Engineered S. elongatus PCC 7942 cscB fixes carbon dioxide using light energy and exports sucrose that directly supports H. boliviensis growth and PHB accumulation.
+The study reports that sucrose secreted by S. elongatus CscB directly supports H. boliviensis in the light-driven consortium. CO2 is the photosynthetic substrate, not the exchanged organic carbon. The record retains its canonical LC1 identity, but the available primary abstract identifies the heterotroph only at species level; strain-specific attribution and complete medium inputs remain unverified.
Source Taxon: Synechococcus elongatus PCC 7942 cscB
@@ -657,8 +657,7 @@Exported cyanobacterial sucrose is the photosynthetically derived organic carbon that H. boliviensis consumes to support PHB accumulation without added external organic carbon. -
+Photosynthetically supplied sucrose supports the PHB-producing Halomonas partner. This preserves the source-supported carbon-to-product route without asserting that the abstract proves exclusion of every external organic input or a quantitative carbon balance.
H. boliviensis uses photosynthetically derived sucrose from the cyanobacterium to support stable polyhydroxybutyrate production without adding external organic carbon.
+The light-driven consortium accumulated PHB in H. boliviensis. The primary abstract reports up to 31% of heterotroph dry weight as PHB and productive coculture persistence for over five months. This is a community production endpoint, not an additional pairwise exchange or direct photosynthesis by Halomonas. Exact assay and LC1 attribution await primary Methods.
-Source Taxon: Synechococcus elongatus PCC 7942 cscB
+Participating Taxa: -
Target Taxon: Halomonas boliviensis LC1
+ Synechococcus elongatus PCC 7942 cscB, + Halomonas boliviensis LC1 + -Metabolites: - sucrose - (CHEBI:17992) -
+Metabolites: + poly(3-hydroxybutyrate) + (CHEBI:53389) +
-Biological Processes:
-Alginate encapsulation of the S. elongatus CscB module enhances sucrose export and coculture stability, physically partitioning the sucrose-producing cyanobacterium from H. boliviensis while maintaining carbohydrate transfer that drives PHB accumulation.
+Alginate encapsulation of S. elongatus CscB increased sucrose export and improved coculture stability in the primary abstract. This is an abiotic partitioning intervention, not organism-driven colonization facilitation. The source supports these positive effects but the abstract does not isolate how much of PHB output is mediated by export versus other effects.
@@ -794,10 +771,6 @@Metabolites: - alginic acid - (CHEBI:17548), - sucrose (CHEBI:17992) @@ -813,7 +786,7 @@
Enhanced sucrose export and improved partitioned-coculture stability increase the reliability of cyanobacterial sucrose delivery that supports Halomonas PHB accumulation.
+HYPOTHESIZED/PARTIAL: alginate-enhanced sucrose export and stability could sustain carbon delivery to the PHB producer. The abstract reports these benefits and PHB production but does not separate their causal contributions to productivity.
Fresh Europe PMC abstract and Crossref DOI metadata were checked. Publisher retrieval failed and bounded author-page/title/DOI/OSTI searches did not recover the full article. The abstract supports species-level sucrose feeding, PHB and enhanced stability, but not LC1 attribution, the complete organic-input accounting or isolated mediation. Obtain authorized primary Methods/supplements before treating these exact-system details as verified; issue #1860 remains open.
+ +Attaches to: ecological_interactions#Photosynthetic Sucrose Transfer To Halomonas, ecological_interactions#Light-Driven Biopolymer Production, ecological_interactions#Alginate-Partitioned Coculture Stabilization
enhances the co-culture stability
+A positive stability finding does not resolve the missing strain and mediation details.
+S. elongatus cscB fixes CO2 using light energy, converts fixed carbon to sucrose, and exports sucrose to support P. putida growth and metabolism.
+S. elongatus cscB supplies photosynthetically derived sucrose to engineered P. putida partners. This record spans distinct implementations: cscAB PHA production, cscRABY and its nitrate-blind derivative, and EM173-derived DNT transformation. Their outcomes and growth-feedback assays are not interchangeable strain-level observations.
Source Taxon: Synechococcus elongatus PCC 7942 cscB
@@ -668,12 +673,12 @@Secreted sucrose provides the carbon source for P. putida PHA biosynthesis.
+Cyanobacterial sucrose supplies carbon for P. putida PHA accumulation in the production assays. Polymer accumulation depends on the tested strain and nitrogen regime; the nitrate-blind comparison measures final accumulation, not a production-rate increase.
Secreted sucrose supports active metabolism of engineered P. putida during pollutant transformation.
+In the separate EM173-derived DNT implementation, sucrose from encapsulated cyanobacteria supports heterotrophic growth and metabolism during DNT biotransformation. This does not equate pollutant disappearance with complete mineralization.
P. putida consumes cyanobacterial sucrose-derived carbon and accumulates medium-chain-length polyhydroxyalkanoates as a bioproduct, with nitrogen limitation or nitrate-blind engineering improving production in related exact species-pair studies.
- +P. putida cscAB accumulated medium-chain-length PHA from cyanobacterial sucrose, with 3-hydroxydecanoate the most abundant monomer. A separate cscRABY nitrate-blind study reported an 8.8-fold increase in final PHA accumulation relative to its nitrate-consuming reference, not a measured rate increase. These production phenotypes are not additional cross-feeding events and do not establish PHB homopolymer identity.
-Source Taxon: Pseudomonas putida engineered sucrose-utilizing partner
@@ -741,9 +743,9 @@In the DNT-remediation implementation, engineered P. putida EM173 consumes cyanobacterial sucrose and transforms 2,4-dinitrotoluene while S. elongatus provides photosynthetically fixed carbon.
- +The EM173-derived P. putida EM.DNT.S partner transformed 2,4-DNT in coculture with alginate-encapsulated S. elongatus CscB. Oxidative-intermediate measurements support pathway activity, whereas disappearance from solution also includes adsorption and reductive transformation. Complete mineralization was not directly established; the paper gives a model-based estimate. The same implementation accumulated PHA under nitrogen depletion, without proving a PHB homopolymer composition.
-Source Taxon: Pseudomonas putida engineered sucrose-utilizing partner
@@ -860,7 +859,7 @@Multi-omics experiments indicate that P. putida cscRABY can improve S. elongatus cscB growth and photosynthetic capacity, with additional molecular exchanges beyond sucrose likely contributing to coculture dynamics.
+In the cscRABY study, P. putida promoted cyanobacterial growth and prevented photobleaching in tested contexts while receiving photosynthetic carbon. MUTUALISM here denotes that conditional carbon-supported partnership, not a universal fitness response: P. putida growth was not improved relative to matched external-sucrose controls. PARTIAL: additional molecular exchange and the mechanism of growth promotion remain hypotheses; mixed-cell omics and transporter regulation do not identify a transferred mediator. Sucrose is not a reverse donation.
Source Taxon: Pseudomonas putida engineered sucrose-utilizing partner
@@ -897,14 +909,6 @@Metabolites: - - sucrose - (CHEBI:17992) - -
- @@ -933,13 +937,26 @@The primary study supports conditional cyanobacterial growth benefit and carbon supply to Pseudomonas, while matched external-sucrose controls show no heterotroph growth advantage. Transport regulation and mixed-cell metabolomics suggest additional interactions but do not resolve donor-recipient flux or distinguish a specific mediator from growth-state differences. Do not transfer this feedback to the cscAB or DNT implementation without exact-system evidence.
+ +Attaches to: ecological_interactions#Growth-Promoting Partner Feedback
attributing core metabolites to a specific co-culture partner is not possible
+Explains why the omics findings cannot directly identify reciprocal transfer.
+Engineered S. elongatus UTEX 2973 converts light and carbon dioxide into D-lactate, which serves as the transferred energy carrier for S. oneidensis MR-1.
+Engineered Syn2973-omcS-ldh produces D-lactate that supports current production by the napA-deletion derivative of S. oneidensis MR-1. The engineered carrier is important but not the exclusive organic input: the paper reports additional cyanobacterial organics and LB supplementation in the consortium assays. Canonical member labels denote their strain backgrounds.
Source Taxon: Synechococcus elongatus UTEX 2973
@@ -621,9 +621,9 @@Metabolites:
- D-lactic acid
- (CHEBI:42111),
+ D-lactate
+ (CHEBI:16004),
carbon dioxide
(Photosynthetic D-Lactate Cross-Feeding
Photosynthetically produced D-lactate is the engineered carrier oxidized by S. oneidensis as it releases electrons to the anode.
- Photosynthetically produced D-lactate is oxidized by the engineered Shewanella partner, supporting electron transfer to the anode. Lactate-free and axenic comparisons support its contribution, not exclusive attribution of all current to D-lactate. S. oneidensis MR-1 oxidizes D-lactate and uses its extracellular electron transfer machinery to release electrons to the anode for current production. The napA-deletion S. oneidensis MR-1 derivative oxidizes D-lactate and transfers electrons to an abiotic anode. This is the consortium electrode-output process, not electron or metabolite donation to Synechococcus. The paper also reports enhanced cyanobacterial growth; it does not isolate CO2 recycling as its cause. Source Taxon: Shewanella oneidensis MR-1 Participating Taxa:
- Target Taxon: Synechococcus elongatus UTEX 2973 Metabolites:
- D-lactic acid
- (CHEBI:42111)
+ D-lactate
+ (CHEBI:16004)
Biological Processes: Physical and temporal separation prevents light- and oxygen-associated inhibition of S. oneidensis while preserving D-lactate transfer from the engineered cyanobacterium.
