently outcompeted RDK17 in batch and multitransfer coculture fermentations,
- even when RDK17 was inoculated at a significantly higher initial abundance
- explanation: Exploitative competition for the shared TPA carbon source drives Pp-TE dominance.
+ snippet: Pp-TE consistently outcompeted RDK17 in batch and multitransfer coculture fermentations, even when
+ RDK17 was inoculated at a significantly higher initial abundance
+ explanation: Supports the observed competitive outcome, not by itself the mechanism of resource competition.
+ - reference: PMID:42324694
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: when TPA metabolism was abolished in Pp-TE, it lost its dominance to RDK17
+ explanation: Supports the source-reported metabolic perturbation and its population outcome, without inventing
+ an exact genetic intervention or separating every competitive contribution.
- name: Interference competition via type VI secretion system
- description: Pp-TE inhibits RDK17 through contact-dependent inhibition mediated by its type VI
- secretion system, which impairs RDK17 growth and reinforces Pp-TE dominance in coculture.
+ description: The authors report assays attributing the main competitive advantage to type-VI-secretion-associated
+ contact inhibition, with a partial contribution from relative growth kinetics. Preserve this experimental attribution;
+ the accessible abstract does not expose the full controls or separate effect sizes.
interaction_type: COMPETITION
scope: PAIRWISE
source_taxon:
@@ -144,22 +151,20 @@ ecological_interactions:
label: protein secretion by the type VI secretion system
downstream:
- target: Pp-TE Dominance During TPA Coculture
- description: >
- Contact-dependent growth inhibition reinforces Pp-TE dominance over RDK17
- in TPA-fed cocultures.
+ description: The source reports that contact-dependent impairment of the partner is the main contributor to
+ dominance, alongside metabolic capability and relative kinetics. This preserves the reported causal attribution
+ without independently certifying unreviewed methods.
evidence:
- reference: PMID:42324694
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: the dominance of Pp-TE was primarily conferred by its type VI secretion system, which
- impaired the growth of RDK17 via contact-dependent inhibition
- explanation: Contact-dependent inhibition through the Pp-TE T6SS is interference competition
- against RDK17.
+ snippet: the dominance of Pp-TE was primarily conferred by its type VI secretion system, which impaired the
+ growth of RDK17 via contact-dependent inhibition
+ explanation: Contact-dependent inhibition through the Pp-TE T6SS is interference competition against RDK17.
- name: Pp-TE Dominance During TPA Coculture
- description: >
- P. putida Pp-TE consistently dominates Rhodococcus sp. RDK17 in batch and
- serial-transfer cocultures supplied with terephthalic acid as the sole
- carbon and energy source.
+ description: Pp-TE consistently outcompetes RDK17 in the reported batch and serial-transfer cocultures. This is
+ the measured population outcome; its mechanistic attribution is represented by the two upstream nodes, not inferred
+ from dominance alone.
interaction_type: COMPETITION
scope: PAIRWISE
source_taxon:
@@ -207,3 +212,38 @@ growth_media:
fermentations
explanation: Cultivation was by batch and multitransfer (serial-transfer) coculture
fermentation.
+discussions:
+- discussion_id: tpa-outcome-versus-competitive-contributions
+ prompt: How are the two competitive contributions distinguished from the dominance observation?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ rationale: All three competition nodes and both existing directions remain. The primary abstract reports contact
+ inhibition, relative kinetics and a metabolism-loss comparison; those positive findings are retained. Full methods
+ and quantitative decomposition were unavailable, which does not imply absent controls. No new resistance-selection
+ details, genetic designs or experimental protocols were added.
+ attaches_to:
+ - ecological_interactions#Exploitative competition for terephthalic acid
+ - ecological_interactions#Interference competition via type VI secretion system
+ - ecological_interactions#Pp-TE Dominance During TPA Coculture
+ evidence:
+ - reference: PMID:42324694
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Pp-TE consistently outcompeted RDK17 in batch and multitransfer coculture fermentations, even when
+ RDK17 was inoculated at a significantly higher initial abundance
+ explanation: Supports the observed competitive outcome, not by itself the mechanism of resource competition.
+ - reference: PMID:42324694
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: the dominance of Pp-TE was primarily conferred by its type VI secretion system, which impaired the
+ growth of RDK17 via contact-dependent inhibition
+ explanation: Contact-dependent inhibition through the Pp-TE T6SS is interference competition against RDK17.
+curation_history:
+- timestamp: '2026-10-07T12:54:50Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Add reported metabolic-perturbation evidence rather than treating dominance alone as mechanism.; Preserve
+ reported contact inhibition and relative-kinetics attribution with source-access limits.; Preserve the measured
+ dominance outcome separately from its explanatory mechanisms. Issue #1739; reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml b/kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
index 92e97dd6f..3f74bfd66 100644
--- a/kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
+++ b/kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
@@ -86,11 +86,10 @@ taxonomy:
explanation: Identifies the engineered Rhodococcus strain as a member of the consortium.
ecological_interactions:
- name: Biochar-bridged direct interspecies electron transfer (DIET)
- description: The conductive S-N-doped biochar matrix bridges the two strains, facilitating direct
- interspecies electron transfer (DIET) and extracellular electron transfer (EET). Pseudomonas
- stutzeri acts as an oxidative bio-anode releasing electrons that are harnessed by the Rhodococcus
- reductive bio-cathode.
- interaction_type: SYNTROPHY
+ description: 'PARTIAL: the authors interpret the conductive material as coupling donor electron release with recipient
+ electron use in a syntrophic model. Retain this reported coupling type, which does not assert obligacy. Electrochemical
+ and multi-omics support do not independently isolate the interspecies route from other material-associated effects
+ in the accessible abstract.'
scope: PAIRWISE
source_taxon:
preferred_term: Pseudomonas stutzeri (overexpressing nahAc and nahB)
@@ -109,33 +108,22 @@ ecological_interactions:
label: electron transport chain
downstream:
- target: Syntrophic naphthalene mineralization circuit
- description: Conductive biochar-mediated electron transfer bridges the engineered
- Pseudomonas bio-anode and Rhodococcus bio-cathode that jointly mineralize
- naphthalene.
+ description: 'PARTIAL: the reported conductive interface is proposed to couple the partners within the authors
+ degradation-circuit model; route-specific mediation is not independently resolved by the accessible abstract.'
evidence:
- reference: PMID:42139785
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: facilitating direct interspecies electron transfer (DIET) and enhancing extracellular
- electron transfer (EET)
- explanation: States the biochar-mediated DIET/EET electron transfer between the two members.
-- name: Syntrophic naphthalene mineralization circuit
- description: Pseudomonas stutzeri initiates naphthalene degradation and releases electrons; the
- directed electron flux is harnessed by Rhodococcus to drive oxygenolytic ring-cleavage catalysis,
- establishing a syntrophic circuit that mineralizes naphthalene while minimizing intermediate
- accumulation.
+ snippet: facilitating direct interspecies electron transfer (DIET) and enhancing extracellular electron transfer
+ (EET)
+ explanation: Supports the authors DIET/EET and coupled-metabolism interpretation, without independently resolving
+ the transfer route or asserting obligacy.
interaction_type: SYNTROPHY
- scope: PAIRWISE
- source_taxon:
- preferred_term: Pseudomonas stutzeri (overexpressing nahAc and nahB)
- term:
- id: NCBITaxon:316
- label: Stutzerimonas stutzeri
- target_taxon:
- preferred_term: Rhodococcus rhodococcus (overexpressing nahH and catA)
- term:
- id: NCBITaxon:1827
- label: Rhodococcus
+- name: Syntrophic naphthalene mineralization circuit
+ description: 'PARTIAL: the authors interpret coordinated electron flux and catabolic responses as a syntrophic
+ degradation circuit. Retain that reported model with canonical participants. The local interaction type does
+ not assert obligacy, and the accessible abstract does not independently isolate every mediator.'
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: naphthalene
term:
@@ -143,22 +131,30 @@ ecological_interactions:
label: naphthalene
downstream:
- target: Enhanced Naphthalene Removal and Mineralization
- description: >
- Biochar-mediated electron flux feeds the Pseudomonas-Rhodococcus
- syntrophic circuit that removes and mineralizes naphthalene.
+ description: 'PARTIAL: the proposed coordinated circuit is offered as an explanation for the reported removal
+ and mineralization endpoints. The abstract does not isolate each mediator from concurrent treatment effects.'
evidence:
- reference: PMID:42139785
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Electrochemical and multi‑omics analyses confirmed the establishment of this syntrophic
- circuit, demonstrating elevated electron flux, coordinated upregulation of catabolic genes
- explanation: Confirms the syntrophic naphthalene-mineralizing circuit between the two members.
-- name: Enhanced Naphthalene Removal and Mineralization
- description: >
- The biochar-bridged engineered circuit achieved more than 98.3% naphthalene
- removal and 89.5% mineralization by coordinating electron flux between
- Pseudomonas and Rhodococcus and limiting intermediate accumulation.
+ snippet: Electrochemical and multi‑omics analyses confirmed the establishment of this syntrophic circuit, demonstrating
+ elevated electron flux, coordinated upregulation of catabolic genes
+ explanation: Supports the reported electron-flux and expression findings and the authors circuit interpretation,
+ not independent necessity of every mediator.
+ participating_taxa:
+ - preferred_term: Pseudomonas stutzeri (overexpressing nahAc and nahB)
+ term:
+ id: NCBITaxon:316
+ label: Stutzerimonas stutzeri
+ - preferred_term: Rhodococcus rhodococcus (overexpressing nahH and catA)
+ term:
+ id: NCBITaxon:1827
+ label: Rhodococcus
interaction_type: SYNTROPHY
+- name: Enhanced Naphthalene Removal and Mineralization
+ description: The source reports more than 98.3% naphthalene removal and 89.5% mineralization. Preserve these separate
+ positive endpoints without treating the measured outcome itself as an electron-transfer interaction or independently
+ auditing a complete carbon balance.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: naphthalene
@@ -169,9 +165,18 @@ ecological_interactions:
- reference: PMID:42139785
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The resulting bioelectrochemical synergy achieved exceptional naphthalene removal
- (>98.3%) and mineralization efficiency (89.5%)
+ snippet: The resulting bioelectrochemical synergy achieved exceptional naphthalene removal (>98.3%) and mineralization
+ efficiency (89.5%)
explanation: Supports the measured removal and mineralization endpoint of the engineered consortium.
+ participating_taxa:
+ - preferred_term: Pseudomonas stutzeri (overexpressing nahAc and nahB)
+ term:
+ id: NCBITaxon:316
+ label: Stutzerimonas stutzeri
+ - preferred_term: Rhodococcus rhodococcus (overexpressing nahH and catA)
+ term:
+ id: NCBITaxon:1827
+ label: Rhodococcus
cultivation_setup:
- system_type: BIOELECTROCHEMICAL_SYSTEM
instrument_detail: Immobilized engineered microbial system (imGEM) co-anchoring engineered Pseudomonas
@@ -195,3 +200,47 @@ cultivation_setup:
snippet: the immobilized system exhibited outstanding operational stability, maintaining high degradation
efficiency over 30 days under varying environmental conditions
explanation: Immobilized bioelectrochemical consortium operated over a 30-day period.
+discussions:
+- discussion_id: naphthalene-model-versus-endpoint
+ prompt: What distinguishes the reported electron-transfer model from the treatment endpoints?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ rationale: 'All three nodes and both existing directions remain. The authors electron-transfer model retains its
+ SYNTROPHY classification with PARTIAL evidence bounds: the local enum does not require obligacy. The community
+ removal/mineralization endpoint is distinct from the coupling mechanism. Only the fresh primary abstract was
+ retrieved; unavailable methods are not proof that route-specific controls were absent. Canonical source labels
+ are preserved, not newly certified strain identities. No new genetic designs, optimization details or experimental
+ procedures were added.'
+ attaches_to:
+ - ecological_interactions#Biochar-bridged direct interspecies electron transfer (DIET)
+ - ecological_interactions#Syntrophic naphthalene mineralization circuit
+ - ecological_interactions#Enhanced Naphthalene Removal and Mineralization
+ evidence:
+ - reference: PMID:42139785
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: facilitating direct interspecies electron transfer (DIET) and enhancing extracellular electron transfer
+ (EET)
+ explanation: Supports the authors DIET/EET interpretation, not independent resolution of the electron-transfer
+ route or obligatory mutual dependence.
+ - reference: PMID:42139785
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The resulting bioelectrochemical synergy achieved exceptional naphthalene removal (>98.3%) and mineralization
+ efficiency (89.5%)
+ explanation: Supports the measured removal and mineralization endpoint of the engineered consortium.
+curation_history:
+- timestamp: '2026-10-07T12:54:50Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Qualify the authors electron-transfer model without asserting obligatory syntrophy.; Represent the composite
+ circuit collectively with explicit canonical participants.; Preserve reported removal and mineralization without
+ conflating endpoints with a specific interaction type. Issue #1740; reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml'
+ llm_assisted: true
+- timestamp: '2026-10-07T13:07:39Z'
+ curator: codex
+ action: CORRECT_PRECOMMIT_SYNTROPHY_REVIEW
+ changes: 'Restore the authors qualified SYNTROPHY model on the transfer and circuit nodes; the local enum explicitly
+ does not assert obligacy. Keep the measurement endpoint distinct. Issue #1740; reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml b/kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml
index 74d621a35..fee2c8d44 100644
--- a/kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml
+++ b/kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml
@@ -49,33 +49,10 @@ taxonomy:
Names Sulfitobacter sp. SA11 as a Pseudo-nitzschia symbiont described in
the Amin et al. 2015 study.
ecological_interactions:
-- name: Diatom-Associated Bacterial Consortium Resolution
- description: >
- The Pseudo-nitzschia study decomposed a diatom-associated bacterial
- consortium to identify a Sulfitobacter species that participates in a
- nutrient and signaling exchange with the phytoplankton host.
- interaction_type: NICHE_PARTITIONING
- scope: COMMUNITY_LEVEL
- biological_processes:
- - preferred_term: interspecies interaction
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
- evidence:
- - reference: PMID:26017307
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >
- Here we tease apart a bacterial consortium associated with a globally
- distributed diatom
- explanation: >
- Supports resolving the diatom-associated bacterial consortium into
- interaction mechanisms.