- HYPOTHESIZED/PARTIAL: the source schematic proposes that CO2 released during Shewanella oxidation can be re-assimilated by cyanobacteria for D-lactate production. The reviewed main text does not demonstrate this carbon-return flux or identify it as the cause of cyanobacterial growth benefit; electrons flow to the anode, not the cyanobacterium. Light and oxygen produced during photosynthesis damaged or inhibited S. oneidensis, so temporal and spatial separation protected the exoelectrogenic partner while allowing D-lactate transfer to support durable power generation. Device-level temporal or spatial separation mitigated incompatible light and oxygen conditions for the Shewanella partner while preserving D-lactate transfer. This is an abiotic compatibility intervention, not colonization facilitation by cyanobacteria. The more-than-40-day spatial-temporal result additionally used continuous medium replenishment and LB supplementation; it is distinct from temporal batch and spatially separated assays. Source Taxon: Synechococcus elongatus UTEX 2973 Participating Taxa:
- Target Taxon: Shewanella oneidensis MR-1 Biological Processes: The primary main text, Results and figure captions were inspected. Figure1 proposes CO2 re-assimilation and Results report cyanobacterial growth enhancement, but these do not isolate a carbon-return mediator. The anode remains the electron recipient. Preserve the existing reverse direction only as a hypothesis pending direct flux evidence; device separation and medium replenishment are distinct interventions. Attaches to: The released CO2 can be re-assimilated by cyanobacteria for d-lactate production. Source-proposed carbon recycling is not demonstrated electron return.Evidence
+ Evidence
Shewanella Anode Electron Transfer
- CROSS_FEEDING
-
-
-
Shewanella Anode Electron Transfer
Evidence
+ Evidence
- SUPPORT (IN_VITRO)
Evidence
Spatial-Temporal Separation for Compatibility
- COLONIZATION_FACILITATION
-
@@ -845,6 +851,19 @@ Evidence
+ Evidence
+ Knowledge gaps & discussions (1)
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Does Shewanella-derived CO2 contribute to cyanobacterial D-lactate production or growth?
+
+ ecological_interactions#Shewanella Anode Electron Transfer, ecological_interactions#Photosynthetic D-Lactate Cross-Feeding1 evidence item(s)
+
+ Evidence
var metabolites = [];
- metabolites.push("D-lactic acid");
+ metabolites.push("D-lactate");
metabolites.push("carbon dioxide");
@@ -1279,7 +1337,7 @@ Evidence
processes.push("interspecies interaction between organisms");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1308,20 +1366,16 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
- metabolites.push("D-lactic acid");
+ metabolites.push("D-lactate");
var processes = [];
-
- processes.push("interspecies interaction between organisms");
-
-
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1334,32 +1388,29 @@ Evidence
});
- var srcKey = "Shewanella oneidensis MR-1";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Synechococcus elongatus UTEX 2973";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Shewanella oneidensis MR-1"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("interspecies interaction between organisms");
-
-
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1372,17 +1423,20 @@ Evidence
});
- var srcKey = "Synechococcus elongatus UTEX 2973";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Shewanella oneidensis MR-1";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Synechococcus elongatus UTEX 2973",
+
+ "Shewanella oneidensis MR-1"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/history/records/Synechococcus_Halomonas_Light_Driven_PHB_Coculture/2026-10-08T053619Z-codex-d68757.yaml b/history/records/Synechococcus_Halomonas_Light_Driven_PHB_Coculture/2026-10-08T053619Z-codex-d68757.yaml
new file mode 100644
index 000000000..2d71c3bd1
--- /dev/null
+++ b/history/records/Synechococcus_Halomonas_Light_Driven_PHB_Coculture/2026-10-08T053619Z-codex-d68757.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml
+ slug: Synechococcus_Halomonas_Light_Driven_PHB_Coculture
+session:
+ id: 2026-10-08T053619Z-codex-d68757
+ timestamp: '2026-10-08T05:36:19Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1857
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain abstract-supported sucrose feeding while exposing unresolved LC1/medium
+ scope.; Retain PHB and persistence as a community phenotype, not duplicate exchange or
+ photosynthesis.; Retain alginate intervention effects without colonization typing or proven
+ PHB mediation.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
diff --git a/history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T053619Z-codex-9a9ab2.yaml b/history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T053619Z-codex-9a9ab2.yaml
new file mode 100644
index 000000000..fb89c9ea4
--- /dev/null
+++ b/history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T053619Z-codex-9a9ab2.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml
+ slug: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+session:
+ id: 2026-10-08T053619Z-codex-9a9ab2
+ timestamp: '2026-10-08T05:36:19Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1858
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain sucrose carbon support with separate production and DNT assay contexts.;
+ Retain PHA phenotype with correct polymer-family grounding and endpoint comparison.; Retain
+ DNT transformation and PHA outcome without inferring complete mineralization.; Preserve
+ conditional growth partnership without reverse sucrose donation or identified mediator.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
diff --git a/history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T054129Z-codex-d4dcce.yaml b/history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T054129Z-codex-d4dcce.yaml
new file mode 100644
index 000000000..0cb916a14
--- /dev/null
+++ b/history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T054129Z-codex-d4dcce.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml
+ slug: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+session:
+ id: 2026-10-08T054129Z-codex-d4dcce
+ timestamp: '2026-10-08T05:41:29Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1858
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ summary: Replace growth-rate excerpt with an exact passage shared by the primary XML and
+ unchanged PDF cache; the initial CLI rejected a PDF word-join artifact. Matched-control
+ growth interpretation and graph topology are unchanged. Issue#1858.
+ details: Reference-validation correction; initial failure retained in batch110 validation
+ provenance.
diff --git a/history/records/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium/2026-10-08T053619Z-codex-a21481.yaml b/history/records/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium/2026-10-08T053619Z-codex-a21481.yaml
new file mode 100644
index 000000000..d5fa509ab
--- /dev/null
+++ b/history/records/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium/2026-10-08T053619Z-codex-a21481.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml
+ slug: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+session:
+ id: 2026-10-08T053619Z-codex-a21481
+ timestamp: '2026-10-08T05:36:19Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1859
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain D-lactate supply and anode support without exclusive organic-input claims.;
+ Correct anode recipient and preserve source-proposed CO2 feedback as hypothetical.; Retain
+ abiotic compatibility and duration with distinct replenished-device context.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
diff --git a/kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml b/kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml
index 8910644ec..75664f79d 100644
--- a/kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml
+++ b/kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml
@@ -124,8 +124,10 @@ taxonomy:
explanation: Supports the PHB-producing functional role assigned to H. boliviensis.
ecological_interactions:
- name: Photosynthetic Sucrose Transfer To Halomonas
- description: Engineered S. elongatus PCC 7942 cscB fixes carbon dioxide using light energy and exports
- sucrose that directly supports H. boliviensis growth and PHB accumulation.
+ description: The study reports that sucrose secreted by S. elongatus CscB directly supports H. boliviensis in
+ the light-driven consortium. CO2 is the photosynthetic substrate, not the exchanged organic carbon. The record
+ retains its canonical LC1 identity, but the available primary abstract identifies the heterotroph only at species
+ level; strain-specific attribution and complete medium inputs remain unverified.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -143,6 +145,7 @@ ecological_interactions:
term:
id: CHEBI:16526
label: carbon dioxide
+ notes: Carbon-fixation substrate, not the transferred organic carbon.
- preferred_term: sucrose
term:
id: CHEBI:17992
@@ -158,62 +161,51 @@ ecological_interactions:
label: sucrose biosynthetic process
downstream:
- target: Light-Driven Biopolymer Production
- description: >
- Exported cyanobacterial sucrose is the photosynthetically derived organic
- carbon that H. boliviensis consumes to support PHB accumulation without
- added external organic carbon.
+ description: Photosynthetically supplied sucrose supports the PHB-producing Halomonas partner. This preserves
+ the source-supported carbon-to-product route without asserting that the abstract proves exclusion of every
+ external organic input or a quantitative carbon balance.
evidence:
- reference: PMID:29061492
supports: SUPPORT
evidence_source: IN_VITRO
snippet: sucrose secreted by S. elongatus CscB directly supports the bacterium Halomonas boliviensis
explanation: Supports direct sucrose cross-feeding from the cyanobacterium to the Halomonas partner.
- - reference: PMID:29061492
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: photoautotroph/chemoheterotroph consortial design
- explanation: Supports the division of labor between phototrophic and heterotrophic members.
- name: Light-Driven Biopolymer Production
- description: H. boliviensis uses photosynthetically derived sucrose from the cyanobacterium to support
- stable polyhydroxybutyrate production without adding external organic carbon.
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Synechococcus elongatus PCC 7942 cscB
- term:
- id: NCBITaxon:32046
- label: Synechococcus elongatus
- target_taxon:
- preferred_term: Halomonas boliviensis LC1
- term:
- id: NCBITaxon:1072583
- label: Vreelandella boliviensis LC1
+ description: The light-driven consortium accumulated PHB in H. boliviensis. The primary abstract reports up to
+ 31% of heterotroph dry weight as PHB and productive coculture persistence for over five months. This is a community
+ production endpoint, not an additional pairwise exchange or direct photosynthesis by Halomonas. Exact assay
+ and LC1 attribution await primary Methods.
+ scope: COMMUNITY_LEVEL
metabolites:
- - preferred_term: sucrose
- term:
- id: CHEBI:17992
- label: sucrose
- biological_processes:
- - preferred_term: photosynthesis
+ - preferred_term: poly(3-hydroxybutyrate)
term:
- id: GO:0015979
- label: photosynthesis
+ id: CHEBI:53389
+ label: poly(3-hydroxybutyrate)
evidence:
- reference: PMID:29061492
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: stable polyhydroxybutyrate production
- explanation: Supports the biopolymer-production outcome in the light-driven coculture.
+ snippet: Consortial H. boliviensis accumulate up to 31% of their dry-weight as PHB
+ explanation: Supports PHB accumulation in the heterotroph, not a second exchange.
- reference: PMID:29061492
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: improved synthetic photoautotroph/chemoheterotroph consortial design
- explanation: Supports the engineered modular design for light-driven PHB production.
+ snippet: cultures were continuously productive for over 5 months
+ explanation: Supports the reported duration without assigning an unverified operating mode.
+ participating_taxa:
+ - preferred_term: Synechococcus elongatus PCC 7942 cscB
+ term:
+ id: NCBITaxon:32046
+ label: Synechococcus elongatus
+ - preferred_term: Halomonas boliviensis LC1
+ term:
+ id: NCBITaxon:1072583
+ label: Vreelandella boliviensis LC1
- name: Alginate-Partitioned Coculture Stabilization
- description: Alginate encapsulation of the S. elongatus CscB module enhances sucrose export and
- coculture stability, physically partitioning the sucrose-producing cyanobacterium from H.
- boliviensis while maintaining carbohydrate transfer that drives PHB accumulation.
- interaction_type: COLONIZATION_FACILITATION
+ description: Alginate encapsulation of S. elongatus CscB increased sucrose export and improved coculture stability
+ in the primary abstract. This is an abiotic partitioning intervention, not organism-driven colonization facilitation.