- name: Tryptophan-Supported Sulfitobacter IAA Synthesis
- description: >
- Sulfitobacter synthesizes indole-3-acetic acid using tryptophan supplied
- both by Pseudo-nitzschia and by endogenous bacterial metabolism.
- interaction_type: MUTUALISM
+ description: The primary abstract reports bacterial IAA production using both diatom-derived and endogenous precursor
+ pools. Preserve this biochemical attribution without treating the individual synthesis process as proof of reciprocal
+ fitness benefits.
scope: PAIRWISE
source_taxon:
preferred_term: Sulfitobacter sp. SA11
@@ -111,25 +88,24 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Auxin-Mediated Diatom Cell Division
- description: >
- Bacterial indole-3-acetic acid secretion was the hormone signal that
- promoted Pseudo-nitzschia cell division.
+ description: 'Bacterial indole-3-acetic acid secretion was the hormone signal that promoted Pseudo-nitzschia
+ cell division.
+
+ '
evidence:
- reference: PMID:26017307
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- indole-3-acetic acid, synthesized by the bacterium using both
- diatom-secreted and endogenous tryptophan
- explanation: >
- Supports bacterial IAA biosynthesis from both diatom-secreted and
- endogenous tryptophan.
+ snippet: 'indole-3-acetic acid, synthesized by the bacterium using both diatom-secreted and endogenous tryptophan
+
+ '
+ explanation: 'Supports bacterial IAA biosynthesis from both diatom-secreted and endogenous tryptophan.
+
+ '
- name: Auxin-Mediated Diatom Cell Division
- description: >
- Sulfitobacter-secreted indole-3-acetic acid promoted Pseudo-nitzschia cell
- division, establishing auxin as a growth-promoting bacterial signal in this
- diatom association.
- interaction_type: MUTUALISM
+ description: The source reports that bacterial IAA promotes diatom cell division. Preserve the existing positive
+ signaling finding and its direction, without making the individual response node a claim of reciprocal partner
+ benefit.
scope: PAIRWISE
source_taxon:
preferred_term: Sulfitobacter sp. SA11
@@ -155,18 +131,17 @@ ecological_interactions:
- reference: PMID:26017307
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- a Sulfitobacter species promotes diatom cell division via secretion of
- the hormone indole-3-acetic acid
- explanation: >
- Supports IAA secretion as the Sulfitobacter-mediated cue promoting
- diatom cell division.
+ snippet: 'a Sulfitobacter species promotes diatom cell division via secretion of the hormone indole-3-acetic
+ acid
+
+ '
+ explanation: 'Supports IAA secretion as the Sulfitobacter-mediated cue promoting diatom cell division.
+
+ '
- name: Infochemical Nutrient Exchange
- description: >
- Indole-3-acetic acid and tryptophan functioned as signaling molecules
- within a nutrient exchange that included diatom organosulfur compounds and
- bacterial-excreted ammonia.
- interaction_type: MUTUALISM
+ description: 'The source describes signaling within a broader nutrient exchange between the partners. PARTIAL:
+ the accessible abstract does not independently establish complete exchange fluxes or the necessity of every
+ component for reciprocal fitness.'
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: indole-3-acetic acid
@@ -190,39 +165,22 @@ ecological_interactions:
- reference: PMID:26017307
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- Indole-3-acetic acid and tryptophan serve as signalling molecules that
- are part of a complex exchange of nutrients, including diatom-excreted
- organosulfur molecules and bacterial-excreted ammonia
- explanation: >
- Supports IAA and tryptophan signaling inside a broader nutrient exchange.
-- name: Coastal Sulfitobacter IAA Prevalence
- description: >
- Metabolite and metatranscriptome analyses detected widespread
- indole-3-acetic acid production by Sulfitobacter-related bacteria,
- especially in coastal environments.
- interaction_type: NICHE_PARTITIONING
- scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: indole-3-acetic acid
+ snippet: 'Indole-3-acetic acid and tryptophan serve as signalling molecules that are part of a complex exchange
+ of nutrients, including diatom-excreted organosulfur molecules and bacterial-excreted ammonia
+
+ '
+ explanation: 'Supports IAA and tryptophan signaling inside a broader nutrient exchange.
+
+ '
+ participating_taxa:
+ - preferred_term: Pseudo-nitzschia multiseries
term:
- id: CHEBI:16411
- label: indole-3-acetic acid
- biological_processes:
- - preferred_term: indole-3-acetic acid biosynthetic process
+ id: NCBITaxon:37319
+ label: Pseudo-nitzschia multiseries
+ - preferred_term: Sulfitobacter sp. SA11
term:
- id: GO:0009684
- label: indoleacetic acid biosynthetic process
- evidence:
- - reference: PMID:26017307
- supports: SUPPORT
- evidence_source: OTHER
- snippet: >
- widespread indole-3-acetic acid production by Sulfitobacter-related
- bacteria, particularly in coastal environments
- explanation: >
- Supports environmental prevalence of Sulfitobacter-related bacterial IAA
- production.
+ id: NCBITaxon:1546519
+ label: Sulfitobacter sp. SA11
environmental_factors:
- name: Auxin signaling
value: widespread
@@ -421,7 +379,49 @@ curation_history:
- timestamp: '2026-10-02T06:04:09Z'
curator: codex
action: REPAIR_CAUSAL_GRAPH
- changes: Removed three Pseudo-nitzschia workflow or umbrella-summary edges
- from consortium resolution and auxin/nutrient-exchange nodes to downstream
- mechanistic or environmental-prevalence findings.
+ changes: Removed three Pseudo-nitzschia workflow or umbrella-summary edges from consortium resolution and auxin/nutrient-exchange
+ nodes to downstream mechanistic or environmental-prevalence findings.
+ llm_assisted: true
+- timestamp: '2026-10-07T12:54:50Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve reported bacterial synthesis without claiming individual-process mutualism.; Preserve the reported
+ signaling response and existing causal direction.; Preserve nutrient-exchange interpretation with exact-pair
+ and flux limits. Issue #1741; reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml'
llm_assisted: true
+discussions:
+- discussion_id: diatom-pair-mechanism-versus-environmental-prevalence
+ prompt: Which observations belong to the exact pair and which describe the broader environment?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ rationale: 'The consortium-resolution workflow and broad coastal-prevalence nodes were removed from the pair-specific
+ interaction graph; the environmental observation remains in environmental_factors. The three biological signal/exchange
+ nodes and existing causal direction are retained. The fresh primary abstract and public publisher preview were
+ read, not the full main methods or supplements. No new growth mechanism, toxin-production guidance, cultivation
+ optimization or experimental design was added. Non-graph citation, culture and metal metadata remain #1742.'
+ attaches_to:
+ - ecological_interactions#Tryptophan-Supported Sulfitobacter IAA Synthesis
+ - ecological_interactions#Auxin-Mediated Diatom Cell Division
+ - ecological_interactions#Infochemical Nutrient Exchange
+ evidence:
+ - reference: PMID:26017307
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 'Indole-3-acetic acid and tryptophan serve as signalling molecules that are part of a complex exchange
+ of nutrients, including diatom-excreted organosulfur molecules and bacterial-excreted ammonia
+
+ '
+ explanation: 'Supports IAA and tryptophan signaling inside a broader nutrient exchange.
+
+ '
+ - reference: PMID:26017307
+ supports: SUPPORT
+ evidence_source: OTHER
+ snippet: 'widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, particularly in coastal
+ environments
+
+ '
+ explanation: 'Supports environmental prevalence of Sulfitobacter-related bacterial IAA production.
+
+ '
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 389550f78..eafa1554a 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,34 @@ 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`.
+## Batch90: Degradation, Competition And Diatom Signaling
+
+[Decisions](decisions/20261007-four-records-batch90.yaml),
+[validation](validation-20261007-batch90.json) and
+[self-adversarial review](adversarial-review-20261007-batch90.yaml) account for
+14 original nodes and seven arrows. Twelve biological nodes and all seven
+directions remain. A diatom workflow and a broad environmental-prevalence node
+are removed from the pair-specific graph; the environmental evidence remains.
+Reported degradation, competition and signaling findings are preserved while
+reverse-feeding implications, categorical interaction types and mediation
+claims are bounded to the available evidence.
+
+Adversarial review caught an incorrect obligacy requirement after the initial
+816-test run. The actual schema explicitly does not assert obligacy for
+SYNTROPHY. The two naphthalene mechanism nodes retain that qualified type;
+the measurement endpoint remains distinct. Six append-only history artifacts
+preserve both the initial edits and correction. The initial validation and
+inputs are archived as superseded; the current report is a fresh full rerun,
+including an additional schema-contract regression.
+
+Four exact-system primary abstracts and two attribution abstracts were read.
+No complete primary main text was retrieved; access failures and the public
+publisher-preview limits are recorded. All 921 caches, 456 other records and
+raw non-graph blocks are preserved. Repairs #1738-#1741 await protected-main
+merge; diatom metadata #1742 remains open. No new causal direction, paid Edison
+job, genetic design, harmful-algal optimization or experimental protocol was
+added. Self-review is not independent approval or whole-corpus completion.
+
## Batch89: Removal Assays And Social Spreading
[Decisions](decisions/20261007-four-records-batch89.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261007-batch90.yaml b/reports/causal_graph_review/adversarial-review-20261007-batch90.yaml
new file mode 100644
index 000000000..8f00872c9
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261007-batch90.yaml
@@ -0,0 +1,304 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: f63d0b98e06bd1e35016fcfd826b03721fe28f0b
+scope:
+- kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
+- kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml
+- kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
+- kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
+validation_report: reports/causal_graph_review/validation-20261007-batch90.json
+findings:
+- issue: 1738
+ severity: P2
+ status: addressed_in_this_change
+ finding: Correct the reverse-feeding implication in chloronitrobenzene degradation
+ disposition: Close only after protected-main merge.
+- issue: 1739
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate TPA dominance observations from evidence for competitive mechanisms
+ disposition: Close only after protected-main merge.
+- issue: 1740
+ severity: P2
+ status: addressed_in_this_change
+ finding: Bound the biochar electron-transfer model separately from removal endpoints
+ disposition: Close only after protected-main merge.
+- issue: 1741
+ severity: P2
+ status: addressed_in_this_change
+ finding: Keep the diatom signaling graph distinct from workflow and environmental prevalence
+ disposition: Close only after protected-main merge.
+- issue: 1742
+ severity: P2
+ status: unresolved_non_graph
+ finding: Re-evidence diatom cultivation and metal metadata against the exact SA11 association
+ disposition: Keep OPEN after graph repairs.
+adversarial_checks:
+- Fresh both-root baseline preceded papers. All14originalnodes7arrows have dispositions:12biologicalnodes and all7directions
+ retained; two out-of-scope diatom nodes removed. No new node or direction and no arrow endpoint changes.
+- Chloronitro preserves chemical identification, sequential transformations and reported conditional mineralization.
+ The downstream Rhodococcus process no longer asserts metabolite provision back to Pseudomonas. Both original causal
+ directions remain.
+- Conditional mineralization is not silently downgraded to disappearance. The endpoint alone does not establish
+ product-removal feedback making upstream metabolism favourable, so it is untyped. Local SYNTROPHY does not require
+ obligacy. Full carbon balances were not inspected; unavailable methods do not prove absent controls.
+- TPA retains all three competition nodes and both arrows. Dominance alone is not evidence for resource competition;
+ the source-reported metabolism-loss comparison is added. Positive contact inhibition and relative-kinetics attribution
+ remain; separate effect sizes are not invented.
+- Naphthalene retains the authors DIET/circuit interpretation as PARTIAL SYNTROPHY on the first two nodes, electrochemical
+ and multi-omics findings and separate untyped removal/mineralization endpoints. Specific interspecies route and
+ mediator necessity remain qualified. Collective nodes use canonical participants.
+- Diatom consortium resolution is a workflow, while coastal prevalence is broader environmental evidence already
+ retained outside the pair graph. Removing those nodes does not erase the three signal/exchange nodes or existing
+ positive causal arrow.
+- Individual diatom signal/exchange processes are not categorical reciprocal fitness measurements. Canonical participants
+ are preserved. H3 taxonomic evidence and another-system background citation do not certify the exact SA11 cultivation
+ fields; metadata1742remains open.
+- Four exact-system primary abstracts and two attribution abstracts read. No complete primary main text retrieved.
+ Chloronitro XML500/PMC challenge/OA metadata404 and Nature redirect/subscription preview disclosed. Cached secondary
+ background paragraphs are not independent fresh primary evidence. No figures, supplements or raw data audited.
+- Adversarial schema reading caught an incorrect obligacy premise after the initial816-test pass. That report and
+ tested inputs are archived as superseded with verified digests. Two appended correction histories preserve the
+ original four histories. A schema-contract regression and fresh full validation bind the corrected state.
+- All921caches456otherrecords and raw non-graph blocks preserved. Six append-only histories and eleven focused tests.
+ Two new explicit-participant users, measured legacy census unchanged, all56oldwarnings retained and zero structural
+ defects. No taxonomy or auditor-rule changes.
+- No new genetic designs, resistance-selection details, harmful-algal optimization, toxin guidance or experimental
+ protocols. No Edison dry run or provider submission. Executed gates and deterministic HTML checks are not browser
+ screenshots or generated-model loader certification. Loader1703remains open. Repairs1738-1741await protected-main
+ merge;1742remains open. Self-review is not independent approval or corpus completion.
+verification:
+ combined_regressions: 817 passed in 280.29s (0:04:40)
+ new_regression_tests: 11
+ primary_graph_snippet_proof:
+ graph_quotations: 16
+ discussion_quotations: 8
+ fresh_primary_matches: 24
+ cached_only_matches: 0
+ retained_nodes: 12
+ removed_nodes: 2
+ retained_arrows: 7
+ removed_arrows: 0
+ mechanical_source_endpoint_corrections: 0
+ new_biological_causal_claims: 0
+ primary_main_texts_read: 0
+ exact_system_primary_abstracts_read: 4
+ attribution_abstracts_read: 2
+ cache_changes: 0
+ references: Four full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks.
+ Sixteen graph and eight discussion quotations match independent fresh-primary abstract and cache text. Literal
+ matching is not entailment or full-text certification.