+ The source supports these positive effects but the abstract does not isolate how much of PHB output is mediated
+ by export versus other effects.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Synechococcus elongatus PCC 7942 cscB
@@ -225,30 +217,27 @@ ecological_interactions:
id: NCBITaxon:1072583
label: Vreelandella boliviensis LC1
metabolites:
- - preferred_term: alginic acid
- term:
- id: CHEBI:17548
- label: alginic acid
- preferred_term: sucrose
term:
id: CHEBI:17992
label: sucrose
downstream:
- target: Light-Driven Biopolymer Production
- description: Enhanced sucrose export and improved partitioned-coculture stability increase the
- reliability of cyanobacterial sucrose delivery that supports Halomonas PHB accumulation.
+ description: 'HYPOTHESIZED/PARTIAL: alginate-enhanced sucrose export and stability could sustain carbon delivery
+ to the PHB producer. The abstract reports these benefits and PHB production but does not separate their causal
+ contributions to productivity.'
evidence:
- reference: PMID:29061492
supports: SUPPORT
evidence_source: IN_VITRO
snippet: alginate encapsulation of S. elongatus CscB enhances sucrose-export rates
- explanation: Supports alginate encapsulation as the engineered community context that increases
- cyanobacterial sucrose export.
+ explanation: Supports alginate encapsulation as the engineered community context that increases cyanobacterial
+ sucrose export.
- reference: PMID:29061492
supports: SUPPORT
evidence_source: IN_VITRO
snippet: enhances the co-culture stability
- explanation: Supports alginate partitioning as a stabilizing influence in the coculture.
+ explanation: Supports a positive stability effect, not an isolated PHB mediation test.
environmental_factors:
- name: Illumination
value: light-driven culture
@@ -361,3 +350,32 @@ rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare earth element processing role is curated for this light-driven PHB
coculture.
+discussions:
+- discussion_id: halomonas-strain-and-production-context
+ prompt: Which primary methods establish LC1 identity and the contribution of encapsulation to PHB output?
+ rationale: 'Fresh Europe PMC abstract and Crossref DOI metadata were checked. Publisher retrieval failed and bounded
+ author-page/title/DOI/OSTI searches did not recover the full article. The abstract supports species-level sucrose
+ feeding, PHB and enhanced stability, but not LC1 attribution, the complete organic-input accounting or isolated
+ mediation. Obtain authorized primary Methods/supplements before treating these exact-system details as verified;
+ issue #1860 remains open.'
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ attaches_to:
+ - ecological_interactions#Photosynthetic Sucrose Transfer To Halomonas
+ - ecological_interactions#Light-Driven Biopolymer Production
+ - ecological_interactions#Alginate-Partitioned Coculture Stabilization
+ evidence:
+ - reference: PMID:29061492
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: enhances the co-culture stability
+ explanation: A positive stability finding does not resolve the missing strain and mediation details.
+curation_history:
+- timestamp: '2026-10-08T05:36:17Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain abstract-supported sucrose feeding while exposing unresolved LC1/medium scope.; Retain PHB and
+ persistence as a community phenotype, not duplicate exchange or photosynthesis.; Retain alginate intervention
+ effects without colonization typing or proven PHB mediation. Issue#1857; reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
+ llm_assisted: true
diff --git a/kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml b/kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml
index 26c85d093..e9fa9a8fd 100644
--- a/kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml
+++ b/kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml
@@ -138,8 +138,10 @@ taxonomy:
explanation: Supports P. putida cscRABY as the heterotrophic partner in the multi-omics coculture.
ecological_interactions:
- name: Photosynthetic Sucrose Cross-Feeding
- description: S. elongatus cscB fixes CO2 using light energy, converts fixed carbon to sucrose, and exports
- sucrose to support P. putida growth and metabolism.
+ description: 'S. elongatus cscB supplies photosynthetically derived sucrose to engineered P. putida partners.
+ This record spans distinct implementations: cscAB PHA production, cscRABY and its nitrate-blind derivative,
+ and EM173-derived DNT transformation. Their outcomes and growth-feedback assays are not interchangeable strain-level
+ observations.'
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -157,6 +159,7 @@ ecological_interactions:
term:
id: CHEBI:16526
label: carbon dioxide
+ notes: Photosynthetic substrate, not the exchanged organic molecule.
- preferred_term: sucrose
term:
id: CHEBI:17992
@@ -172,10 +175,13 @@ ecological_interactions:
label: sucrose biosynthetic process
downstream:
- target: Heterotrophic PHA Accumulation
- description: Secreted sucrose provides the carbon source for P. putida PHA biosynthesis.
+ description: Cyanobacterial sucrose supplies carbon for P. putida PHA accumulation in the production assays.
+ Polymer accumulation depends on the tested strain and nitrogen regime; the nitrate-blind comparison measures
+ final accumulation, not a production-rate increase.
- target: DNT Biotransformation with Photosynthetic Carbon Input
- description: Secreted sucrose supports active metabolism of engineered P. putida during pollutant
- transformation.
+ description: In the separate EM173-derived DNT implementation, sucrose from encapsulated cyanobacteria supports
+ heterotrophic growth and metabolism during DNT biotransformation. This does not equate pollutant disappearance
+ with complete mineralization.
evidence:
- reference: PMID:28814973
supports: SUPPORT
@@ -186,13 +192,12 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: cyanobacteria fix CO2 through photosynthetic metabolism and secrete sufficient carbohydrates
- explanation: Supports photosynthetic CO2 fixation and carbohydrate secretion as the basis for P. putida
- growth.
+ explanation: Supports photosynthetic CO2 fixation and carbohydrate secretion as the basis for P. putida growth.
- name: Heterotrophic PHA Accumulation
- description: P. putida consumes cyanobacterial sucrose-derived carbon and accumulates medium-chain-length
- polyhydroxyalkanoates as a bioproduct, with nitrogen limitation or nitrate-blind engineering improving
- production in related exact species-pair studies.
- interaction_type: CROSS_FEEDING
+ description: P. putida cscAB accumulated medium-chain-length PHA from cyanobacterial sucrose, with 3-hydroxydecanoate
+ the most abundant monomer. A separate cscRABY nitrate-blind study reported an 8.8-fold increase in final PHA
+ accumulation relative to its nitrate-consuming reference, not a measured rate increase. These production phenotypes
+ are not additional cross-feeding events and do not establish PHB homopolymer identity.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Synechococcus elongatus PCC 7942 cscB
@@ -203,20 +208,15 @@ ecological_interactions:
term:
id: NCBITaxon:303
label: Pseudomonas putida
- source_taxon:
- preferred_term: Pseudomonas putida engineered sucrose-utilizing partner
- term:
- id: NCBITaxon:303
- label: Pseudomonas putida
metabolites:
- preferred_term: sucrose
term:
id: CHEBI:17992
label: sucrose
- - preferred_term: poly(3-hydroxybutyrate)
+ - preferred_term: polyhydroxyalkanoate
term:
- id: CHEBI:53389
- label: poly(3-hydroxybutyrate)
+ id: CHEBI:78037
+ label: polyhydroxyalkanoate
biological_processes:
- preferred_term: sucrose catabolic process
term:
@@ -226,18 +226,19 @@ ecological_interactions:
- reference: PMID:28814973
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: maximal PHA production rate of 23.8
- explanation: Supports PHA accumulation by the coculture under nitrogen-limiting conditions.
+ snippet: with 3-hydroxydecanoic acid being the most abundant monomer
+ explanation: The directly measured polymer composition is medium-chain-length PHA, not PHB.
- reference: PMID:32523942
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: PHA produced from light and CO2 was 8.8 fold increased
- explanation: Supports improved PHA production in a nitrate-blind P. putida variant of the same species-pair
- platform.
+ snippet: these numbers are based on the snapshot at the end of the experiment
+ explanation: Bounds the strain comparison to final accumulation rather than production rate.
- name: DNT Biotransformation with Photosynthetic Carbon Input
- description: In the DNT-remediation implementation, engineered P. putida EM173 consumes cyanobacterial
- sucrose and transforms 2,4-dinitrotoluene while S. elongatus provides photosynthetically fixed carbon.
- interaction_type: CROSS_FEEDING
+ description: The EM173-derived P. putida EM.DNT.S partner transformed 2,4-DNT in coculture with alginate-encapsulated
+ S. elongatus CscB. Oxidative-intermediate measurements support pathway activity, whereas disappearance from
+ solution also includes adsorption and reductive transformation. Complete mineralization was not directly established;
+ the paper gives a model-based estimate. The same implementation accumulated PHA under nitrogen depletion, without
+ proving a PHB homopolymer composition.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Synechococcus elongatus PCC 7942 cscB
@@ -248,11 +249,6 @@ ecological_interactions:
term:
id: NCBITaxon:303
label: Pseudomonas putida
- source_taxon:
- preferred_term: Pseudomonas putida engineered sucrose-utilizing partner
- term:
- id: NCBITaxon:303
- label: Pseudomonas putida
metabolites:
- preferred_term: 2,4-dinitrotoluene
term:
@@ -271,17 +267,24 @@ ecological_interactions:
- reference: PMID:32064751
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: degrade the environmental pollutant 2,4-dinitrotoluene (2,4-DNT)
- explanation: Supports engineered P. putida-mediated DNT transformation in the photosynthetic coculture.
+ snippet: a portion of 2,4-DNT is also transformed via reductive processes
+ explanation: The source explicitly distinguishes alternative fates from the oxidative route.
+ - reference: PMID:32064751
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: we could not precisely quantitate the flux through the oxidative pathway with our data
+ explanation: Soluble pollutant loss is not a direct measure of complete oxidative mineralization.
- reference: PMID:32064751
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: remediate the industrial pollutant 2,4-DNT while simultaneously synthesizing biopolymers
- explanation: Supports the dual bioremediation and bioproduct function of the coculture.
+ snippet: Both engineered P. putida strains were able to accumulate the polymer under nitrogen-limited conditions
+ explanation: Supports the production endpoint in this implementation with its nitrogen boundary.
- name: Growth-Promoting Partner Feedback
- description: Multi-omics experiments indicate that P. putida cscRABY can improve S. elongatus cscB growth
- and photosynthetic capacity, with additional molecular exchanges beyond sucrose likely contributing
- to coculture dynamics.
+ description: 'In the cscRABY study, P. putida promoted cyanobacterial growth and prevented photobleaching in tested
+ contexts while receiving photosynthetic carbon. MUTUALISM here denotes that conditional carbon-supported partnership,
+ not a universal fitness response: P. putida growth was not improved relative to matched external-sucrose controls.