+ snippet_counts_by_record:
+ kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml:
+ MATCH: 22
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml:
+ MATCH: 10
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml:
+ MATCH: 9
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml:
+ MATCH: 10
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ caveat: Both-root recipe executed. Informational exit0 does not certify a clean corpus; four focused snippet
+ gates pass independently.
+ output: "# 8929 evidence snippets scanned across 460 files\n MATCH 8794\n RENDERING 20\n ASSEMBLED\
+ \ 1\n WEAK 0\n MISMATCH 38\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but\
+ \ snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n\
+ \ 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n\
+ \ 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\nuv run python scripts/evidence_snippet_audit.py\
+ \ \n"
+ network:
+ existing_findings_preserved: 56
+ added_findings: {}
+ removed_findings: {}
+ interpretation: All56existing warnings preserved, zero structural defects. No edge endpoint changes; two out-of-scope
+ nodes removed. No taxonomy or auditor-rule changes.
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml: bdcd291bfeb14293712b5b408e7ef8cc396a18317827618ed75fee517b1f9d58
+ tests/test_causal_review_batch90.py: 12dfffa68bd63e815e76f50dd9cb52ac459390f0bf48a0a1da3521134a3a98be
+ tests/test_participating_taxa.py: 89d6e67cd3a8401b2fe96f3e83d2aa5737f6f123cc849a0afdbab40eb25a4942
+ kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml: 2638bb5668d31d6c8a59d616e36777b22d38f03e1fef80dc58fada489628e41e
+ kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml: 6416089a1d115f7834f71f98182476728a7f936f8b544c6551103c712a2bb825
+ kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml: d987d0d184c409b62a9e96034e7dd8f294742b10bc3adefe4617ddd7208c97f8
+ kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml: 1a0fd950b4dc5fbb21331be3995a2fffb05ac8d4e3df772f5008cb88a9b9d4e6
+ reports/causal_graph_review/README.md: 727ecad74acba894907ac59be451da98bb734ae08bf099e7970f1cf9c493cc48
+ unchanged_records: 456
+ unchanged_caches: 921
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: No new node or direction. Existing source-backed arrows retained; non-biological and out-of-scope
+ nodes removed.
+ post_commit_docs_current: Separate publication gate, not preasserted.
+ superseded_precommit_validation:
+ report: /private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/validation-20261007-batch90.json
+ sha256: 313fe985877fc7e3b5bb5a92bc7b68e68d91918954f824213265e7b25f875f18
+ regressions: 816 passed in 296.55s (0:04:56)
+ reason: Adversarial reading of the actual enum shows SYNTROPHY does not assert obligacy. Preserve the authors
+ qualified metabolic-coupling model; classify endpoints by their meaning, not an obsolete obligation requirement.
+ original_logs_verified: true
+ archived_inputs_verified: true
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 396
+ mixed: 126
+ community_level_only: 270
+ taxa: 1523
+ credited_solely_by_the_rule: 1249
+ current:
+ records: 460
+ with_community_level: 396
+ mixed: 126
+ community_level_only: 270
+ taxa: 1523
+ credited_solely_by_the_rule: 1249
+ delta:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ interpretation: Legacy community-level census unchanged; two new explicit-participant users. No canonical taxon
+ or auditor-rule change.
+corpus:
+ records: 460
+ nodes: 1420
+ edges: 584
+ review_status_counts:
+ needs_research: 48
+ pending: 132
+ reviewed: 280
+limitations:
+- Fresh both-root baseline before papers:460records921caches1422nodes584arrows56warnings0structural defects. All14originalnodes7arrows
+ accounted for;12biologicalnodes and all7directions retained. Two out-of-scope diatom nodes removed, with environmental
+ evidence preserved outside the graph.
+- Four fresh exact-system primary abstracts and two attribution abstracts read. No complete fresh primary main text.
+ Chloronitro XML500 after bounded retries, PMC challenge and open-access metadata404. Nature public search-index
+ preview read, with explicit subscription notice; direct publisher redirect failed. No challenges or paywalls bypassed.
+ No figure pixels, supplements or raw data inspected.
+- Chloronitro chemically supported upstream conversion, downstream degradation and conditional mineralization remain.
+ The intermediate-degradation node no longer implies reverse metabolite provision. The endpoint itself does not
+ demonstrate product-removal feedback on upstream metabolism; lack of obligacy is not a reason to reject SYNTROPHY.
+- TPA preserves three competition nodes and both directions, including reported contact inhibition, relative kinetics
+ and metabolism-loss comparison. Dominance is an outcome, not standalone evidence for resource competition. Full
+ controls and separate effect sizes remain uninspected; positive causal findings are not removed.
+- Naphthalene retains the authors SYNTROPHY classification on the PARTIAL electron-transfer/circuit model. The actual
+ enum does not require obligacy. The measured removal/mineralization endpoint is kept distinct from the proposed
+ coupling interaction; route-specific mediation remains qualified.
+- Diatom workflow resolution and broad environmental prevalence are not pair-specific biological interactions. Three
+ signal/exchange nodes and the existing positive signaling arrow remain. Individual processes are not categorical
+ reciprocal fitness measurements. No new harmful-algal growth optimization, toxin guidance or experimental designs
+ were added.
+- The fresh H3 taxonomic abstract is not the exact SA11 study. PMID30228381 is another-system primary whose cached
+ background discussion mentions SA11; only relevant background paragraphs were inspected, not independently fresh
+ main text. Public Nature preview identifies the canonical pair. Non-graph citation, culture and metal claims remain
+ the metadata issue, not silently corrected or certified.
+- 456otherrecords, all921caches and raw non-graph blocks preserved. Two new explicit participant users; legacy community-level
+ census is to be measured. No taxon IDs, taxonomy or auditor rules changed. No new genetic designs, resistance-selection
+ details or optimization protocols.
+- Dedup1006all-state issue titles/bodies with broad aliases; nine matching bodies read and49local ignored/hidden
+ matches found, excluding .git/docs/site/references_cache. Relevant caches separately inspected. Explicit529/573/605read.
+ Matching1091is a general DOI-cache case issue; these graph evidence references use PMIDs. Comments and PRs not
+ exhaustively searched.
+- No new node, direction, Edison dry run or provider submission. Earlier pending and denied spend scopes remain
+ unchanged. Four repair issues close only after protected-main merge; the metadata follow-up remains open. Validation,
+ rendering and publication are subsequent gates, not preasserted. Self-review is not independent approval, generated-model
+ loader certification or corpus completion. Loader1703remains open.
+- Adversarial review caught an obsolete obligacy premise after the initial816-test pass. Corrected before publication,
+ retained initial inputs/results as superseded, appended two additional histories without rewriting the four earlier
+ artifacts, and required a fresh full validation run. A schema-contract regression guards the distinction.
+precommit_adversarial_correction:
+ reason: Adversarial reading of the actual enum shows SYNTROPHY does not assert obligacy. Preserve the authors
+ qualified metabolic-coupling model; classify endpoints by their meaning, not an obsolete obligation requirement.
+ schema_path: src/communitymech/schema/communitymech.yaml
+ schema_sha256: 99079e7712d0c6b5eef0f278822a6b04fdb9a3a55b446e1f73f0752e4e626d04
+ schema_definition: 'Metabolic cooperation in which one partner''s product is another''s substrate, and removing
+ that product is what makes the first partner''s metabolism favourable.
+
+ **Obligacy is not asserted.** This value used to read "Obligate metabolic cooperation", which the corpus''s
+ 135 uses do not honour and which a single record can rarely establish: showing that neither partner grows alone
+ needs a monoculture arm, and where sources have one they often disprove obligacy. CommunityMech:000336 is the
+ worked case - every paper calls that pairing a syntrophy and its seed paper grows both species as monocultures
+ in the same experiment (#752).
+
+ Where the distinction matters, state it in the interaction''s `description` with the evidence for it. METPO:1007200
+ obligate syntrophy interaction and METPO:1007201 facultative syntrophy interaction are proposed in `proposals/metpo_communitymech_interaction_semantics_v1/`
+ so it can eventually be typed rather than narrated.'
+ superseded_validation: /private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/validation-20261007-batch90.json
+ superseded_validation_sha256: 313fe985877fc7e3b5bb5a92bc7b68e68d91918954f824213265e7b25f875f18
+ superseded_regressions: 816 passed in 296.55s (0:04:56)
+ archived_inputs:
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T125451Z-codex-edc25d.yaml
+ : 271a08af4cba3eabb3cf7a342e8e9a281083767ce6c50f24b07a87137cc276f2
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/history/records/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium/2026-10-07T125451Z-codex-55758a.yaml
+ : 8b5c559e995515bca1f98cb6a3e7c8be078de36235b7597948d54cd04127d663
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T125451Z-codex-1ff079.yaml
+ : d175709b5dc8d6f6b60ed8db6e52b5a697c84c3470316f9f97702853cdaf5f74
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/history/records/Pseudonitzschia_Sulfitobacter_Association/2026-10-07T125452Z-codex-a42433.yaml
+ : 5d914980c60f787a52d05932653e4ef7a5d32da0faee8e1fb64ef381b3cd73d8
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
+ : 931c479671d16ea771c7e1a45356e4fefa166a823dbcf1863f184058ae167d07
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml
+ : 6416089a1d115f7834f71f98182476728a7f936f8b544c6551103c712a2bb825
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
+ : 5acea2e42c6ce0d29a2602ce285bb4d8853cedbd5ce3fbef9038f46b78c0410a
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml
+ : 1a0fd950b4dc5fbb21331be3995a2fffb05ac8d4e3df772f5008cb88a9b9d4e6
+ /private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/README.md: 0219db95d1142cee2c9b69a7b845976e83bcebc6a63384120469ae9b4ceb794c
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
+ : 59d039596548e55dbeda8456ae93999e7131f1e3759ba22b3b0b35ddda6aea18
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/validation-20261007-batch90.json
+ : 313fe985877fc7e3b5bb5a92bc7b68e68d91918954f824213265e7b25f875f18
+ /private/tmp/communitymech-batch90/before-syntrophy-correction/tests/test_causal_review_batch90.py: baa964c9086a4a568a2ed2829e1f8bbdb61403f52fa537c87119ab2e23162756
+ /private/tmp/communitymech-batch90/before-syntrophy-correction/tests/test_participating_taxa.py: 89d6e67cd3a8401b2fe96f3e83d2aa5737f6f123cc849a0afdbab40eb25a4942
+ records:
+ - path: kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
+ before_sha256: 931c479671d16ea771c7e1a45356e4fefa166a823dbcf1863f184058ae167d07
+ after_sha256: 2638bb5668d31d6c8a59d616e36777b22d38f03e1fef80dc58fada489628e41e
+ history: history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T130739Z-codex-a070e2.yaml
+ summary: 'Correct the precommit syntrophy rationale: the local enum does not require obligacy; an endpoint alone
+ does not establish product-removal feedback.'
+ - path: kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
+ before_sha256: 5acea2e42c6ce0d29a2602ce285bb4d8853cedbd5ce3fbef9038f46b78c0410a
+ after_sha256: d987d0d184c409b62a9e96034e7dd8f294742b10bc3adefe4617ddd7208c97f8
+ history: history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T130739Z-codex-d6881b.yaml
+ summary: Restore the authors qualified SYNTROPHY model on the transfer and circuit nodes; the local enum explicitly
+ does not assert obligacy. Keep the measurement endpoint distinct.
+issue_rationale_correction:
+ issue: 1740
+ original_sha256: 9a15e63beaaa1ba3c792d904a62963946968e4f7eb3fd3e0d12b2337d4afd76f
+ corrected_sha256: f36150f31e55f3db383554c05a0f3ce670432a5664f56d920b020924a57cbd3f
+ comments:
+ - issue: 1738
+ url: https://github.com/CultureBotAI/CommunityMech/issues/1738#issuecomment-6038701522
+ - issue: 1740
+ url: https://github.com/CultureBotAI/CommunityMech/issues/1740#issuecomment-6038702011
+issue_rationale_correction_sha256: 8fe52cd28c1d024ae6e48fdc38c0798aad6a22190c56cb1343723d072f1731fc
diff --git a/reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml b/reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
new file mode 100644
index 000000000..357475eca
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
@@ -0,0 +1,671 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+source_access:
+- reference: PMID:10049867
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A10049867+AND+SRC%3AMED&format=json&resultType=core
+ accessed_scope: Primary abstract only; full text not available through Europe PMC.
+ fulltext_error: Primary XML request returned HTTP500; no full text retrieved.
+- reference: PMID:42324694
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42324694+AND+SRC%3AMED&format=json&resultType=core
+ accessed_scope: Primary abstract only; full text not available through Europe PMC.
+ fulltext_error: null
+- reference: PMID:42139785
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42139785+AND+SRC%3AMED&format=json&resultType=core
+ accessed_scope: Primary abstract only; full text not available through Europe PMC.
+ fulltext_error: null
+- reference: PMID:26017307
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A26017307+AND+SRC%3AMED&format=json&resultType=core
+ accessed_scope: Primary abstract only; full text not available through Europe PMC.
+ fulltext_error: null
+- reference: PMID:25278561
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A25278561+AND+SRC%3AMED&format=json&resultType=core
+ accessed_scope: Abstract only; attribution reference, not a full-text or primary exact-system review.
+ fulltext_error: null
+- reference: PMID:30228381
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A30228381+AND+SRC%3AMED&format=json&resultType=core
+ accessed_scope: Abstract only; attribution reference, not a full-text or primary exact-system review.
+ fulltext_error: null
+base_commit: f63d0b98e06bd1e35016fcfd826b03721fe28f0b
+baseline_commit: f63d0b98e06bd1e35016fcfd826b03721fe28f0b
+base_tree: 8323cd500b8d327c50030d13c9bfea0dd3f8d903
+pre_source_baseline_sha256: 9bf34b0998d64a7441e0f65c5ef9543df83e9755c4d313f7572d3b67e0f45475
+issues:
+- 1738
+- 1739
+- 1740
+- 1741
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1742
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 1006
+ explicitly_read_issues:
+ - 529
+ - 573
+ - 605
+ ignored_hidden_local_search: true
+ matching_issues:
+ - 1716
+ - 1712
+ - 1664
+ - 1660
+ - 1250
+ - 1091
+ - 1029
+ - 833
+ - 832
+primary_artifacts:
+ /private/tmp/communitymech-batch90/baseline.json: 9bf34b0998d64a7441e0f65c5ef9543df83e9755c4d313f7572d3b67e0f45475
+ /private/tmp/communitymech-batch90/chloronitro-metadata.json: 1a4331e0133148db3885a1406990d6d7f8baa2c41e61bab3eb6a3adf3bb4f6f7
+ /private/tmp/communitymech-batch90/chloronitro-primary.txt: 57c0d96d71b004ca74536d7abc440daa279c384aa6b70dc463031972460cd722
+ /private/tmp/communitymech-batch90/created-issues.json: 69a24faa193aafdc6fd03ad05363291c9f7e20eb8d8a6c6eafb2b5e016cd5273
+ /private/tmp/communitymech-batch90/diatom-metadata.json: 275efc565d9080db643360ea68b5884d0fa0eda95b3b9ef9b942984c10aaa62a
+ /private/tmp/communitymech-batch90/diatom-primary.txt: 85d4adc94376971363158c043f4ec21e5000c192d0076565a3fa19e746a5db75
+ /private/tmp/communitymech-batch90/diatom-secondary-metadata.json: 4090b8e12410080cff01a3e6869b2901fdefc6c6e49add37941c89d9b7db5225
+ /private/tmp/communitymech-batch90/diatom-secondary-primary.txt: e741219f2e52f12603bb6a529abbb6c586a7f4872bc93c1dac8a1678dfc6d929
+ /private/tmp/communitymech-batch90/diatom-taxon-metadata.json: 3013c34cf35bb58bcbb0d049eca9063160ad99ef5481d71eba411a8d8eff6fc9
+ /private/tmp/communitymech-batch90/diatom-taxon-primary.txt: e0e474b216c59e48ec0ed62cc28b318995213071f4f410b0a449ff3d900cee9c
+ /private/tmp/communitymech-batch90/issue-matches-current.json: 670446e6dbbbec064b12effade07a2a9bb55c03081506202dfc3ef6d0ca6da01
+ /private/tmp/communitymech-batch90/issue-matches.json: 998a4ebf253b10811bec9d5a3ac59bee11c23f7e1fcf1f1252d797ba4dd0f05e
+ /private/tmp/communitymech-batch90/issues-current.json: 12cbeb6806f6fb0139af3b5af5803fcca74221dc47e9d6fdd9bbcc4f0ac46fba
+ /private/tmp/communitymech-batch90/issues.json: 721957caeea9b1b327c8e0db5bc32ab8d580c77b83dc4aa475870c7a1f5c37ff
+ /private/tmp/communitymech-batch90/local-matches-current.txt: b32ca05e528862c3dc0eacacdcbf887d51cf4a5425ee173f622885b2a2d330b9
+ /private/tmp/communitymech-batch90/local-matches.txt: b079e9d455348d083398c52b16135b2f5262190e44b47eb614d1743a8bc1ea9d
+ /private/tmp/communitymech-batch90/naphthalene-metadata.json: c4d6850388ef38877fa72ac4aa4af02341d9e901d3ef6420b1a1307e2204d5be
+ /private/tmp/communitymech-batch90/naphthalene-primary.txt: 4dc8f806efa7962c3ba07392d3cba7155ca348a9ce9fb3355b2a937fef192a37
+ /private/tmp/communitymech-batch90/primary-manifest.json: c0ab117a1b13bc6eb5e630888dc695a483f30fb4d81709c44291915f3b0a8f3d
+ /private/tmp/communitymech-batch90/source-access-limits.json: 1bc763eb8b04a7f7a3fc1034ebb89415043a36f8ebef5ddc4329425fbe3dfa2e
+ /private/tmp/communitymech-batch90/tpa-metadata.json: be7394814f2ee19727002e4ff80336da92263ce849341b3b361f2ada023d9bda
+ /private/tmp/communitymech-batch90/tpa-primary.txt: 6a8867182d70aa4b39805f8773811f28bfbba8526972addaaad12b44176a1588
+ references_cache/PMID_10049867.txt: 864e5e8ae2f8db67e4f80181c4b8a34d0d4c2609a695f49b53f18b22155544be
+ references_cache/PMID_25278561.md: 2a6e0578f788ef608228bbbf351021400e26a81292d7242ea8618f558a4ed54d
+ references_cache/PMID_26017307.txt: 73002aeab17f66c3f4335473c65cf2fec08b255b18ec928877f55ad4636af2ec
+ references_cache/PMID_30228381.txt: 5219e0c6d1c1ca3b629ad25df87cd5edd628f613c66311250968515e51d781fc
+ references_cache/PMID_42139785.md: 3dc162fe4c8935f7f5dafa5fddf54d09980e78691ff2a786a9a3e2e4b44accf0
+ references_cache/PMID_42324694.md: c8216f9b203d325e0f2ce7bce97a175613c18d8e41d01373eeb0eb22029de89c
+ /private/tmp/communitymech-batch90/syntrophy-correction.json: 0bf5eaf021429affcb06fe022fb6e9ed022c37072c25f672b21f4f10018e5ba3
+primary_graph_snippet_count: 16
+snippet_checks:
+- record: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+ node: Pseudomonas Partial Chloronitrobenzene Transformation
+ evidence_index: 0
+ reference: PMID:10049867
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/chloronitro-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+ node: Pseudomonas Partial Chloronitrobenzene Transformation
+ evidence_index: 1
+ reference: PMID:10049867
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/chloronitro-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+ node: Rhodococcus Intermediate Degradation
+ evidence_index: 0
+ reference: PMID:10049867
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/chloronitro-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+ node: Rhodococcus Intermediate Degradation
+ evidence_index: 1
+ reference: PMID:10049867
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/chloronitro-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+ node: Coculture Chloronitrobenzene Mineralization
+ evidence_index: 0
+ reference: PMID:10049867
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/chloronitro-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+ node: Coculture Chloronitrobenzene Mineralization
+ evidence_index: 1
+ reference: PMID:10049867
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/chloronitro-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium
+ node: Exploitative competition for terephthalic acid
+ evidence_index: 0
+ reference: PMID:42324694
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/tpa-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium
+ node: Exploitative competition for terephthalic acid
+ evidence_index: 1
+ reference: PMID:42324694
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/tpa-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium
+ node: Interference competition via type VI secretion system
+ evidence_index: 0
+ reference: PMID:42324694
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/tpa-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium
+ node: Pp-TE Dominance During TPA Coculture
+ evidence_index: 0
+ reference: PMID:42324694
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/tpa-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium
+ node: Biochar-bridged direct interspecies electron transfer (DIET)
+ evidence_index: 0
+ reference: PMID:42139785
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/naphthalene-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium
+ node: Syntrophic naphthalene mineralization circuit
+ evidence_index: 0
+ reference: PMID:42139785
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/naphthalene-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium
+ node: Enhanced Naphthalene Removal and Mineralization
+ evidence_index: 0
+ reference: PMID:42139785
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/naphthalene-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudonitzschia_Sulfitobacter_Association
+ node: Tryptophan-Supported Sulfitobacter IAA Synthesis
+ evidence_index: 0
+ reference: PMID:26017307
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/diatom-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudonitzschia_Sulfitobacter_Association
+ node: Auxin-Mediated Diatom Cell Division
+ evidence_index: 0
+ reference: PMID:26017307
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/diatom-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudonitzschia_Sulfitobacter_Association
+ node: Infochemical Nutrient Exchange
+ evidence_index: 0
+ reference: PMID:26017307
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/diatom-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+discussion_snippet_checks:
+- record: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+ node: chloronitro-direction-and-mineralization
+ evidence_index: 0
+ reference: PMID:10049867
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/chloronitro-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture
+ node: chloronitro-direction-and-mineralization
+ evidence_index: 1
+ reference: PMID:10049867
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/chloronitro-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium
+ node: tpa-outcome-versus-competitive-contributions
+ evidence_index: 0
+ reference: PMID:42324694
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/tpa-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium
+ node: tpa-outcome-versus-competitive-contributions
+ evidence_index: 1
+ reference: PMID:42324694
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/tpa-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium
+ node: naphthalene-model-versus-endpoint
+ evidence_index: 0
+ reference: PMID:42139785
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/naphthalene-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium
+ node: naphthalene-model-versus-endpoint
+ evidence_index: 1
+ reference: PMID:42139785
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/naphthalene-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudonitzschia_Sulfitobacter_Association
+ node: diatom-pair-mechanism-versus-environmental-prevalence
+ evidence_index: 0
+ reference: PMID:26017307
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/diatom-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+- record: Pseudonitzschia_Sulfitobacter_Association
+ node: diatom-pair-mechanism-versus-environmental-prevalence
+ evidence_index: 1
+ reference: PMID:26017307
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch90/diatom-primary.txt
+ method: Normalized contiguous match; literal match is not scientific entailment.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: No new node or direction. Existing source-backed arrows retained; non-biological and out-of-scope
+ nodes removed.
+limitations:
+- Fresh both-root baseline before papers:460records921caches1422nodes584arrows56warnings0structural defects. All14originalnodes7arrows
+ accounted for;12biologicalnodes and all7directions retained. Two out-of-scope diatom nodes removed, with environmental
+ evidence preserved outside the graph.
+- Four fresh exact-system primary abstracts and two attribution abstracts read. No complete fresh primary main text.
+ Chloronitro XML500 after bounded retries, PMC challenge and open-access metadata404. Nature public search-index
+ preview read, with explicit subscription notice; direct publisher redirect failed. No challenges or paywalls bypassed.
+ No figure pixels, supplements or raw data inspected.
+- Chloronitro chemically supported upstream conversion, downstream degradation and conditional mineralization remain.
+ The intermediate-degradation node no longer implies reverse metabolite provision. The endpoint itself does not
+ demonstrate product-removal feedback on upstream metabolism; lack of obligacy is not a reason to reject SYNTROPHY.
+- TPA preserves three competition nodes and both directions, including reported contact inhibition, relative kinetics
+ and metabolism-loss comparison. Dominance is an outcome, not standalone evidence for resource competition. Full
+ controls and separate effect sizes remain uninspected; positive causal findings are not removed.
+- Naphthalene retains the authors SYNTROPHY classification on the PARTIAL electron-transfer/circuit model. The actual
+ enum does not require obligacy. The measured removal/mineralization endpoint is kept distinct from the proposed
+ coupling interaction; route-specific mediation remains qualified.
+- Diatom workflow resolution and broad environmental prevalence are not pair-specific biological interactions. Three
+ signal/exchange nodes and the existing positive signaling arrow remain. Individual processes are not categorical
+ reciprocal fitness measurements. No new harmful-algal growth optimization, toxin guidance or experimental designs
+ were added.
+- The fresh H3 taxonomic abstract is not the exact SA11 study. PMID30228381 is another-system primary whose cached
+ background discussion mentions SA11; only relevant background paragraphs were inspected, not independently fresh
+ main text. Public Nature preview identifies the canonical pair. Non-graph citation, culture and metal claims remain
+ the metadata issue, not silently corrected or certified.
+- 456otherrecords, all921caches and raw non-graph blocks preserved. Two new explicit participant users; legacy community-level
+ census is to be measured. No taxon IDs, taxonomy or auditor rules changed. No new genetic designs, resistance-selection
+ details or optimization protocols.
+- Dedup1006all-state issue titles/bodies with broad aliases; nine matching bodies read and49local ignored/hidden
+ matches found, excluding .git/docs/site/references_cache. Relevant caches separately inspected. Explicit529/573/605read.
+ Matching1091is a general DOI-cache case issue; these graph evidence references use PMIDs. Comments and PRs not
+ exhaustively searched.
+- No new node, direction, Edison dry run or provider submission. Earlier pending and denied spend scopes remain
+ unchanged. Four repair issues close only after protected-main merge; the metadata follow-up remains open. Validation,
+ rendering and publication are subsequent gates, not preasserted. Self-review is not independent approval, generated-model
+ loader certification or corpus completion. Loader1703remains open.
+- Adversarial review caught an obsolete obligacy premise after the initial816-test pass. Corrected before publication,
+ retained initial inputs/results as superseded, appended two additional histories without rewriting the four earlier
+ artifacts, and required a fresh full validation run. A schema-contract regression guards the distinction.
+records:
+- path: kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
+ id: CommunityMech:000181
+ original_sha256: 298c55daea0a8c85c2dc73a7193091872b724bd484201d4ca3ee382c861602e7
+ record_sha256: 2638bb5668d31d6c8a59d616e36777b22d38f03e1fef80dc58fada489628e41e
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
+ scope: Whole record and all existing nodes/arrows; not non-graph certification or exhaustive new-mechanism discovery.
+ summary: Preserve chemically supported upstream transformation with transfer limits.; Remove the reverse-feeding
+ implication while retaining downstream degradation.; Preserve conditional mineralization without treating the
+ outcome as evidence of product-removal feedback.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Pseudomonas Partial Chloronitrobenzene Transformation
+ original_node: Pseudomonas Partial Chloronitrobenzene Transformation
+ rationale: Preserve chemically supported upstream transformation with transfer limits.
+ - node: Rhodococcus Intermediate Degradation
+ original_node: Rhodococcus Intermediate Degradation
+ rationale: Remove the reverse-feeding implication while retaining downstream degradation.
+ - node: Coculture Chloronitrobenzene Mineralization
+ original_node: Coculture Chloronitrobenzene Mineralization
+ rationale: Preserve conditional mineralization without treating the outcome as evidence of product-removal feedback.
+ removed_node_decisions: []
+ edges_before:
+ - source: Pseudomonas Partial Chloronitrobenzene Transformation
+ target: Rhodococcus Intermediate Degradation
+ description: 'P. putida HS12 partial reduction and acetylation generate chlorohydroxyacetanilide intermediates
+ that Rhodococcus sp. strain HS51 further degrades in the sequential two-strain pathway.
+
+ '
+ - source: Rhodococcus Intermediate Degradation
+ target: Coculture Chloronitrobenzene Mineralization
+ description: 'Rhodococcus degradation of the Pseudomonas-derived chlorohydroxyacetanilide intermediates completes
+ the sequential pathway needed for 3- and 4-chloronitrobenzene mineralization by the coculture.