+ PARTIAL: additional molecular exchange and the mechanism of growth promotion remain hypotheses; mixed-cell omics
+ and transporter regulation do not identify a transferred mediator. Sucrose is not a reverse donation.'
interaction_type: MUTUALISM
scope: PAIRWISE
source_taxon:
@@ -294,11 +297,6 @@ ecological_interactions:
term:
id: NCBITaxon:32046
label: Synechococcus elongatus
- metabolites:
- - preferred_term: sucrose
- term:
- id: CHEBI:17992
- label: sucrose
evidence:
- reference: PMID:38609451
supports: SUPPORT
@@ -306,10 +304,15 @@ ecological_interactions:
snippet: up to 80% increase in the growth rate and enhanced photosynthetic capacity
explanation: Supports a positive effect of P. putida on the cyanobacterial partner.
- reference: PMID:38609451
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: exchange of further molecules beyond the unidirectional feeding with sucrose
- explanation: Supports additional interaction mechanisms beyond the engineered sucrose cross-feeding link.
+ explanation: The source strongly hints at additional exchange; it does not demonstrate its mediator or direction.
+ - reference: PMID:38609451
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: which aligns with the expected outcome due to the same growth rate
+ explanation: Pseudomonas growth-rate comparison used matched sucrose-supplied axenic controls.
cultivation_setup:
- cultivation_mode: BATCH
system_type: FLASK
@@ -605,3 +608,38 @@ related_ingredients:
evidence_source: IN_VITRO
snippet: promote dehydration of 3‐hydroxybutyrate into crotonic acid
explanation: Names crotonic acid as the analytical proxy for PHA quantification.
+discussions:
+- discussion_id: pseudomonas-growth-feedback-mediator
+ prompt: Which mechanism causes cyanobacterial growth promotion in the cscRABY coculture?
+ rationale: The primary study supports conditional cyanobacterial growth benefit and carbon supply to Pseudomonas,
+ while matched external-sucrose controls show no heterotroph growth advantage. Transport regulation and mixed-cell
+ metabolomics suggest additional interactions but do not resolve donor-recipient flux or distinguish a specific
+ mediator from growth-state differences. Do not transfer this feedback to the cscAB or DNT implementation without
+ exact-system evidence.
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ attaches_to:
+ - ecological_interactions#Growth-Promoting Partner Feedback
+ evidence:
+ - reference: PMID:38609451
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: attributing core metabolites to a specific co-culture partner is not possible
+ explanation: Explains why the omics findings cannot directly identify reciprocal transfer.
+curation_history:
+- timestamp: '2026-10-08T05:36:18Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain sucrose carbon support with separate production and DNT assay contexts.; Retain PHA phenotype
+ with correct polymer-family grounding and endpoint comparison.; Retain DNT transformation and PHA outcome without
+ inferring complete mineralization.; Preserve conditional growth partnership without reverse sucrose donation
+ or identified mediator. Issue#1858; reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
+ llm_assisted: true
+- timestamp: '2026-10-08T05:41:27Z'
+ curator: codex
+ action: CORRECT_EVIDENCE_SNIPPET
+ changes: Replace growth-rate excerpt with an exact passage shared by the primary XML and unchanged PDF cache;
+ the initial CLI rejected a PDF word-join artifact. Matched-control growth interpretation and graph topology
+ are unchanged. Issue#1858.
+ llm_assisted: true
diff --git a/kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml b/kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml
index b54d17e76..d8dee4531 100644
--- a/kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml
+++ b/kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml
@@ -117,8 +117,10 @@ taxonomy:
explanation: Supports the engineered nitrate-reductase mutant used as the Shewanella partner.
ecological_interactions:
- name: Photosynthetic D-Lactate Cross-Feeding
- description: Engineered S. elongatus UTEX 2973 converts light and carbon dioxide into D-lactate,
- which serves as the transferred energy carrier for S. oneidensis MR-1.
+ description: 'Engineered Syn2973-omcS-ldh produces D-lactate that supports current production by the napA-deletion
+ derivative of S. oneidensis MR-1. The engineered carrier is important but not the exclusive organic input: the
+ paper reports additional cyanobacterial organics and LB supplementation in the consortium assays. Canonical
+ member labels denote their strain backgrounds.'
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -132,15 +134,15 @@ ecological_interactions:
id: NCBITaxon:211586
label: Shewanella oneidensis MR-1
metabolites:
- - preferred_term: D-lactic acid
+ - preferred_term: D-lactate
term:
- id: CHEBI:42111
- label: (R)-lactic acid
- notes: Source uses D-lactate as the transferred energy carrier; CHEBI:42111 represents D-lactic acid.
+ id: CHEBI:16004
+ label: (R)-lactate
- preferred_term: carbon dioxide
term:
id: CHEBI:16526
label: carbon dioxide
+ notes: Photosynthetic carbon-fixation substrate, not the exchanged organic carrier.
biological_processes:
- preferred_term: photosynthesis
term:
@@ -152,83 +154,69 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Shewanella Anode Electron Transfer
- description: >
- Photosynthetically produced D-lactate is the engineered carrier oxidized
- by S. oneidensis as it releases electrons to the anode.
+ description: Photosynthetically produced D-lactate is oxidized by the engineered Shewanella partner, supporting
+ electron transfer to the anode. Lactate-free and axenic comparisons support its contribution, not exclusive
+ attribution of all current to D-lactate.
evidence:
- reference: PMID:31537786
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: D-lactate mediated microbial consortium consisting of photosynthetic cyanobacteria and exoelectrogenic Shewanella
+ snippet: D-lactate mediated microbial consortium consisting of photosynthetic cyanobacteria and exoelectrogenic
+ Shewanella
explanation: Supports D-lactate-mediated cross-feeding between the photosynthetic and exoelectrogenic partners.
- reference: PMID:31537786
supports: SUPPORT
evidence_source: IN_VITRO
snippet: D-lactate is selected as the energy carrier
explanation: Supports D-lactate as the curated exchanged metabolite.
+ - reference: PMID:31537786
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: d-lactate which is the dominant secreted metabolite
+ explanation: Supports a dominant carrier rather than the sole organic substrate.
- name: Shewanella Anode Electron Transfer
- description: S. oneidensis MR-1 oxidizes D-lactate and uses its extracellular electron transfer
- machinery to release electrons to the anode for current production.
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Shewanella oneidensis MR-1
- term:
- id: NCBITaxon:211586
- label: Shewanella oneidensis MR-1
- target_taxon:
- preferred_term: Synechococcus elongatus UTEX 2973
- term:
- id: NCBITaxon:1350461
- label: Synechococcus elongatus UTEX 2973
+ description: The napA-deletion S. oneidensis MR-1 derivative oxidizes D-lactate and transfers electrons to an
+ abiotic anode. This is the consortium electrode-output process, not electron or metabolite donation to Synechococcus.
+ The paper also reports enhanced cyanobacterial growth; it does not isolate CO2 recycling as its cause.
+ scope: COMMUNITY_LEVEL
metabolites:
- - preferred_term: D-lactic acid
- term:
- id: CHEBI:42111
- label: (R)-lactic acid
- biological_processes:
- - preferred_term: interspecies interaction between organisms
+ - preferred_term: D-lactate
term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
+ id: CHEBI:16004
+ label: (R)-lactate
downstream:
- target: Photosynthetic D-Lactate Cross-Feeding
- description: >
- Physical and temporal separation prevents light- and oxygen-associated
- inhibition of S. oneidensis while preserving D-lactate transfer from the
- engineered cyanobacterium.
+ description: 'HYPOTHESIZED/PARTIAL: the source schematic proposes that CO2 released during Shewanella oxidation
+ can be re-assimilated by cyanobacteria for D-lactate production. The reviewed main text does not demonstrate
+ this carbon-return flux or identify it as the cause of cyanobacterial growth benefit; electrons flow to the
+ anode, not the cyanobacterium.'
evidence:
- reference: PMID:31537786
supports: SUPPORT
evidence_source: IN_VITRO
snippet: releases electrons from D-lactate and transfers them to the anode
explanation: Supports the Shewanella D-lactate oxidation and anode electron transfer role.
+ - reference: PMID:31537786
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: The released CO2 can be re-assimilated by cyanobacteria for d-lactate production.
+ explanation: Figure1 schematic proposes the existing reverse direction; it is not a transfer measurement.
- reference: PMID:31537786
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: converting organic compounds into electricity using its efficient EET capacity
- explanation: Supports the exoelectrogenic function assigned to S. oneidensis MR-1.
-- name: Spatial-Temporal Separation for Compatibility
- description: Light and oxygen produced during photosynthesis damaged or inhibited S. oneidensis,
- so temporal and spatial separation protected the exoelectrogenic partner while allowing D-lactate
- transfer to support durable power generation.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Synechococcus elongatus UTEX 2973
- term:
- id: NCBITaxon:1350461
- label: Synechococcus elongatus UTEX 2973
- target_taxon:
- preferred_term: Shewanella oneidensis MR-1
+ snippet: enhanced the growth of cyanobacteria
+ explanation: The primary Results report a positive cyanobacterial growth response without isolating its mediator.
+ participating_taxa:
+ - preferred_term: Shewanella oneidensis MR-1
term:
id: NCBITaxon:211586
label: Shewanella oneidensis MR-1
- biological_processes:
- - preferred_term: interspecies interaction between organisms
- term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
+- name: Spatial-Temporal Separation for Compatibility
+ description: Device-level temporal or spatial separation mitigated incompatible light and oxygen conditions for
+ the Shewanella partner while preserving D-lactate transfer. This is an abiotic compatibility intervention, not
+ colonization facilitation by cyanobacteria. The more-than-40-day spatial-temporal result additionally used continuous
+ medium replenishment and LB supplementation; it is distinct from temporal batch and spatially separated assays.
+ scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:31537786
supports: SUPPORT
@@ -240,6 +228,20 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: temporal/spatial separation design conquered the physiological incompatibility
explanation: Supports the spatial-temporal device organization as the compatibility mechanism.
+ - reference: PMID:31537786
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: spatial-temporal separation setup with medium replenishment enables stable operation for over 40 days
+ explanation: The duration belongs to the replenished device format.
+ participating_taxa:
+ - preferred_term: Synechococcus elongatus UTEX 2973
+ term:
+ id: NCBITaxon:1350461
+ label: Synechococcus elongatus UTEX 2973
+ - preferred_term: Shewanella oneidensis MR-1
+ term:
+ id: NCBITaxon:211586
+ label: Shewanella oneidensis MR-1
cultivation_setup:
- cultivation_mode: BATCH
system_type: BIOELECTROCHEMICAL_SYSTEM
@@ -476,3 +478,30 @@ rare_earth_elements_present: []
metal_relevance: INCIDENTAL
metal_notes: The community uses Shewanella extracellular electron transfer to an electrode; no metal
or rare earth extraction, cycling, or stress mechanism is curated for this record.
+discussions:
+- discussion_id: shewanella-carbon-return-versus-electrode-output
+ prompt: Does Shewanella-derived CO2 contribute to cyanobacterial D-lactate production or growth?
+ rationale: The primary main text, Results and figure captions were inspected. Figure1 proposes CO2 re-assimilation
+ and Results report cyanobacterial growth enhancement, but these do not isolate a carbon-return mediator. The
+ anode remains the electron recipient. Preserve the existing reverse direction only as a hypothesis pending direct
+ flux evidence; device separation and medium replenishment are distinct interventions.
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ attaches_to:
+ - ecological_interactions#Shewanella Anode Electron Transfer
+ - ecological_interactions#Photosynthetic D-Lactate Cross-Feeding
+ evidence:
+ - reference: PMID:31537786
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: The released CO2 can be re-assimilated by cyanobacteria for d-lactate production.
+ explanation: Source-proposed carbon recycling is not demonstrated electron return.
+curation_history:
+- timestamp: '2026-10-08T05:36:18Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain D-lactate supply and anode support without exclusive organic-input claims.; Correct anode recipient
+ and preserve source-proposed CO2 feedback as hypothetical.; Retain abiotic compatibility and duration with distinct
+ replenished-device context. Issue#1859; reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 8da03ca82..bec4597bc 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,32 @@ 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`.
+## Batch110: Polymer And Electron-Recipient Boundaries
+
+[Decisions](decisions/20261008-three-records-batch110.yaml),
+[provenance](cache-provenance-20261008-batch110.json),
+[validation](validation-20261008-batch110.json), and
+[self-adversarial review](adversarial-review-20261008-batch110.yaml) cover
+the Synechococcus-Halomonas, -Pseudomonas and -Shewanella records.
+All ten nodes and six directions remain. PHA is distinguished from PHB,
+DNT transformation from complete mineralization, and the abiotic anode
+from a cyanobacterial recipient. Positive production and growth findings
+remain; unmeasured mediation stays explicitly hypothetical.
+
+Five primary main texts were read in bounded spans and one primary abstract
+in full. Twenty-seven graph/discussion quotations match fresh primary text
+and unchanged caches. Four append-only histories include a quotation
+correction; its initial failed check is retained. A separate PDF fi-ligature
+false positive remains explicitly recorded under validator issue #1863,
+not silently counted as a clean snippet audit. Four in-memory mutation
+probes reject claim inflation. All 923 caches and 457 other records remain
+unchanged. No new topology or Edison spend.
+
+Repairs #1857-#1859 await protected-main merge. Halomonas remains
+`needs_research` for primary-methods access and exact-system scope (#1860).
+Non-graph follow-ups #1861-#1862 and validator #1863 remain open. Self-review
+is not independent approval or completion of the whole corpus review.
+
## Batch109: Strain And Assay Boundaries
[Decisions](decisions/20261008-six-records-batch109.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch110.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch110.yaml
new file mode 100644
index 000000000..87d087fe3
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch110.yaml
@@ -0,0 +1,358 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 9b429a9fa64f383ece90031645efbb8f913e111b
+scope:
+- kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml
+- kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml
+- kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch110.json
+findings:
+- issue: 1857
+ severity: P2
+ finding: Separate Halomonas PHB phenotype and alginate intervention from ecological typing
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1858
+ severity: P2
+ finding: Bound Pseudomonas PHA and DNT graph outcomes by polymer and assay
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1859
+ severity: P2
+ finding: Correct anode recipient and qualify CO2-return arrow in biophotovoltaic graph
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1860
+ severity: P2
+ finding: Obtain Halomonas PHB primary methods to verify LC1 scope and encapsulation mediation
+ status: open_research_follow_up
+ disposition: Remains open; source and non-graph scope limits are explicit.
+- issue: 1861
+ severity: P2
+ finding: Review Pseudomonas PHB ingredient attribution outside repaired PHA graph
+ status: open_non_graph_follow_up
+ disposition: Remains open; source and non-graph scope limits are explicit.
+- issue: 1862
+ severity: P2
+ finding: Reconcile biophotovoltaic cultivation mode and medium with primary device arms
+ status: open_non_graph_follow_up
+ disposition: Remains open; source and non-graph scope limits are explicit.
+- issue: 1863
+ severity: P2
+ finding: Snippet auditor drops PDF fi ligature and reports a false MISMATCH.
+ status: open_validator_follow_up
+ disposition: Exact single-quote exception documented; fix shared normalization in a separate tested change.
+adversarial_checks:
+- Whole original targets and all changed graph/discussion diffs reviewed. All ten nodes and six existing directions
+ retained. No renamed, removed or new topology; no Edison job or spend.
+- 'Challenge overcorrection: preserve photosynthetic carbon supply, PHB/PHA accumulation, DNT transformation, cyanobacterial
+ growth benefits, anode current and device-compatibility benefits. Qualification distinguishes observed outcomes
+ from isolated causal mediation, not positive from negative results.'
+- 'Halomonas: abstract supports sucrose feeding, PHB up to 31% dry weight, productive persistence over five months
+ and alginate-enhanced export/stability. It does not identify LC1, resolve all organic inputs or isolate encapsulation-to-PHB
+ mediation. Preserve existing identities but mark graph needs_research and retain the mediation arrow as HYPOTHESIZED/PARTIAL.
+ PHB output and alginate intervention are untyped community processes, not duplicate exchange or colonization facilitation.'
+- 'Pseudomonas: distinguish cscAB PHA, cscRABY/nitrate-blind and EM173 DNT implementations. Measured medium-chain-length
+ PHA is not PHB homopolymer; 8.8-fold final accumulation is not a rate comparison. DNT disappearance includes adsorption
+ and reductive fates; oxidative intermediates support transformation, not measured complete mineralization. Preserve
+ nitrogen-limited PHA outcome without importing polymer identity from a crotonic-acid assay.'
+- 'Pseudomonas feedback: retain conditional carbon-supported partnership and positive cyanobacterial growth. The
+ heterotroph does not gain growth rate over matched externally fed axenic controls. Mixed-cell omics and transporter
+ responses do not establish a donor/recipient mediator or reverse sucrose donation. The unresolved mechanism remains
+ PARTIAL with a discussion, not a new exchange node.'
+- 'Shewanella: retain D-lactate contribution using lactate rather than acid grounding, without exclusive organic-carbon
+ attribution. The anode is abiotic, not the cyanobacterium. Source Figure1 proposes CO2 return, so the existing
+ reverse arrow remains explicitly hypothetical; positive cyanobacterial growth is retained separately. Temporal
+ batch, spatial and replenished spatial-temporal devices are distinct. More-than-40-day output is qualified by
+ medium replenishment and LB supplementation; no protocol optimization is added.'
+- Twenty-four graph and three new discussion quotations match fresh primary text and unchanged caches under documented
+ normalization. Five primary main texts were read in bounded spans and one primary abstract in full; remaining
+ Methods, supplements, figure pixels and raw data were not certified. Halomonas full article was not retrieved
+ in bounded searches, not declared globally unavailable.
+- Initial reference failure came from a PDF word join. A replacement excerpt from the same primary paragraph passes
+ CLI validation, with append-only correction history and the failed attempt retained. One remaining local snippet-audit
+ MISMATCH is an exact, independently proven fi-ligature false positive; issue1863 stays open. No shared validator
+ change, cache rewrite or claim that all snippet classifications are clean.
+- Three guarded records and four append-only histories preserve all prior history and decision files, 457 other
+ records, all 923 caches and non-graph raw blocks. Shewanella adds one community-level/mixed record and two taxa
+ to the survey denominator, with no new taxa credited solely by the broad rule. Measurement-based census expectations
+ are updated; connectivity and share logic are unchanged.
+- Four in-memory control/mutation/restored-control probes reject PHA-to-PHB inflation, complete-mineralization inflation,
+ a cyanobacterial anode recipient and unsupported growth-mediator certainty. Canonical files remain unchanged;
+ probes are not added to the pytest count.
+- Seven focused tests and 994 combined regressions pass. Three full-record schema/strict/term/reference validations
+ and four histories pass. Local snippet checks retain the one explicitly documented ligature discrepancy. Network
+ preserves 56 baseline warnings with zero structural defects. Deterministic rendering and exact HTML descriptions
+ cover 456 pages, 1367 nodes and 536 arrows; this is not screenshot QA.
+- Repairs1857-1859 await protected-main merge. Research1860, non-graph1861-1862 and validator1863 remain open. Existing
+ loader1703, DOI-case1091 and cache-policy949/1093 are not certified. Denied/unanswered Edison scopes are untouched.
+ Self-review is not independent approval, and no CI/protection bypass or premature branch deletion is allowed.
+- Corpus status is 352 reviewed, 55 pending and 53 needs_research. The whole goal remains incomplete. Exact-head
+ publication and postcommit docs-current are separate gates, not preasserted here.
+- Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: PHA family inflated to PHB homopolymer
+ test: test_pha_is_not_phb_or_a_rate_comparison
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 35
+ assertion: assert product["metabolites"][1]["term"] == {
+ restored_control: PASS
+ - mutation: DNT disappearance promoted to complete mineralization
+ test: test_dnt_removal_does_not_prove_complete_mineralization
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 49
+ assertion: assert "Complete mineralization was not directly established" in dnt["description"]
+ restored_control: PASS
+ - mutation: Anode output assigned to cyanobacterial recipient
+ test: test_anode_is_not_a_cyanobacterial_recipient_and_carbon_return_is_hypothetical
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 72
+ assertion: assert "source_taxon" not in anode and "target_taxon" not in anode
+ restored_control: PASS
+ - mutation: Unresolved growth mediator promoted to SUPPORT
+ test: test_growth_feedback_preserves_positive_context_without_reverse_sucrose
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 60
+ assertion: assert feedback["evidence"][1]["supports"] == "PARTIAL"
+ restored_control: PASS
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml: 6f80bc26157b469b40d247d9d8bdf08aacee7ce6009e53527820248179397b3c
+ kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml: 76fe4a6229c920128650e889592471c220a7a42283bc97c605c6d9615983cf8a
+ kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml: 826172b3e4ec14cb21b506f830175d55dc982b3ee809bc7811e9a29cb67e231c
+ tests/test_causal_review_batch110.py: 39b08c28d3140ebbd608ca57317d51e1302d36d8a5474c186873d918858f3b69
+ scope: In-memory evidence mutations with control and restored-control; no canonical writes or inflated pytest
+ count.