+
+ '
+ edges_after:
+ - source: Pseudomonas Partial Chloronitrobenzene Transformation
+ target: Rhodococcus Intermediate Degradation
+ description: 'The reported upstream transformation produces the intermediates that the downstream partner degrades,
+ coupling the two steps. PARTIAL: the accessible abstract does not resolve every transfer or assimilation step.'
+ - source: Rhodococcus Intermediate Degradation
+ target: Coculture Chloronitrobenzene Mineralization
+ description: 'The reported downstream intermediate degradation contributes to the proposed two-strain pathway
+ and conditional coculture mineralization. PARTIAL: the full pathway and carbon-balance measurements were not
+ independently inspected.'
+ retained_edge_decisions:
+ - source: Pseudomonas Partial Chloronitrobenzene Transformation
+ target: Rhodococcus Intermediate Degradation
+ description: 'The reported upstream transformation produces the intermediates that the downstream partner degrades,
+ coupling the two steps. PARTIAL: the accessible abstract does not resolve every transfer or assimilation step.'
+ rationale: Existing source-backed causal direction retained with explicit evidence limits; no edge endpoint
+ changes.
+ - source: Rhodococcus Intermediate Degradation
+ target: Coculture Chloronitrobenzene Mineralization
+ description: 'The reported downstream intermediate degradation contributes to the proposed two-strain pathway
+ and conditional coculture mineralization. PARTIAL: the full pathway and carbon-balance measurements were not
+ independently inspected.'
+ rationale: Existing source-backed causal direction retained with explicit evidence limits; no edge endpoint
+ changes.
+ removed_edge_decisions: []
+ mechanical_edge_source_corrections: []
+ references:
+ - PMID:10049867
+ issues:
+ - 1738
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 2
+ history_files:
+ - history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T125451Z-codex-edc25d.yaml
+ - history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T130739Z-codex-a070e2.yaml
+- path: kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml
+ id: CommunityMech:000289
+ original_sha256: f210209ef928cb79871d6e29901b721878edb7022d9d5c5597b7b9e48f763dd0
+ record_sha256: 6416089a1d115f7834f71f98182476728a7f936f8b544c6551103c712a2bb825
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
+ scope: Whole record and all existing nodes/arrows; not non-graph certification or exhaustive new-mechanism discovery.
+ summary: Add reported metabolic-perturbation evidence rather than treating dominance alone as mechanism.; Preserve
+ reported contact inhibition and relative-kinetics attribution with source-access limits.; Preserve the measured
+ dominance outcome separately from its explanatory mechanisms.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Exploitative competition for terephthalic acid
+ original_node: Exploitative competition for terephthalic acid
+ rationale: Add reported metabolic-perturbation evidence rather than treating dominance alone as mechanism.
+ - node: Interference competition via type VI secretion system
+ original_node: Interference competition via type VI secretion system
+ rationale: Preserve reported contact inhibition and relative-kinetics attribution with source-access limits.
+ - node: Pp-TE Dominance During TPA Coculture
+ original_node: Pp-TE Dominance During TPA Coculture
+ rationale: Preserve the measured dominance outcome separately from its explanatory mechanisms.
+ removed_node_decisions: []
+ edges_before:
+ - source: Exploitative competition for terephthalic acid
+ target: Pp-TE Dominance During TPA Coculture
+ description: 'Competition for terephthalic acid contributes to Pp-TE dominance in the two-member TPA coculture
+ fermentations.
+
+ '
+ - source: Interference competition via type VI secretion system
+ target: Pp-TE Dominance During TPA Coculture
+ description: 'Contact-dependent growth inhibition reinforces Pp-TE dominance over RDK17 in TPA-fed cocultures.
+
+ '
+ edges_after:
+ - source: Exploitative competition for terephthalic acid
+ target: Pp-TE Dominance During TPA Coculture
+ description: 'The source-reported metabolic perturbation supports a contribution of substrate use to dominance,
+ alongside contact inhibition. PARTIAL: their separate effect sizes are not resolved by the accessible abstract.'
+ - source: Interference competition via type VI secretion system
+ target: Pp-TE Dominance During TPA Coculture
+ description: The source reports that contact-dependent impairment of the partner is the main contributor to
+ dominance, alongside metabolic capability and relative kinetics. This preserves the reported causal attribution
+ without independently certifying unreviewed methods.
+ retained_edge_decisions:
+ - source: Exploitative competition for terephthalic acid
+ target: Pp-TE Dominance During TPA Coculture
+ description: 'The source-reported metabolic perturbation supports a contribution of substrate use to dominance,
+ alongside contact inhibition. PARTIAL: their separate effect sizes are not resolved by the accessible abstract.'
+ rationale: Existing source-backed causal direction retained with explicit evidence limits; no edge endpoint
+ changes.
+ - source: Interference competition via type VI secretion system
+ target: Pp-TE Dominance During TPA Coculture
+ description: The source reports that contact-dependent impairment of the partner is the main contributor to
+ dominance, alongside metabolic capability and relative kinetics. This preserves the reported causal attribution
+ without independently certifying unreviewed methods.
+ rationale: Existing source-backed causal direction retained with explicit evidence limits; no edge endpoint
+ changes.
+ removed_edge_decisions: []
+ mechanical_edge_source_corrections: []
+ references:
+ - PMID:42324694
+ issues:
+ - 1739
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium/2026-10-07T125451Z-codex-55758a.yaml
+- path: kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
+ id: CommunityMech:000291
+ original_sha256: ee4c4d20acf4e636663a9d6d0e69237986d15c41018d7992172f8488eab4c209
+ record_sha256: d987d0d184c409b62a9e96034e7dd8f294742b10bc3adefe4617ddd7208c97f8
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
+ scope: Whole record and all existing nodes/arrows; not non-graph certification or exhaustive new-mechanism discovery.
+ summary: Retain the authors qualified syntrophic electron-transfer model without an obligacy requirement.; Represent
+ the composite circuit collectively with explicit canonical participants.; Preserve reported removal and mineralization
+ without conflating endpoints with a specific interaction type.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Biochar-bridged direct interspecies electron transfer (DIET)
+ original_node: Biochar-bridged direct interspecies electron transfer (DIET)
+ rationale: Retain the authors qualified syntrophic electron-transfer model without an obligacy requirement.
+ - node: Syntrophic naphthalene mineralization circuit
+ original_node: Syntrophic naphthalene mineralization circuit
+ rationale: Represent the composite circuit collectively with explicit canonical participants.
+ - node: Enhanced Naphthalene Removal and Mineralization
+ original_node: Enhanced Naphthalene Removal and Mineralization
+ rationale: Preserve reported removal and mineralization without conflating endpoints with a specific interaction
+ type.
+ removed_node_decisions: []
+ edges_before:
+ - source: Biochar-bridged direct interspecies electron transfer (DIET)
+ target: Syntrophic naphthalene mineralization circuit
+ description: Conductive biochar-mediated electron transfer bridges the engineered Pseudomonas bio-anode and
+ Rhodococcus bio-cathode that jointly mineralize naphthalene.
+ - source: Syntrophic naphthalene mineralization circuit
+ target: Enhanced Naphthalene Removal and Mineralization
+ description: 'Biochar-mediated electron flux feeds the Pseudomonas-Rhodococcus syntrophic circuit that removes
+ and mineralizes naphthalene.
+
+ '
+ edges_after:
+ - source: Biochar-bridged direct interspecies electron transfer (DIET)
+ target: Syntrophic naphthalene mineralization circuit
+ description: 'PARTIAL: the reported conductive interface is proposed to couple the partners within the authors
+ degradation-circuit model; route-specific mediation is not independently resolved by the accessible abstract.'
+ - source: Syntrophic naphthalene mineralization circuit
+ target: Enhanced Naphthalene Removal and Mineralization
+ description: 'PARTIAL: the proposed coordinated circuit is offered as an explanation for the reported removal
+ and mineralization endpoints. The abstract does not isolate each mediator from concurrent treatment effects.'
+ retained_edge_decisions:
+ - source: Biochar-bridged direct interspecies electron transfer (DIET)
+ target: Syntrophic naphthalene mineralization circuit
+ description: 'PARTIAL: the reported conductive interface is proposed to couple the partners within the authors
+ degradation-circuit model; route-specific mediation is not independently resolved by the accessible abstract.'
+ rationale: Existing source-backed causal direction retained with explicit evidence limits; no edge endpoint
+ changes.
+ - source: Syntrophic naphthalene mineralization circuit
+ target: Enhanced Naphthalene Removal and Mineralization
+ description: 'PARTIAL: the proposed coordinated circuit is offered as an explanation for the reported removal
+ and mineralization endpoints. The abstract does not isolate each mediator from concurrent treatment effects.'
+ rationale: Existing source-backed causal direction retained with explicit evidence limits; no edge endpoint
+ changes.
+ removed_edge_decisions: []
+ mechanical_edge_source_corrections: []
+ references:
+ - PMID:42139785
+ issues:
+ - 1740
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 2
+ history_files:
+ - history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T125451Z-codex-1ff079.yaml
+ - history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T130739Z-codex-d6881b.yaml
+- path: kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml
+ id: CommunityMech:000056
+ original_sha256: 5726093fb463f13eb9d2806a56352c813b649b4371aa9479cad385779fb97e34
+ record_sha256: 1a0fd950b4dc5fbb21331be3995a2fffb05ac8d4e3df772f5008cb88a9b9d4e6
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
+ scope: Whole record and all existing nodes/arrows; not non-graph certification or exhaustive new-mechanism discovery.
+ summary: Preserve reported bacterial synthesis without claiming individual-process mutualism.; Preserve the reported
+ signaling response and existing causal direction.; Preserve nutrient-exchange interpretation with exact-pair
+ and flux limits.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Tryptophan-Supported Sulfitobacter IAA Synthesis
+ original_node: Tryptophan-Supported Sulfitobacter IAA Synthesis
+ rationale: Preserve reported bacterial synthesis without claiming individual-process mutualism.
+ - node: Auxin-Mediated Diatom Cell Division
+ original_node: Auxin-Mediated Diatom Cell Division
+ rationale: Preserve the reported signaling response and existing causal direction.
+ - node: Infochemical Nutrient Exchange
+ original_node: Infochemical Nutrient Exchange
+ rationale: Preserve nutrient-exchange interpretation with exact-pair and flux limits.
+ removed_node_decisions:
+ - node: Diatom-Associated Bacterial Consortium Resolution
+ rationale: Resolving an associated consortium is an experimental workflow, not a biological interaction or niche
+ partitioning.
+ - node: Coastal Sulfitobacter IAA Prevalence
+ rationale: Broader environmental prevalence is not an exact-pair interaction. The positive environmental observation
+ remains in unchanged environmental_factors and the new scope discussion.
+ edges_before:
+ - source: Tryptophan-Supported Sulfitobacter IAA Synthesis
+ target: Auxin-Mediated Diatom Cell Division
+ description: 'Bacterial indole-3-acetic acid secretion was the hormone signal that promoted Pseudo-nitzschia
+ cell division.
+
+ '
+ edges_after:
+ - source: Tryptophan-Supported Sulfitobacter IAA Synthesis
+ target: Auxin-Mediated Diatom Cell Division
+ description: 'Bacterial indole-3-acetic acid secretion was the hormone signal that promoted Pseudo-nitzschia
+ cell division.
+
+ '
+ retained_edge_decisions:
+ - source: Tryptophan-Supported Sulfitobacter IAA Synthesis
+ target: Auxin-Mediated Diatom Cell Division
+ description: 'Bacterial indole-3-acetic acid secretion was the hormone signal that promoted Pseudo-nitzschia
+ cell division.
+
+ '
+ rationale: Existing source-backed causal direction retained with explicit evidence limits; no edge endpoint
+ changes.
+ removed_edge_decisions: []
+ mechanical_edge_source_corrections: []
+ references:
+ - PMID:26017307
+ issues:
+ - 1741
+ - 1742
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Pseudonitzschia_Sulfitobacter_Association/2026-10-07T125452Z-codex-a42433.yaml
+precommit_adversarial_correction:
+ reason: Adversarial reading of the actual enum shows SYNTROPHY does not assert obligacy. Preserve the authors
+ qualified metabolic-coupling model; classify endpoints by their meaning, not an obsolete obligation requirement.
+ schema_path: src/communitymech/schema/communitymech.yaml
+ schema_sha256: 99079e7712d0c6b5eef0f278822a6b04fdb9a3a55b446e1f73f0752e4e626d04
+ schema_definition: 'Metabolic cooperation in which one partner''s product is another''s substrate, and removing
+ that product is what makes the first partner''s metabolism favourable.
+
+ **Obligacy is not asserted.** This value used to read "Obligate metabolic cooperation", which the corpus''s
+ 135 uses do not honour and which a single record can rarely establish: showing that neither partner grows alone
+ needs a monoculture arm, and where sources have one they often disprove obligacy. CommunityMech:000336 is the
+ worked case - every paper calls that pairing a syntrophy and its seed paper grows both species as monocultures
+ in the same experiment (#752).
+
+ Where the distinction matters, state it in the interaction''s `description` with the evidence for it. METPO:1007200
+ obligate syntrophy interaction and METPO:1007201 facultative syntrophy interaction are proposed in `proposals/metpo_communitymech_interaction_semantics_v1/`
+ so it can eventually be typed rather than narrated.'