+ artifact: /private/tmp/communitymech-batch110/adversarial-regression-proof.json
+ sha256: 3dcf04022bd3717c8c8b58e7cd0524e808b53972cea3d83f285d075d3be59eba
+verification:
+ combined_regressions: 994 passed in 335.27s (0:05:35)
+ new_regression_tests: 7
+ total_recorded_gate_outputs: 35
+ primary_graph_snippet_proof:
+ graph_quotations: 24
+ new_discussion_quotations: 3
+ fresh_primary_literal_matches: 27
+ all_cached_literal_matches: 27
+ retained_nodes: 10
+ removed_nodes: 0
+ retained_arrows: 6
+ removed_arrows: 0
+ new_nodes_or_directions: 0
+ scope: All reviewed quotations match fresh primary text and unchanged caches;source entailment separately reviewed.
+ Primary abstract and bounded main-text/caption spans documented in ledger;no raw-data,figure-pixel or supplement
+ certification.
+ references: Three full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal
+ matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks.
+ Loader1703 not certified.
+ initial_failed_attempt:
+ artifact: /private/tmp/communitymech-batch110/validation-attempt1.json
+ sha256: 9e7c4bf7ac745ae0463afc6a1183360eb6df042af6ef52819c5df5ad53393b4b
+ failed_check:
+ check: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-references
+ command:
+ - /Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator
+ - validate
+ - data
+ - kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml
+ - -s
+ - src/communitymech/schema/communitymech.yaml
+ - --config
+ - conf/reference_validator.yaml
+ exit_code: 1
+ expected_exit_codes:
+ - 0
+ log: /private/tmp/communitymech-batch110/verification-attempt1/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-references.log
+ log_sha256: cd0ab1221ff4111d88fd313d59beee8da5682f9860f1c1f3149d37461385a475
+ output_tail: "Validating kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml against schema\
+ \ src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (1):\n\
+ \ [ERROR] Text part not found as substring: 'they did not differ within the same experiment'\n Location:\
+ \ ecological_interactions[3].evidence[2].snippet\n Reference: PMID:38609451\n\nValidation Summary:\n\
+ \ Total checks: 1\n Issues found: 1\n"
+ explained_output_tail: "Validating kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml against\
+ \ schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues\
+ \ (1):\n [ERROR] Text part not found as substring: 'they did not differ within the same experiment'\n \
+ \ Location: ecological_interactions[3].evidence[2].snippet\n Reference: PMID:38609451\n\nValidation\
+ \ Summary:\n Total checks: 1\n Issues found: 1\n"
+ disposition: PDF word join rejected the initial excerpt; replaced with another literal passage from the same
+ primary paragraph, appended correction history, reran every gate. Caches and scientific interpretation unchanged.
+ known_snippet_audit_false_positive:
+ issue: 1863
+ path: kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml.discussions[0].evidence[0]
+ reference: PMID:38609451
+ snippet: attributing core metabolites to a specific co-culture partner is not possible
+ reported_class: MISMATCH
+ reported_coverage: 0.0
+ independent_normalization: NFKD/case/whitespace/punctuation contiguous match
+ source_sha256:
+ /private/tmp/communitymech-causal-batch110/references_cache/PMID_38609451.md: 823040c434fe5d39a55b9b7efe43ee277021dd2f22c979c71cd40142d6025b96
+ /private/tmp/communitymech-batch110/omics-primary.txt: d0297a40f3662014578949cac1f4e8434449b29db9f5887642006be0088bb8c8
+ disposition: Explicit single-quote exception for PDF fi ligature stripped by auditor. Primary and cache checked;
+ CLI references pass. Initial audit assertion stopped validation; shared auditor and canonical quote unchanged.
+ Follow-up1863 remains open.
+ snippet_counts_by_record:
+ kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml:
+ MATCH: 20
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml:
+ MATCH: 37
+ RENDERING: 2
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 1
+ NOCONTENT: 0
+ kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml:
+ MATCH: 37
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 8998
+ categories:
+ MATCH: 8858
+ RENDERING: 23
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 76
+ caveat: Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment.
+ network:
+ existing_findings_preserved: 56
+ added_findings: {}
+ removed_findings: {}
+ interpretation: Ten nodes and six existing directions retained. All56existing warnings unchanged;zero structural
+ defects. Halomonas needs research1860;non-graph follow-ups1861-1862.
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml: 814876819500a172c6d4423086c5299d62b15e9915c1f96ed66fdaaf3367fb2e
+ tests/test_causal_review_batch110.py: 39b08c28d3140ebbd608ca57317d51e1302d36d8a5474c186873d918858f3b69
+ tests/test_causal_review_batch109.py: 2b244b24479edf6025412c2a42459e92151d4602a20f571fef8fade9769d92d5
+ tests/test_participating_taxa.py: f70e3c12c1c295edda98a5b9c60f0b791213a49b060be96071409fe0164188bc
+ tests/test_community_level_connectivity_credit.py: 4d13eaa74d04b6730e5e88c5aba5df1c2bc9aeea4597084274c48b9df9cd5247
+ reports/causal_graph_review/cache-provenance-20261008-batch110.json: 7fb379fd4c081d4251b9f6599018a5db9a2fdab31ccdf852957b06cc4107dbac
+ kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml: 6f80bc26157b469b40d247d9d8bdf08aacee7ce6009e53527820248179397b3c
+ kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml: 76fe4a6229c920128650e889592471c220a7a42283bc97c605c6d9615983cf8a
+ kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml: 826172b3e4ec14cb21b506f830175d55dc982b3ee809bc7811e9a29cb67e231c
+ history_sha256:
+ history/records/Synechococcus_Halomonas_Light_Driven_PHB_Coculture/2026-10-08T053619Z-codex-d68757.yaml: 29a2002ea46efe7131363d795998e84f55922a89ac49c3e15bd0b12e4176b9f0
+ history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T053619Z-codex-9a9ab2.yaml: 530d6eb19253d8f043ec446dacd61e44f748057e590bde24b093b69e18ff812b
+ history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T054129Z-codex-d4dcce.yaml: 344a6752a0d6009012e4ee7dd69684556e9b384d9ac6c27601398d7a472d5b1c
+ history/records/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium/2026-10-08T053619Z-codex-a21481.yaml: 14157eebb8d1446fc0613b16cd2f9c2c39e1a884658eab29249c639d241d2d27
+ unchanged_records: 457
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 840
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Existing node scope/evidence repairs and qualification of identical existing directions. Missing
+ primary methods are an access/scope follow-up,not topology extension.
+ post_commit_docs_current: Separate publication gate, not preasserted.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 407
+ mixed: 132
+ community_level_only: 275
+ taxa: 1552
+ credited_solely_by_the_rule: 1270
+ current:
+ records: 460
+ with_community_level: 408
+ mixed: 133
+ community_level_only: 275
+ taxa: 1554
+ credited_solely_by_the_rule: 1270
+ delta:
+ records: 0
+ with_community_level: 1
+ mixed: 1
+ community_level_only: 0
+ taxa: 2
+ credited_solely_by_the_rule: 0
+ interpretation: Shewanella electrode output and device intervention gain community-level identity-only scope.
+ One additional mixed-scope record and two taxa in survey;zero new solely-credited taxa. Exact census and observational
+ bounds updated;connectivity and share rules unchanged.
+corpus:
+ records: 460
+ nodes: 1381
+ edges: 544
+ review_status_counts:
+ needs_research: 53
+ pending: 55
+ reviewed: 352
+lint_limitation: Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies
+ unchanged. Not a complete embedding runtime.
+limitations:
+- Fresh both-root baseline before primary reads:460 records,923 caches,56 existing warnings,zero structural defects.
+ Three full targets and ten nodes/six arrows reviewed. All topology retained; no new nodes/directions or Edison
+ spend.
+- Primary texts independently retrieved via EuropePMC with exact Crossref DOI checks. Read spans:PHA abstract/background/Results/Discussion/Conclusions
+ and initial Methods lines1-114;DNT summary/main Results/Discussion/Methods/captions lines1-145;omics abstract/main
+ Results/Discussion/captions lines1-160;Shewanella abstract/main Results/Discussion/captions/initial Methods lines1-128;nitrate
+ abstract/introduction1-18 and coculture Results/Discussion/Conclusion55-94. Truncated spans were reread; remaining
+ Methods, supplementary files, figure pixels and raw datasets not audited.
+- Halomonas independently retrieved primary abstract and whole committed abstract cache read. No PMCID;DOI landing
+ inaccessible,publisher403,author pagecitation only. Bounded title/DOI/OSTI search did not retrieve primary full
+ article. This is not global absence. LC1/complete organic inputs/isolated encapsulation mediation remain1860 and
+ needs_research;not silently certified. Existing canonical taxonomy untouched.
+- Other five cache content-type/section headers inspected,not whole caches. All graph/discussion quotations checked
+ against fresh primary and unchanged caches. Case/spacing/hyphen normalization accommodates XML/PDF rendering;matches
+ alone do not prove entailment. DNT oxidation/mineralization distinction comes from direct Results/Discussion,not
+ a removal-only assay. No source-cache changes.
+- Retain Halomonas feeding,PHB/persistence and alginate intervention;remove duplicate exchange/colonization typing
+ and unsupported organic-input exclusion. Keep alginate mechanism in text without asserting alginic-acid protonation.
+ Existing alginate-to-PHB direction stays HYPOTHESIZED/PARTIAL.
+- Pseudomonas preserves separate cscAB,cscRABY/nitrate-blind and EM173 implementations. PHA family not PHB;8.8-fold
+ endpoint not rate;DNT disappearance not complete mineralization. Conditional mutualism retains carbon supply/cyanobacterial
+ benefit,not heterotroph advantage over externally fed controls. Additional molecular exchange unresolved,not reverse
+ sucrose. General PHA term reused from same record.
+- Shewanella retains D-lactate contribution,not substrate exclusivity. Anode is abiotic recipient;positive cyanobacterial
+ growth is retained separately from hypothetical CO2-return mediation. Retain existing reverse direction using
+ source Fig1 proposal,not device-separation wording. Device modes and replenishment/LB context qualified. D-lactate
+ CHEBI16004 canonical label checked against EBI acid/base relation and focused term validation. No new engineering/cultivation/protocol
+ instructions.
+- Whole reviewed Azotobacter neighboring record and reusable Shewanella MR1 taxon record read as modeling context,not
+ evidence for targets. Reusable record is not linked automatically to the engineered derivative;no gene claims
+ copied. Ignored/hidden kb/taxa search found only that matching reusable taxon. Fresh all-state title/body dedup
+ matched1093,258,1851,1669,1606,1605,837,836,835;all wholebodies and related529 read. Local matching-path index
+ read,not every report;PRs/comments not exhaustive.
+- Only ecological_interactions,discussions,curation_history change. Preserve other457records,all923caches,non-graph
+ rawblocks and prior history/decisionfiles. Issues1857-1859 remainopen untilprotectedmainmerge;research1860 and
+ nongraph1861-1862 remainopen afterward. Self-review is not independent approval or full corpus completion. No
+ schema/validator/runtime change. Participantcensus updates must be measurement-based with unchanged connectivity/share
+ rules. Loader1703,DOIcase1091,cachepolicy949/1093 not certified. Denied/unanswered Edison scopes untouched.
+- Replace growth-rate excerpt with an exact passage shared by the primary XML and unchanged PDF cache; the initial
+ CLI rejected a PDF word-join artifact. Matched-control growth interpretation and graph topology are unchanged.
+ Issue#1858. Four append-only histories across three records; no prior history rewritten.
+- Local snippet auditor reports one exact known MISMATCH for the Pseudomonas discussion because it drops the PDF
+ fi ligature. Primary XML and unchanged cache match under independent NFKD normalization; CLI references pass.
+ Preserve the faithful quote and record the exact classification rather than claiming a clean snippet audit. Shared-auditor
+ follow-up1863 remains open; related257/596 and fresh all-state title/body dedup reviewed. Initial audit assertion
+ failure is retained; no shared validator change.
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch110.json b/reports/causal_graph_review/cache-provenance-20261008-batch110.json
new file mode 100644
index 000000000..32daf6e72
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch110.json
@@ -0,0 +1,372 @@
+{
+ "changes": [],
+ "unchanged_cache_files": 923,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch110/baseline.json": "2d61587c414ad3b2ef5fbdc650b81772d471574f15c35d8c7dbd57e56d2a30ea",
+ "/private/tmp/communitymech-batch110/dedup-local-current.txt": "c9c9f9d438450928edc05384a25f765678d8d2fd4b0b4408b4f97255469ed3ac",
+ "/private/tmp/communitymech-batch110/dnt-abstract.txt": "b6e9c4ab7cace0d0ef29b1726ff8eb4942244cd125cbe3987ab41fc44ddbf6d4",
+ "/private/tmp/communitymech-batch110/dnt-crossref.json": "184149be5823a9e4b1684a0344adc74340023f4ad9eba9219844a28a79a36390",
+ "/private/tmp/communitymech-batch110/dnt-metadata.json": "154834ded50858b67c2514387282426a85286464d0c2a04947b040b54a6c94ad",
+ "/private/tmp/communitymech-batch110/dnt-primary.txt": "8f3f442f6892761829ce27b43766cd9d6f331d9b039bab5d33771b3c29bac51c",
+ "/private/tmp/communitymech-batch110/dnt-primary.xml": "a4a8e42b6f8c85c62947ec7106147082bf4446093e9fdedfcb52491282e7fcc0",
+ "/private/tmp/communitymech-batch110/halomonas-abstract.txt": "b868eefc2a9142bca52838ec23dee3ce50915b0fc12f30b0b754528b6d7d73b5",
+ "/private/tmp/communitymech-batch110/halomonas-crossref.json": "824b0951ae3ae72cf654ac78fb28b94af1d63a5d9dfac6ca4204ed07c7cc20b9",
+ "/private/tmp/communitymech-batch110/halomonas-metadata.json": "3ee4bb9699d6787306348303002e5ebcad8a59f7744fbac5e57fab2cd0801e70",
+ "/private/tmp/communitymech-batch110/issue-dedup-current.json": "af05eaaf59a0ec9ad8b34670607630bcd09768d9060c7dde985cde0307b5c28b",
+ "/private/tmp/communitymech-batch110/nitrate-abstract.txt": "4fa0999fb18f1d0d07a32121ba889901aad4baf4a0da27ecc61df1b7e965b635",
+ "/private/tmp/communitymech-batch110/nitrate-crossref.json": "e9ec5824fbe0eed19243b6d8d89df2590ecde066c7498fe610ed1401f03cc154",
+ "/private/tmp/communitymech-batch110/nitrate-metadata.json": "e1c5908d99176ffb94d88ead705b3fd7c3ddfef07e703fae224bed6b352e46f9",
+ "/private/tmp/communitymech-batch110/nitrate-primary.txt": "fe01a626b490ac32bef31fb500fb27f502407bb0ea7237c103fff3061d3f5de0",
+ "/private/tmp/communitymech-batch110/nitrate-primary.xml": "6e2fdb0a75a40423c0a89b1eb10b0ec69d3567fd007edfea1cc5802bfb934b79",
+ "/private/tmp/communitymech-batch110/omics-abstract.txt": "02ad6aa0500370c45c0aa822ea952b0eebc888f1b9ee2a088eeaffd1bf8328c7",
+ "/private/tmp/communitymech-batch110/omics-crossref.json": "04f8ba720123113007e4ba9cad89797f79eed0a20224c2212b2abe37a280009a",
+ "/private/tmp/communitymech-batch110/omics-metadata.json": "fa14cbdc872eac703ec9c78220fb37acc42932d0525a075ca5b2441455096726",
+ "/private/tmp/communitymech-batch110/omics-primary.txt": "d0297a40f3662014578949cac1f4e8434449b29db9f5887642006be0088bb8c8",
+ "/private/tmp/communitymech-batch110/omics-primary.xml": "c4d0c5a3b1d591c01d646680533feb9120f4c3c50a70c59eb3aca6c58ece3401",
+ "/private/tmp/communitymech-batch110/pha-abstract.txt": "b7a325beb7d96b8ad94d2f08157ce49e5beaa9698964b70c3b239f58ca8338d3",
+ "/private/tmp/communitymech-batch110/pha-crossref.json": "b1b3dabd9c57a01f06985c9d8300b07dafbd4970a9c6ba5f2efe8d8910a354d0",
+ "/private/tmp/communitymech-batch110/pha-metadata.json": "c0a71d945741a7d3e2fcac0e70eeeaf73b377e7a40efaa94a4479fad8e058f1b",
+ "/private/tmp/communitymech-batch110/pha-primary.txt": "1de61ab6b36360fd4d1c1a4a740e20ec2cf803b066a670062f42a0df943f4db9",
+ "/private/tmp/communitymech-batch110/pha-primary.xml": "433ffdbbe24ed62e1207c6dc608638e84fef6a792317c065d20d07d628cf322d",
+ "/private/tmp/communitymech-batch110/primary-manifest.json": "559dd1bccc435efd5fbc16269bffe9474d3651ed392e5e2502751f30ca2ddb88",
+ "/private/tmp/communitymech-batch110/shewanella-abstract.txt": "a70dd2377d0e8341a94290c489b5c9144d670e6da089d22a822170409c8781c3",
+ "/private/tmp/communitymech-batch110/shewanella-crossref.json": "1c9c86d88af3b5725083eadc39437ee8044436528596bd6b7dd70c8725901a92",
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+ "license": [
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+ ],
+ "crossref": "/private/tmp/communitymech-batch110/dnt-crossref.json",
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+ "doi": "10.3389/fbioe.2020.00486",
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+ "title": "A Nitrate-Blind P. putida Strain Boosts PHA Production in a Synthetic Mixed Culture.",
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+ "abstract": "/private/tmp/communitymech-batch110/nitrate-abstract.txt",
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+ "xml_sha256": "6e2fdb0a75a40423c0a89b1eb10b0ec69d3567fd007edfea1cc5802bfb934b79",
+ "primary_text": "/private/tmp/communitymech-batch110/nitrate-primary.txt",
+ "primary_text_sha256": "fe01a626b490ac32bef31fb500fb27f502407bb0ea7237c103fff3061d3f5de0",
+ "license": [
+ "This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms."
+ ],
+ "crossref": "/private/tmp/communitymech-batch110/nitrate-crossref.json",
+ "crossref_sha256": "e9ec5824fbe0eed19243b6d8d89df2590ecde066c7498fe610ed1401f03cc154",
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+ "omics": {
+ "pmid": "38609451",
+ "doi": "10.1038/s42003-024-06098-5",
+ "pmcid": "PMC11014904",
+ "title": "Pseudomonas putida as saviour for troubled Synechococcus elongatus in a synthetic co-culture - interaction studies based on a multi-OMICs approach.",
+ "metadata": "/private/tmp/communitymech-batch110/omics-metadata.json",
+ "metadata_sha256": "fa14cbdc872eac703ec9c78220fb37acc42932d0525a075ca5b2441455096726",
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+ "status": "retrieved"
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11014904/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch110/omics-abstract.txt",
+ "abstract_sha256": "02ad6aa0500370c45c0aa822ea952b0eebc888f1b9ee2a088eeaffd1bf8328c7",
+ "xml": "/private/tmp/communitymech-batch110/omics-primary.xml",
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+ "primary_text_sha256": "d0297a40f3662014578949cac1f4e8434449b29db9f5887642006be0088bb8c8",
+ "license": [
+ "https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article\u2019s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article\u2019s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/."