+ superseded_validation: /private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/validation-20261007-batch90.json
+ superseded_validation_sha256: 313fe985877fc7e3b5bb5a92bc7b68e68d91918954f824213265e7b25f875f18
+ superseded_regressions: 816 passed in 296.55s (0:04:56)
+ archived_inputs:
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T125451Z-codex-edc25d.yaml
+ : 271a08af4cba3eabb3cf7a342e8e9a281083767ce6c50f24b07a87137cc276f2
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/history/records/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium/2026-10-07T125451Z-codex-55758a.yaml
+ : 8b5c559e995515bca1f98cb6a3e7c8be078de36235b7597948d54cd04127d663
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T125451Z-codex-1ff079.yaml
+ : d175709b5dc8d6f6b60ed8db6e52b5a697c84c3470316f9f97702853cdaf5f74
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/history/records/Pseudonitzschia_Sulfitobacter_Association/2026-10-07T125452Z-codex-a42433.yaml
+ : 5d914980c60f787a52d05932653e4ef7a5d32da0faee8e1fb64ef381b3cd73d8
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
+ : 931c479671d16ea771c7e1a45356e4fefa166a823dbcf1863f184058ae167d07
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml
+ : 6416089a1d115f7834f71f98182476728a7f936f8b544c6551103c712a2bb825
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
+ : 5acea2e42c6ce0d29a2602ce285bb4d8853cedbd5ce3fbef9038f46b78c0410a
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml
+ : 1a0fd950b4dc5fbb21331be3995a2fffb05ac8d4e3df772f5008cb88a9b9d4e6
+ /private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/README.md: 0219db95d1142cee2c9b69a7b845976e83bcebc6a63384120469ae9b4ceb794c
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml
+ : 59d039596548e55dbeda8456ae93999e7131f1e3759ba22b3b0b35ddda6aea18
+ ? /private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/validation-20261007-batch90.json
+ : 313fe985877fc7e3b5bb5a92bc7b68e68d91918954f824213265e7b25f875f18
+ /private/tmp/communitymech-batch90/before-syntrophy-correction/tests/test_causal_review_batch90.py: baa964c9086a4a568a2ed2829e1f8bbdb61403f52fa537c87119ab2e23162756
+ /private/tmp/communitymech-batch90/before-syntrophy-correction/tests/test_participating_taxa.py: 89d6e67cd3a8401b2fe96f3e83d2aa5737f6f123cc849a0afdbab40eb25a4942
+ records:
+ - path: kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml
+ before_sha256: 931c479671d16ea771c7e1a45356e4fefa166a823dbcf1863f184058ae167d07
+ after_sha256: 2638bb5668d31d6c8a59d616e36777b22d38f03e1fef80dc58fada489628e41e
+ history: history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T130739Z-codex-a070e2.yaml
+ summary: 'Correct the precommit syntrophy rationale: the local enum does not require obligacy; an endpoint alone
+ does not establish product-removal feedback.'
+ - path: kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml
+ before_sha256: 5acea2e42c6ce0d29a2602ce285bb4d8853cedbd5ce3fbef9038f46b78c0410a
+ after_sha256: d987d0d184c409b62a9e96034e7dd8f294742b10bc3adefe4617ddd7208c97f8
+ history: history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T130739Z-codex-d6881b.yaml
+ summary: Restore the authors qualified SYNTROPHY model on the transfer and circuit nodes; the local enum explicitly
+ does not assert obligacy. Keep the measurement endpoint distinct.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 9cab4d3a1..266afdf4f 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -324,10 +324,10 @@ kb/communities/Pseudomonas_Bacillus_Waxy_Oil_Biodegradation_Consortium.yaml Comm
kb/communities/Pseudomonas_Klebsiella_Alcaligenes_FeII_Nitrogen_Removal_SynCom.yaml CommunityMech:000372 0e4ab9a02b384bc08912fba28e9873d6c98d408ebd7aa68187adbc423a7b4c38 1 0 55.0 reports/causal_graph_review/decisions/20261007-four-records-batch89.yaml reviewed
kb/communities/Pseudomonas_Paracoccus_Bifenthrin_Degradation_Consortium.yaml CommunityMech:000331 84251088dd9fe5c30bdab428f7edf3bba20a00b5433b232ac867658eb189d9ce 3 2 93.3 reports/causal_graph_review/decisions/20261007-four-records-batch89.yaml reviewed
kb/communities/Pseudomonas_Pedobacter_Social_Spreading_Coculture.yaml CommunityMech:000161 0b23d93e9c3dee9108cc63022eee2c241c9df15ea94840600a6d44d4a3f2f0f8 3 2 90.0 reports/causal_graph_review/decisions/20261007-four-records-batch89.yaml reviewed
-kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml CommunityMech:000181 298c55daea0a8c85c2dc73a7193091872b724bd484201d4ca3ee382c861602e7 3 2 100.0 pending
-kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml CommunityMech:000289 f210209ef928cb79871d6e29901b721878edb7022d9d5c5597b7b9e48f763dd0 3 2 100.0 pending
-kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml CommunityMech:000291 ee4c4d20acf4e636663a9d6d0e69237986d15c41018d7992172f8488eab4c209 3 2 100.0 pending
-kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml CommunityMech:000056 5726093fb463f13eb9d2806a56352c813b649b4371aa9479cad385779fb97e34 5 1 90.0 pending
+kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml CommunityMech:000181 2638bb5668d31d6c8a59d616e36777b22d38f03e1fef80dc58fada489628e41e 3 2 93.3 reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml reviewed
+kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml CommunityMech:000289 6416089a1d115f7834f71f98182476728a7f936f8b544c6551103c712a2bb825 3 2 100.0 reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml reviewed
+kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml CommunityMech:000291 d987d0d184c409b62a9e96034e7dd8f294742b10bc3adefe4617ddd7208c97f8 3 2 96.7 reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml reviewed
+kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml CommunityMech:000056 1a0fd950b4dc5fbb21331be3995a2fffb05ac8d4e3df772f5008cb88a9b9d4e6 3 1 80.0 reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml reviewed
kb/communities/Puer_FloralFruity_Fungal_SynCom.yaml CommunityMech:000430 ce86bf2668f811e616cd1feef671d7580920303cc0714a82a6cce5ec7c7bec97 1 0 55.0 pending
kb/communities/QY2S1_Dehalogenimonas_BFR_Bioremediation_Consortium.yaml CommunityMech:000424 1c3034feff5fe4328d79ca67a2811c340fca4c297b1bdaf32f609a04a0cebda0 1 0 65.0 pending
kb/communities/Quinoa_SCDY1_Salt_Stress_SynCom.yaml CommunityMech:000459 d1af81a5ffedb3dcc2ffeb32271eb3d66282f82db96b85335e21fdc449b90aac 1 0 60.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 2cebcafc7..4734d87ed 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": 1422,
+ "nodes": 1420,
"edges": 584,
"records_without_nodes": 8,
"records_without_edges": 173,
"review_status_counts": {
"needs_research": 48,
- "pending": 136,
- "reviewed": 276
+ "pending": 132,
+ "reviewed": 280
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261007-batch90.json b/reports/causal_graph_review/validation-20261007-batch90.json
new file mode 100644
index 000000000..59b215bf2
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261007-batch90.json
@@ -0,0 +1,1120 @@
+{
+ "base_commit": "f63d0b98e06bd1e35016fcfd826b03721fe28f0b",
+ "scope": [
+ "kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml",
+ "kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml",
+ "kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml",
+ "kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-strict.tsv",
+ "kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-strict.log",
+ "log_sha256": "e6f9374e78065633f68d866324a81f559b164b8b966b2c0a4300c43611a0fbcf",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch90/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-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-references.log",
+ "log_sha256": "715999d7a98167c8cc5e98398ed42c49de97e4442dd1182c9870ca3a992416e5",
+ "output_tail": "Validating kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-snippets.log",
+ "log_sha256": "96a23c88588d68e990af5d62f9c27df12879566b4125e7703a275c3bfa7adcd7",
+ "output_tail": "# 22 evidence snippets scanned across 1 files\n MATCH 22\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-rank.log",
+ "log_sha256": "074cd530a081860766fa6d79388bfbb5c6334ade016bd05fc5e2c6af277d141f",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000181\",\n \"name\": \"Pseudomonas-Rhodococcus Chloronitrobenzene Coculture\",\n \"score\": 93.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T125451Z-codex-edc25d.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-history-1",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T130739Z-codex-a070e2.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture-history-1.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch90/v2-Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-strict.tsv",
+ "kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-strict.log",
+ "log_sha256": "b6beb748d106af1d012e95a2a4cdcac6d5a40f9330c2ed26e614d44bad1575ea",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch90/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-batch90/v2-Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-references.log",
+ "log_sha256": "de599f8795d6e68c219adf00cc931e8e1d0f4d36da889ce5c004941c469adc09",
+ "output_tail": "Validating kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-snippets.log",
+ "log_sha256": "1835af07ebf0373785ca2d25de18c6984a3cbcfdec0d2610f1d8437504408710",
+ "output_tail": "# 10 evidence snippets scanned across 1 files\n MATCH 10\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-rank.log",
+ "log_sha256": "3cb7721d91efb108291da9a9260dd6d10909f5b847414a4aa3d92181a7b05fb9",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000289\",\n \"name\": \"Pseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium\",\n \"score\": 100.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [],\n \"path\": \"kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium/2026-10-07T125451Z-codex-55758a.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-strict.tsv",
+ "kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-strict.log",
+ "log_sha256": "6e8922002cf39eea96266c1ebfa9a1beedc74b5b42b1bc0cf908a695579601a5",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch90/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-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-references.log",
+ "log_sha256": "709787a511463ba1fcfa973b68ac16c3cba814ed0684c2254b381190c916cb77",
+ "output_tail": "Validating kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-snippets.log",
+ "log_sha256": "32e79f5bf36e5c97f219c301b9924d6a9da1ff1bf07e2b076f93f0d0ee74a358",
+ "output_tail": "# 9 evidence snippets scanned across 1 files\n MATCH 9\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-rank.log",
+ "log_sha256": "417824e038c6f182ea9ad5da235a274e30b7c2711b92198fb0ca2726ee74a5a8",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000291\",\n \"name\": \"Pseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium\",\n \"score\": 96.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T125451Z-codex-1ff079.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-history-1",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T130739Z-codex-d6881b.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium-history-1.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pseudonitzschia_Sulfitobacter_Association-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudonitzschia_Sulfitobacter_Association-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Pseudonitzschia_Sulfitobacter_Association-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch90/v2-Pseudonitzschia_Sulfitobacter_Association-strict.tsv",
+ "kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudonitzschia_Sulfitobacter_Association-strict.log",
+ "log_sha256": "9a1941588d65a1fe330c6378153d9fe3e5cbea22d4c9e5930bc5991e6d19cf76",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch90/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-batch90/v2-Pseudonitzschia_Sulfitobacter_Association-strict.tsv\n"
+ },
+ {
+ "check": "Pseudonitzschia_Sulfitobacter_Association-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudonitzschia_Sulfitobacter_Association-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Pseudonitzschia_Sulfitobacter_Association-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudonitzschia_Sulfitobacter_Association-references.log",
+ "log_sha256": "944243207c11e3c4fd0cd4b698903661476691a0dbfc49f82a50ee3aba43cf37",
+ "output_tail": "Validating kb/communities/Pseudonitzschia_Sulfitobacter_Association.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/Pseudonitzschia_Sulfitobacter_Association.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": "Pseudonitzschia_Sulfitobacter_Association-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudonitzschia_Sulfitobacter_Association-snippets.log",
+ "log_sha256": "1835af07ebf0373785ca2d25de18c6984a3cbcfdec0d2610f1d8437504408710",
+ "output_tail": "# 10 evidence snippets scanned across 1 files\n MATCH 10\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Pseudonitzschia_Sulfitobacter_Association-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudonitzschia_Sulfitobacter_Association-rank.log",
+ "log_sha256": "367ca3ed65189e30c1b7533f0f4d40293275dfc10a6ae9456dee0117a7320f03",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000056\",\n \"name\": \"Pseudo-nitzschia-Sulfitobacter Marine Association\",\n \"score\": 80.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Pseudonitzschia_Sulfitobacter_Association-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Pseudonitzschia_Sulfitobacter_Association/2026-10-07T125452Z-codex-a42433.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-Pseudonitzschia_Sulfitobacter_Association-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-batch90/v2-inventory.log",
+ "log_sha256": "beb676def27914d03e3c57f8cd243729b37ac50f1c39d0da197815fea5122264",
+ "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\": 1420,\n \"edges\": 584,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 173,\n \"review_status_counts\": {\n \"needs_research\": 48,\n \"pending\": 132,\n \"reviewed\": 280\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-batch90/v2-network.log",
+ "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+ "output_tail": " \"total_genomes\": 17191,\n \"is_reclassified\": false,\n \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n },\n \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"mexZ\"\n },\n \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n \"evidence\": [\n {\n \"reference\": \"PMID:42153623\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-just-network-json.log",
+ "log_sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-rank-all.log",
+ "log_sha256": "132ee89400717a2ccf119304af6536d19f8108d7b98bd7bcb313da0f92805faa",
+ "output_tail": "ities/Soybean_N_Fixation_sfSynCom.yaml\tCommunityMech:000064\tSoybean N-Fixation Simplified SynCom\t4\t4\t0\t3\t2\t3\t\t0\t0\n402\t100.0\tkb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml\tCommunityMech:000267\tSphingobium-Rhodococcus Lignin-Dimer Valorization Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n403\t100.0\tkb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml\tCommunityMech:000326\tStaphylococcus-Candida Context-Dependent Biofilm Coculture\t2\t2\t0\t6\t2\t13\t\t0\t0\n404\t100.0\tkb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml\tCommunityMech:000254\tStordalen Mire Methylotrophic Methanogenesis Community\t3\t3\t0\t4\t4\t9\t\t0\t0\n405\t100.0\tkb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml\tCommunityMech:000335\tStreptomyces A2-A5-A11-M7 Pesticide-Bioremediation Consortium\t4\t4\t0\t4\t2\t5\t\t0\t0\n406\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t5\t2\t5\t\t0\t0\n407\t100.0\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t4\t\t0\t0\n408\t100.0\tkb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml\tCommunityMech:000222\tSulfide Spring Autotrophic CPR-Hosting Biofilm\t3\t3\t0\t3\t2\t4\t\t0\t0\n409\t100.0\tkb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml\tCommunityMech:000127\tSynComBac10 Chicken Intestinal SynCom\t3\t3\t0\t3\t2\t3\t\t0\t0\n410\t100.0\tkb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\tCommunityMech:000314\tSynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community\t5\t5\t0\t3\t2\t3\t\t0\t0\n411\t100.0\tkb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\tCommunityMech:000278\tSynCom BsBv Cigar Tobacco Leaf Fermentation\t2\t2\t0\t3\t2\t3\t\t0\t0\n412\t100.0\tkb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\tCommunityMech:000285\tSynCom + Chlorella sorokiniana Biogas-slurry Coupling System\t2\t2\t0\t5\t3\t5\t\t0\t0\n413\t100.0\tkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\tCommunityMech:000302\tSynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\t2\t2\t0\t3\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n417\t100.0\tkb/communities/Synechococcus_Bacillus_SPC.yaml\tCommunityMech:000065\tSynechococcus-Bacillus Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n418\t100.0\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n419\t100.0\tkb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\tCommunityMech:000198\tSynechococcus-Halomonas Light-Driven PHB Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\tCommunityMech:000167\tSynechococcus-Pseudomonas Phototrophic PHA and DNT Coculture\t2\t2\t0\t4\t2\t8\t\t0\t0\n421\t100.0\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n422\t100.0\tkb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\tCommunityMech:000211\tSynechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n424\t100.0\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t8\t\t0\t0\n425\t100.0\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t5\t\t0\t0\n426\t100.0\tkb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml\tCommunityMech:000189\tSyntrophomonas-Methanococcus Butyrate Growth Coordination Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n427\t100.0\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n428\t100.0\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\t\t0\t0\n429\t100.0\tkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml\tCommunityMech:000187\tSyntrophus-Methanospirillum Gentianae Benzoate Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n431\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n432\t100.0\tkb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\tCommunityMech:000100\tTeosinte-Derived Maize Biofertilizer SynCom7\t4\t4\t0\t6\t2\t12\t\t0\t0\n433\t100.0\tkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml\tCommunityMech:000259\tThalassiosira-Marinobacter Marine Snow Coculture\t2\t2\t0\t4\t2\t10\t\t0\t0\n434\t100.0\tkb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml\tCommunityMech:000162\tThalassiosira-Ruegeria Phycosphere Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n435\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n436\t100.0\tkb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\tCommunityMech:000282\tThermophilic Lignocellulose-degrading Composting SynCom\t5\t5\t0\t3\t2\t3\t\t0\t0\n437\t100.0\tkb/communities/Thermophilic_Pyrite_QS_Consortium.yaml\tCommunityMech:000073\tThermophilic Pyrite Quorum Sensing Consortium\t3\t3\t0\t6\t2\t14\t\t0\t0\n438\t100.0\tkb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\tCommunityMech:000186\tThermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\t2\t2\t0\t3\t2\t8\t\t0\t0\n439\t100.0\tkb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml\tCommunityMech:000239\tThiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community\t3\t3\t0\t3\t2\t3\t\t0\t0\n440\t100.0\tkb/communities/Tinto_River_Iron_Cycling_Community.yaml\tCommunityMech:000074\tTinto River Iron Cycling Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-render.log",
+ "log_sha256": "293aa0b73490c12a0a15c29d431d6736c1b0e5012ed2e8108eb5aa8c17536f94",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch90/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch90/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch90/docs/index.html\n"
+ },
+ {
+ "check": "render-repeat",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-render-repeat.log",
+ "log_sha256": "293aa0b73490c12a0a15c29d431d6736c1b0e5012ed2e8108eb5aa8c17536f94",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch90/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch90/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch90/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch90/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-batch89')),('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-batch90/v2-connectivity-survey.log",
+ "log_sha256": "0a3e2264d8517443edbaf49c24795268ac88303e6a1ac2a60b435487f48e5c07",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 396, \"mixed\": 126, \"community_level_only\": 270, \"taxa\": 1523, \"credited_solely_by_the_rule\": 1249}, \"current\": {\"records\": 460, \"with_community_level\": 396, \"mixed\": 126, \"community_level_only\": 270, \"taxa\": 1523, \"credited_solely_by_the_rule\": 1249}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_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-batch90/v2-regressions.log",
+ "log_sha256": "7b9bb1c1e1bd83b9e81f78abc38de93338d489f1a5fa6bd58474f48c942d7ff6",
+ "output_tail": "........................................................................ [ 8%]\n........................................................................ [ 17%]\n........................................................................ [ 26%]\n........................................................................ [ 35%]\n........................................................................ [ 44%]\n........................................................................ [ 52%]\n........................................................................ [ 61%]\n........................................................................ [ 70%]\n........................................................................ [ 79%]\n........................................................................ [ 88%]\n........................................................................ [ 96%]\n......................... [100%]\n817 passed in 280.29s (0:04:40)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-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_batch90.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/v2-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-batch90/v2-diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ },
+ {
+ "check": "primary-graph-proof",
+ "command": [
+ "in-process normalized per-evidence source checks in finalize.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/primary-graph-proof.log",
+ "log_sha256": "7e911a325969e4523cc87422ef659f5e2bfeb16677e5fe9ea411ba496f2674bf",
+ "output_tail": "{\n \"graph_quotations\": 16,\n \"discussion_quotations\": 8,\n \"fresh_primary_matches\": 24,\n \"cached_only_matches\": 0,\n \"retained_nodes\": 12,\n \"removed_nodes\": 2,\n \"retained_arrows\": 7,\n \"removed_arrows\": 0,\n \"mechanical_source_endpoint_corrections\": 0,\n \"new_biological_causal_claims\": 0,\n \"primary_main_texts_read\": 0,\n \"exact_system_primary_abstracts_read\": 4,\n \"attribution_abstracts_read\": 2,\n \"cache_changes\": 0\n}\n"
+ },
+ {
+ "check": "focused-final",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch90.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/focused-final.log",
+ "log_sha256": "7d56aa14837fa0f9abef1041bd4f8231442681774bfd29e2c4e2d43c8907e51b",
+ "output_tail": "........... [100%]\n11 passed in 1.88s\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch90/audit-snippets-all.log",
+ "log_sha256": "e29b60b478ba1baba9fedf26e58ec8a06bd38a16d431540aae41a30ec7df6190",
+ "output_tail": "# 8929 evidence snippets scanned across 460 files\n MATCH 8794\n RENDERING 20\n ASSEMBLED 1\n WEAK 0\n MISMATCH 38\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ }
+ ],
+ "limitations": [
+ "Fresh both-root baseline before papers:460records921caches1422nodes584arrows56warnings0structural defects. All14originalnodes7arrows accounted for;12biologicalnodes and all7directions retained. Two out-of-scope diatom nodes removed, with environmental evidence preserved outside the graph.",
+ "Four fresh exact-system primary abstracts and two attribution abstracts read. No complete fresh primary main text. Chloronitro XML500 after bounded retries, PMC challenge and open-access metadata404. Nature public search-index preview read, with explicit subscription notice; direct publisher redirect failed. No challenges or paywalls bypassed. No figure pixels, supplements or raw data inspected.",
+ "Chloronitro chemically supported upstream conversion, downstream degradation and conditional mineralization remain. The intermediate-degradation node no longer implies reverse metabolite provision. The endpoint itself does not demonstrate product-removal feedback on upstream metabolism; lack of obligacy is not a reason to reject SYNTROPHY.",
+ "TPA preserves three competition nodes and both directions, including reported contact inhibition, relative kinetics and metabolism-loss comparison. Dominance is an outcome, not standalone evidence for resource competition. Full controls and separate effect sizes remain uninspected; positive causal findings are not removed.",
+ "Naphthalene retains the authors SYNTROPHY classification on the PARTIAL electron-transfer/circuit model. The actual enum does not require obligacy. The measured removal/mineralization endpoint is kept distinct from the proposed coupling interaction; route-specific mediation remains qualified.",
+ "Diatom workflow resolution and broad environmental prevalence are not pair-specific biological interactions. Three signal/exchange nodes and the existing positive signaling arrow remain. Individual processes are not categorical reciprocal fitness measurements. No new harmful-algal growth optimization, toxin guidance or experimental designs were added.",
+ "The fresh H3 taxonomic abstract is not the exact SA11 study. PMID30228381 is another-system primary whose cached background discussion mentions SA11; only relevant background paragraphs were inspected, not independently fresh main text. Public Nature preview identifies the canonical pair. Non-graph citation, culture and metal claims remain the metadata issue, not silently corrected or certified.",
+ "456otherrecords, all921caches and raw non-graph blocks preserved. Two new explicit participant users; legacy community-level census is to be measured. No taxon IDs, taxonomy or auditor rules changed. No new genetic designs, resistance-selection details or optimization protocols.",
+ "Dedup1006all-state issue titles/bodies with broad aliases; nine matching bodies read and49local ignored/hidden matches found, excluding .git/docs/site/references_cache. Relevant caches separately inspected. Explicit529/573/605read. Matching1091is a general DOI-cache case issue; these graph evidence references use PMIDs. Comments and PRs not exhaustively searched.",
+ "No new node, direction, Edison dry run or provider submission. Earlier pending and denied spend scopes remain unchanged. Four repair issues close only after protected-main merge; the metadata follow-up remains open. Validation, rendering and publication are subsequent gates, not preasserted. Self-review is not independent approval, generated-model loader certification or corpus completion. Loader1703remains open.",
+ "Adversarial review caught an obsolete obligacy premise after the initial816-test pass. Corrected before publication, retained initial inputs/results as superseded, appended two additional histories without rewriting the four earlier artifacts, and required a fresh full validation run. A schema-contract regression guards the distinction.",
+ "Exact HTML-description parser and repeat-render checks, not browser screenshots. Post-commit docs-current is separate."
+ ],
+ "superseded_precommit_validation": {
+ "report": "/private/tmp/communitymech-batch90/before-syntrophy-correction/reports/causal_graph_review/validation-20261007-batch90.json",
+ "sha256": "313fe985877fc7e3b5bb5a92bc7b68e68d91918954f824213265e7b25f875f18",
+ "regressions": "816 passed in 296.55s (0:04:56)",
+ "reason": "Adversarial reading of the actual enum shows SYNTROPHY does not assert obligacy. Preserve the authors qualified metabolic-coupling model; classify endpoints by their meaning, not an obsolete obligation requirement.",
+ "original_logs_verified": true,
+ "archived_inputs_verified": true
+ },
+ "snippet_counts_by_record": {
+ "kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml": {
+ "MATCH": 22,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml": {
+ "MATCH": 10,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml": {
+ "MATCH": 9,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml": {
+ "MATCH": 10,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 48,
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 921,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [],
+ "repair_scope": "No new node or direction. Existing source-backed arrows retained; non-biological and out-of-scope nodes removed."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch90/baseline.json": "9bf34b0998d64a7441e0f65c5ef9543df83e9755c4d313f7572d3b67e0f45475",
+ "/private/tmp/communitymech-batch90/chloronitro-metadata.json": "1a4331e0133148db3885a1406990d6d7f8baa2c41e61bab3eb6a3adf3bb4f6f7",
+ "/private/tmp/communitymech-batch90/chloronitro-primary.txt": "57c0d96d71b004ca74536d7abc440daa279c384aa6b70dc463031972460cd722",
+ "/private/tmp/communitymech-batch90/created-issues.json": "69a24faa193aafdc6fd03ad05363291c9f7e20eb8d8a6c6eafb2b5e016cd5273",
+ "/private/tmp/communitymech-batch90/diatom-metadata.json": "275efc565d9080db643360ea68b5884d0fa0eda95b3b9ef9b942984c10aaa62a",
+ "/private/tmp/communitymech-batch90/diatom-primary.txt": "85d4adc94376971363158c043f4ec21e5000c192d0076565a3fa19e746a5db75",
+ "/private/tmp/communitymech-batch90/diatom-secondary-metadata.json": "4090b8e12410080cff01a3e6869b2901fdefc6c6e49add37941c89d9b7db5225",
+ "/private/tmp/communitymech-batch90/diatom-secondary-primary.txt": "e741219f2e52f12603bb6a529abbb6c586a7f4872bc93c1dac8a1678dfc6d929",
+ "/private/tmp/communitymech-batch90/diatom-taxon-metadata.json": "3013c34cf35bb58bcbb0d049eca9063160ad99ef5481d71eba411a8d8eff6fc9",
+ "/private/tmp/communitymech-batch90/diatom-taxon-primary.txt": "e0e474b216c59e48ec0ed62cc28b318995213071f4f410b0a449ff3d900cee9c",
+ "/private/tmp/communitymech-batch90/issue-matches-current.json": "670446e6dbbbec064b12effade07a2a9bb55c03081506202dfc3ef6d0ca6da01",
+ "/private/tmp/communitymech-batch90/issue-matches.json": "998a4ebf253b10811bec9d5a3ac59bee11c23f7e1fcf1f1252d797ba4dd0f05e",
+ "/private/tmp/communitymech-batch90/issues-current.json": "12cbeb6806f6fb0139af3b5af5803fcca74221dc47e9d6fdd9bbcc4f0ac46fba",
+ "/private/tmp/communitymech-batch90/issues.json": "721957caeea9b1b327c8e0db5bc32ab8d580c77b83dc4aa475870c7a1f5c37ff",
+ "/private/tmp/communitymech-batch90/local-matches-current.txt": "b32ca05e528862c3dc0eacacdcbf887d51cf4a5425ee173f622885b2a2d330b9",
+ "/private/tmp/communitymech-batch90/local-matches.txt": "b079e9d455348d083398c52b16135b2f5262190e44b47eb614d1743a8bc1ea9d",
+ "/private/tmp/communitymech-batch90/naphthalene-metadata.json": "c4d6850388ef38877fa72ac4aa4af02341d9e901d3ef6420b1a1307e2204d5be",
+ "/private/tmp/communitymech-batch90/naphthalene-primary.txt": "4dc8f806efa7962c3ba07392d3cba7155ca348a9ce9fb3355b2a937fef192a37",
+ "/private/tmp/communitymech-batch90/primary-manifest.json": "c0ab117a1b13bc6eb5e630888dc695a483f30fb4d81709c44291915f3b0a8f3d",
+ "/private/tmp/communitymech-batch90/source-access-limits.json": "1bc763eb8b04a7f7a3fc1034ebb89415043a36f8ebef5ddc4329425fbe3dfa2e",
+ "/private/tmp/communitymech-batch90/tpa-metadata.json": "be7394814f2ee19727002e4ff80336da92263ce849341b3b361f2ada023d9bda",
+ "/private/tmp/communitymech-batch90/tpa-primary.txt": "6a8867182d70aa4b39805f8773811f28bfbba8526972addaaad12b44176a1588",
+ "references_cache/PMID_10049867.txt": "864e5e8ae2f8db67e4f80181c4b8a34d0d4c2609a695f49b53f18b22155544be",
+ "references_cache/PMID_25278561.md": "2a6e0578f788ef608228bbbf351021400e26a81292d7242ea8618f558a4ed54d",
+ "references_cache/PMID_26017307.txt": "73002aeab17f66c3f4335473c65cf2fec08b255b18ec928877f55ad4636af2ec",
+ "references_cache/PMID_30228381.txt": "5219e0c6d1c1ca3b629ad25df87cd5edd628f613c66311250968515e51d781fc",
+ "references_cache/PMID_42139785.md": "3dc162fe4c8935f7f5dafa5fddf54d09980e78691ff2a786a9a3e2e4b44accf0",
+ "references_cache/PMID_42324694.md": "c8216f9b203d325e0f2ce7bce97a175613c18d8e41d01373eeb0eb22029de89c",
+ "/private/tmp/communitymech-batch90/syntrophy-correction.json": "0bf5eaf021429affcb06fe022fb6e9ed022c37072c25f672b21f4f10018e5ba3"
+ },
+ "network_delta": {
+ "existing_findings_preserved": 56,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "All56existing warnings preserved, zero structural defects. No edge endpoint changes; two out-of-scope nodes removed. No taxonomy or auditor-rule changes."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1406,
+ "arrows": 576
+ },
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 396,
+ "mixed": 126,
+ "community_level_only": 270,
+ "taxa": 1523,
+ "credited_solely_by_the_rule": 1249
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 396,
+ "mixed": 126,
+ "community_level_only": 270,
+ "taxa": 1523,
+ "credited_solely_by_the_rule": 1249
+ }
+ },
+ "delta": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "interpretation": "Legacy community-level census unchanged; two new explicit-participant users. No canonical taxon or auditor-rule change."
+ },
+ "network_warning_count": 56,
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1420,
+ "edges": 584,
+ "records_without_nodes": 8,
+ "records_without_edges": 173,
+ "review_status_counts": {
+ "needs_research": 48,
+ "pending": 132,
+ "reviewed": 280
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml": "bdcd291bfeb14293712b5b408e7ef8cc396a18317827618ed75fee517b1f9d58",
+ "tests/test_causal_review_batch90.py": "12dfffa68bd63e815e76f50dd9cb52ac459390f0bf48a0a1da3521134a3a98be",
+ "tests/test_participating_taxa.py": "89d6e67cd3a8401b2fe96f3e83d2aa5737f6f123cc849a0afdbab40eb25a4942",
+ "kb/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml": "2638bb5668d31d6c8a59d616e36777b22d38f03e1fef80dc58fada489628e41e",
+ "kb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml": "6416089a1d115f7834f71f98182476728a7f936f8b544c6551103c712a2bb825",
+ "kb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml": "d987d0d184c409b62a9e96034e7dd8f294742b10bc3adefe4617ddd7208c97f8",
+ "kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml": "1a0fd950b4dc5fbb21331be3995a2fffb05ac8d4e3df772f5008cb88a9b9d4e6",
+ "reports/causal_graph_review/README.md": "727ecad74acba894907ac59be451da98bb734ae08bf099e7970f1cf9c493cc48"
+ },
+ "status": "verified_assay_boundary_graph_review",
+ "pre_correction_histories_preserved": [
+ "history/records/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture/2026-10-07T125451Z-codex-edc25d.yaml",
+ "history/records/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium/2026-10-07T125451Z-codex-55758a.yaml",
+ "history/records/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium/2026-10-07T125451Z-codex-1ff079.yaml",
+ "history/records/Pseudonitzschia_Sulfitobacter_Association/2026-10-07T125452Z-codex-a42433.yaml"
+ ],
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 8929,
+ "categories": {
+ "MATCH": 8794,
+ "RENDERING": 20,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 38,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Both-root recipe executed. Informational exit0 does not certify a clean corpus; four focused snippet gates pass independently.",
+ "pre_research_baseline": {
+ "base_commit": "f63d0b98e06bd1e35016fcfd826b03721fe28f0b",
+ "base_tree": "8323cd500b8d327c50030d13c9bfea0dd3f8d903",
+ "research_worktree": "/private/tmp/communitymech-causal-batch89",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch90/baseline-rank.log",
+ "sha256": "ee8d3999d942c7888b056d36f54e71e9ef67f36c7ecf03a1d1e5cd91650e7d96",
+ "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-batch90/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-batch90/baseline-network.log",
+ "sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+ "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-batch90/baseline-downstream.log",
+ "sha256": "612533c9f55a6a2b48e05aa5b1f9f7f923f27a728a742167a5d14df82228a138",
+ "output_tail": "_Plume_Succession.yaml:241: downstream:\nkb/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.yaml:157: downstream:\nkb/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.yaml:196: 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/Synechococcus_Bacillus_SPC.yaml:120: downstream:\nkb/communities/Synechococcus_Bacillus_SPC.yaml:152: downstream:\nkb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml:143: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:69: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:88: downstream:\nkb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml:191: downstream:\nkb/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.yaml:121: downstream:\nkb/communities/Chlorella_Azospirillum_Synthetic_Mutualism.yaml:207: downstream:\nkb/communities/Chlorella_Azospirillum_Synthetic_Mutualism.yaml:252: downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:104: downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:127: downstream:\nkb/communities/OMM12_Gnotobiotic_Mouse_Gut_Community.yaml:89: downstream:\nkb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml:136: downstream:\nkb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml:201: downstream:\nkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml:179: downstream:\nkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml:232: 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/Salar_Atacama_Lithium_Brine_Community.yaml:295: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:339: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "9bf34b0998d64a7441e0f65c5ef9543df83e9755c4d313f7572d3b67e0f45475"
+ },
+ "reference_validator_caveat": "Four full-record reference-validator runs passed. CLI Total checks counts issues, not executed checks. Sixteen graph and eight discussion quotations match independent fresh-primary abstract and cache text. Literal matching is not entailment or full-text certification."
+}
diff --git a/tests/test_causal_review_batch90.py b/tests/test_causal_review_batch90.py
new file mode 100644
index 000000000..17eb22909
--- /dev/null
+++ b/tests/test_causal_review_batch90.py
@@ -0,0 +1,165 @@
+"""Keep reported causal findings distinct from reversed transfers and scope drift."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261007-four-records-batch90.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / row["path"]).read_text()) for row in rows]
+
+
+def test_chloronitro_downstream_step_does_not_imply_reverse_feeding():
+ _, rows, docs = records()
+ upstream, downstream, endpoint = docs[0]["ecological_interactions"]
+ assert len(rows[0]["edges_after"]) == 2
+ assert upstream["interaction_type"] == "CROSS_FEEDING"
+ assert downstream["scope"] == "COMMUNITY_LEVEL"
+ assert "source_taxon" not in downstream and "target_taxon" not in downstream
+ assert "interaction_type" not in downstream and "interaction_type" not in endpoint
+ assert "not evidence of Rhodococcus supplying a metabolite back" in downstream["description"]
+
+
+def test_chloronitro_conditional_mineralization_is_preserved():
+ _, _, docs = records()
+ endpoint = docs[0]["ecological_interactions"][-1]
+ assert "reports coculture mineralization" in endpoint["description"]
+ assert "additional carbon source" in endpoint["description"]
+ assert len(endpoint["evidence"]) == 2
+ assert "not evidence that controls were absent" in docs[0]["discussions"][-1]["rationale"]
+
+
+def test_tpa_competition_has_metabolic_evidence_not_only_dominance():
+ _, _, docs = records()
+ exploit, interference, dominance = docs[1]["ecological_interactions"]
+ assert all(n["interaction_type"] == "COMPETITION" for n in [exploit, interference, dominance])
+ assert len(exploit["evidence"]) == 2
+ assert "TPA metabolism was abolished" in exploit["evidence"][1]["snippet"]
+ assert "not by itself the mechanism" in exploit["evidence"][0]["explanation"]
+ assert "measured population outcome" in dominance["description"]
+
+
+def test_tpa_positive_contact_inhibition_attribution_survives():
+ _, rows, docs = records()
+ node = docs[1]["ecological_interactions"][1]
+ assert len(rows[1]["edges_after"]) == 2
+ assert "authors report assays" in node["description"]
+ assert "main contributor to dominance" in node["downstream"][0]["description"]
+ assert "relative growth kinetics" in node["description"]
+ assert "does not imply absent controls" in docs[1]["discussions"][-1]["rationale"]
+
+
+def test_naphthalene_model_and_positive_endpoints_are_separate():
+ _, _, docs = records()
+ transfer, circuit, endpoint = docs[2]["ecological_interactions"]
+ assert transfer["interaction_type"] == circuit["interaction_type"] == "SYNTROPHY"
+ assert "interaction_type" not in endpoint
+ assert transfer["description"].startswith("PARTIAL:")
+ assert circuit["description"].startswith("PARTIAL:")
+ assert circuit["scope"] == endpoint["scope"] == "COMMUNITY_LEVEL"
+ assert "98.3%" in endpoint["description"] and "89.5%" in endpoint["description"]
+ assert "complete carbon balance" in endpoint["description"]
+
+
+def test_syntrophy_review_follows_the_current_schema_not_an_obligacy_requirement():
+ ledger, _, docs = records()
+ schema = yaml.safe_load((ROOT / "src/communitymech/schema/communitymech.yaml").read_text())
+ definition = schema["enums"]["InteractionTypeEnum"]["permissible_values"]["SYNTROPHY"][
+ "description"
+ ]
+ assert "Obligacy is not asserted." in definition
+ correction = ledger["precommit_adversarial_correction"]
+ assert correction["schema_definition"] == definition
+ assert correction["superseded_regressions"].startswith("816 passed")
+ assert len(correction["records"]) == 2
+ for node in docs[2]["ecological_interactions"][:2]:
+ assert node["interaction_type"] == "SYNTROPHY"
+ assert "does not assert obligacy" in " ".join(node["description"].split())
+
+
+def test_diatom_workflow_and_environmental_scope_do_not_become_pair_mechanisms():
+ _, rows, docs = records()
+ synthesis, response, exchange = docs[3]["ecological_interactions"]
+ removed = {n["node"] for n in rows[3]["removed_node_decisions"]}
+ assert removed == {
+ "Diatom-Associated Bacterial Consortium Resolution",
+ "Coastal Sulfitobacter IAA Prevalence",
+ }
+ assert synthesis["downstream"][0]["target"] == response["name"]
+ assert "IAA promotes diatom cell division" in response["description"]
+ assert all("interaction_type" not in n for n in [synthesis, response, exchange])
+ assert "widespread" in docs[3]["environmental_factors"][0]["value"]
+ assert "#1742" in docs[3]["discussions"][-1]["rationale"]
+
+
+def test_all_original_nodes_edges_and_graph_anchors_have_dispositions():
+ _, rows, docs = records()
+ assert sum(len(r["node_decisions"]) for r in rows) == 12
+ assert sum(len(r["removed_node_decisions"]) for r in rows) == 2
+ assert sum(len(r["edges_before"]) for r in rows) == 7
+ assert sum(len(r["retained_edge_decisions"]) for r in rows) == 7
+ assert all(
+ not r["removed_edge_decisions"] and not r["mechanical_edge_source_corrections"]
+ for r in rows
+ )
+ for row, doc in zip(rows, docs, strict=True):
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ assert names == {n["node"] for n in row["node_decisions"]}
+ assert {(e["source"], e["target"]) for e in row["edges_before"]} == {
+ (e["source"], e["target"]) for e in row["edges_after"]
+ }
+ assert all(
+ a.split("#", 1)[1] in names
+ for d in doc["discussions"]
+ for a in d["attaches_to"]
+ if a.startswith("ecological_interactions#")
+ )
+
+
+def test_abstract_matches_are_not_full_text_certification():
+ ledger, _, _ = records()
+ assert ledger["primary_graph_snippet_count"] == 16
+ assert len(ledger["discussion_snippet_checks"]) == 8
+ checks = ledger["snippet_checks"] + ledger["discussion_snippet_checks"]
+ assert len(checks) == 24 and all(c["independent_primary_match"] for c in checks)
+ assert len(ledger["source_access"]) == 6
+ assert all("abstract" in r["accessed_scope"].lower() for r in ledger["source_access"])
+
+
+def test_history_no_spend_and_unfinished_followups_are_explicit():
+ ledger, rows, docs = records()
+ assert not ledger["independent_approval"]
+ assert ledger["issues"] == [1738, 1739, 1740, 1741]
+ assert ledger["unresolved_non_graph_issues"] == [1742]
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert ledger["edison"]["dry_runs"] == []
+ assert sum(len(row["history_files"]) for row in rows) == 6
+ for index, (row, doc) in enumerate(zip(rows, docs, strict=True)):
+ assert (
+ row["curation_events_added"]
+ == len(row["history_files"])
+ == (2 if index in [0, 2] else 1)
+ )
+ assert row["status"] == "reviewed" and doc["curation_history"][-1]["llm_assisted"]
+
+
+def test_reviewed_records_canonical_participants_and_caches_are_hash_bound():
+ ledger, rows, docs = records()
+ assert ledger["cache_changes"] == []
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ canonical = [
+ {k: t["taxon_term"][k] for k in ["preferred_term", "term"]} for t in doc["taxonomy"]
+ ]
+ for node in doc["ecological_interactions"]:
+ if node.get("participating_taxa"):
+ assert node["participating_taxa"] == canonical
+ for path, digest in ledger["primary_artifacts"].items():
+ if path.startswith("references_cache/"):
+ assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == digest
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 190037307..6016489c0 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -379,6 +379,8 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Pseudomonas_Paracoccus_Bifenthrin_Degradation_Consortium.yaml",
"Pseudomonas_Pedobacter_Social_Spreading_Coculture.yaml",
"Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.yaml",
+ "Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml",
+ "Pseudonitzschia_Sulfitobacter_Association.yaml",
"Rhizorhabdus_Cupriavidus_BDE47_Degradation_SynCom.yaml",
"Rhodococcus_Acinetobacter_RAMC_Mixed_Plastic_Upcycling_SynCom.yaml",
"Rhodococcus_Pseudomonas_PPOW_Consortium.yaml",