+ ],
+ "crossref": "/private/tmp/communitymech-batch110/omics-crossref.json",
+ "crossref_sha256": "04f8ba720123113007e4ba9cad89797f79eed0a20224c2212b2abe37a280009a",
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+ },
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+ "delay-in-days": 0,
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+ }
+ ]
+ },
+ "shewanella": {
+ "pmid": "31537786",
+ "doi": "10.1038/s41467-019-12190-w",
+ "pmcid": "PMC6753107",
+ "title": "Development of a longevous two-species biophotovoltaics with constrained electron flow.",
+ "metadata": "/private/tmp/communitymech-batch110/shewanella-metadata.json",
+ "metadata_sha256": "986590bf3b94aaca2023e4f4e4253a141f37daf5b6a69eb579c4fdb866838e0c",
+ "retrievals": [
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+ "status": "retrieved"
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6753107/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch110/shewanella-abstract.txt",
+ "abstract_sha256": "a70dd2377d0e8341a94290c489b5c9144d670e6da089d22a822170409c8781c3",
+ "xml": "/private/tmp/communitymech-batch110/shewanella-primary.xml",
+ "xml_sha256": "52316f1590836be781beaba85238f8839d064f350ac3c953135a8855213e0f2c",
+ "primary_text": "/private/tmp/communitymech-batch110/shewanella-primary.txt",
+ "primary_text_sha256": "a63997f2d187c4d97b1651a4526ab8b76b3ee414f33230d57cd9d8f25e4da05a",
+ "license": [
+ "https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article\u2019s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article\u2019s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/."
+ ],
+ "crossref": "/private/tmp/communitymech-batch110/shewanella-crossref.json",
+ "crossref_sha256": "1c9c86d88af3b5725083eadc39437ee8044436528596bd6b7dd70c8725901a92",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2019,
+ 9,
+ 19
+ ]
+ ],
+ "date-time": "2019-09-19T00:00:00Z",
+ "timestamp": 1568851200000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2019,
+ 9,
+ 19
+ ]
+ ],
+ "date-time": "2019-09-19T00:00:00Z",
+ "timestamp": 1568851200000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0"
+ }
+ ]
+ }
+ },
+ "actual_read_scope": [
+ "Primary texts independently retrieved via EuropePMC with exact Crossref DOI checks. Read spans:PHA abstract/background/Results/Discussion/Conclusions and initial Methods lines1-114;DNT summary/main Results/Discussion/Methods/captions lines1-145;omics abstract/main Results/Discussion/captions lines1-160;Shewanella abstract/main Results/Discussion/captions/initial Methods lines1-128;nitrate abstract/introduction1-18 and coculture Results/Discussion/Conclusion55-94. Truncated spans were reread; remaining Methods, supplementary files, figure pixels and raw datasets not audited.",
+ "Halomonas independently retrieved primary abstract and whole committed abstract cache read. No PMCID;DOI landing inaccessible,publisher403,author pagecitation only. Bounded title/DOI/OSTI search did not retrieve primary full article. This is not global absence. LC1/complete organic inputs/isolated encapsulation mediation remain1860 and needs_research;not silently certified. Existing canonical taxonomy untouched.",
+ "Other five cache content-type/section headers inspected,not whole caches. All graph/discussion quotations checked against fresh primary and unchanged caches. Case/spacing/hyphen normalization accommodates XML/PDF rendering;matches alone do not prove entailment. DNT oxidation/mineralization distinction comes from direct Results/Discussion,not a removal-only assay. No source-cache changes."
+ ],
+ "bounded_fulltext_search": {
+ "doi": "https://doi.org/10.1016/j.ymben.2017.10.009",
+ "publisher": "https://www.sciencedirect.com/science/article/abs/pii/S1096717617301763",
+ "author": "https://faculty.engineering.asu.edu/taylorlweiss/publications/",
+ "fulltext_retrieved": false
+ }
+ },
+ "limitations": [
+ "Fresh both-root baseline before primary reads:460 records,923 caches,56 existing warnings,zero structural defects. Three full targets and ten nodes/six arrows reviewed. All topology retained; no new nodes/directions or Edison spend.",
+ "Primary texts independently retrieved via EuropePMC with exact Crossref DOI checks. Read spans:PHA abstract/background/Results/Discussion/Conclusions and initial Methods lines1-114;DNT summary/main Results/Discussion/Methods/captions lines1-145;omics abstract/main Results/Discussion/captions lines1-160;Shewanella abstract/main Results/Discussion/captions/initial Methods lines1-128;nitrate abstract/introduction1-18 and coculture Results/Discussion/Conclusion55-94. Truncated spans were reread; remaining Methods, supplementary files, figure pixels and raw datasets not audited.",
+ "Halomonas independently retrieved primary abstract and whole committed abstract cache read. No PMCID;DOI landing inaccessible,publisher403,author pagecitation only. Bounded title/DOI/OSTI search did not retrieve primary full article. This is not global absence. LC1/complete organic inputs/isolated encapsulation mediation remain1860 and needs_research;not silently certified. Existing canonical taxonomy untouched.",
+ "Other five cache content-type/section headers inspected,not whole caches. All graph/discussion quotations checked against fresh primary and unchanged caches. Case/spacing/hyphen normalization accommodates XML/PDF rendering;matches alone do not prove entailment. DNT oxidation/mineralization distinction comes from direct Results/Discussion,not a removal-only assay. No source-cache changes.",
+ "Retain Halomonas feeding,PHB/persistence and alginate intervention;remove duplicate exchange/colonization typing and unsupported organic-input exclusion. Keep alginate mechanism in text without asserting alginic-acid protonation. Existing alginate-to-PHB direction stays HYPOTHESIZED/PARTIAL.",
+ "Pseudomonas preserves separate cscAB,cscRABY/nitrate-blind and EM173 implementations. PHA family not PHB;8.8-fold endpoint not rate;DNT disappearance not complete mineralization. Conditional mutualism retains carbon supply/cyanobacterial benefit,not heterotroph advantage over externally fed controls. Additional molecular exchange unresolved,not reverse sucrose. General PHA term reused from same record.",
+ "Shewanella retains D-lactate contribution,not substrate exclusivity. Anode is abiotic recipient;positive cyanobacterial growth is retained separately from hypothetical CO2-return mediation. Retain existing reverse direction using source Fig1 proposal,not device-separation wording. Device modes and replenishment/LB context qualified. D-lactate CHEBI16004 canonical label checked against EBI acid/base relation and focused term validation. No new engineering/cultivation/protocol instructions.",
+ "Whole reviewed Azotobacter neighboring record and reusable Shewanella MR1 taxon record read as modeling context,not evidence for targets. Reusable record is not linked automatically to the engineered derivative;no gene claims copied. Ignored/hidden kb/taxa search found only that matching reusable taxon. Fresh all-state title/body dedup matched1093,258,1851,1669,1606,1605,837,836,835;all wholebodies and related529 read. Local matching-path index read,not every report;PRs/comments not exhaustive.",
+ "Only ecological_interactions,discussions,curation_history change. Preserve other457records,all923caches,non-graph rawblocks and prior history/decisionfiles. Issues1857-1859 remainopen untilprotectedmainmerge;research1860 and nongraph1861-1862 remainopen afterward. Self-review is not independent approval or full corpus completion. No schema/validator/runtime change. Participantcensus updates must be measurement-based with unchanged connectivity/share rules. Loader1703,DOIcase1091,cachepolicy949/1093 not certified. Denied/unanswered Edison scopes untouched."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml b/reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
new file mode 100644
index 000000000..fc390a233
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
@@ -0,0 +1,846 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 9b429a9fa64f383ece90031645efbb8f913e111b
+baseline_commit: 9b429a9fa64f383ece90031645efbb8f913e111b
+base_tree: 5b3c9f4f87ad147d839e896d6388695107f9fed3
+pre_source_baseline_sha256: 2d61587c414ad3b2ef5fbdc650b81772d471574f15c35d8c7dbd57e56d2a30ea
+issues:
+- 1857
+- 1858
+- 1859
+unresolved_research_issues:
+- 1860
+unresolved_non_graph_issues:
+- 1861
+- 1862
+source_access:
+ retrieval_manifest:
+ halomonas:
+ pmid: '29061492'
+ doi: 10.1016/j.ymben.2017.10.009
+ pmcid: null
+ title: A synthetic, light-driven consortium of cyanobacteria and heterotrophic bacteria enables stable polyhydroxybutyrate
+ production.
+ metadata: /private/tmp/communitymech-batch110/halomonas-metadata.json
+ metadata_sha256: 3ee4bb9699d6787306348303002e5ebcad8a59f7744fbac5e57fab2cd0801e70
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A29061492+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ abstract: /private/tmp/communitymech-batch110/halomonas-abstract.txt
+ abstract_sha256: b868eefc2a9142bca52838ec23dee3ce50915b0fc12f30b0b754528b6d7d73b5
+ crossref: /private/tmp/communitymech-batch110/halomonas-crossref.json
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+ crossref_license:
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+ title: Photoautotrophic production of polyhydroxyalkanoates in a synthetic mixed culture of Synechococcus
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+ nitrate:
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+ pmcid: PMC7261876
+ title: A Nitrate-Blind P. putida Strain Boosts PHA Production in a Synthetic Mixed Culture.
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+ license:
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+ \ Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction\
+ \ in any medium or format, as long as you give appropriate credit to the original author(s) and the source,\
+ \ provide a link to the Creative Commons licence, and indicate if changes were made. The images or other\
+ \ third party material in this article are included in the article\u2019s Creative Commons licence, unless\
+ \ indicated otherwise in a credit line to the material. If material is not included in the article\u2019\
+ s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the\
+ \ permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of\
+ \ this licence, visit http://creativecommons.org/licenses/by/4.0/."
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+ shewanella:
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+ doi: 10.1038/s41467-019-12190-w
+ pmcid: PMC6753107
+ title: Development of a longevous two-species biophotovoltaics with constrained electron flow.
+ metadata: /private/tmp/communitymech-batch110/shewanella-metadata.json
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+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6753107/fullTextXML
+ status: retrieved_not_yet_read
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+ abstract_sha256: a70dd2377d0e8341a94290c489b5c9144d670e6da089d22a822170409c8781c3
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+ primary_text_sha256: a63997f2d187c4d97b1651a4526ab8b76b3ee414f33230d57cd9d8f25e4da05a
+ license:
+ - "https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons\
+ \ Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction\
+ \ in any medium or format, as long as you give appropriate credit to the original author(s) and the source,\
+ \ provide a link to the Creative Commons license, and indicate if changes were made. The images or other\
+ \ third party material in this article are included in the article\u2019s Creative Commons license, unless\
+ \ indicated otherwise in a credit line to the material. If material is not included in the article\u2019\
+ s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the\
+ \ permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of\
+ \ this license, visit http://creativecommons.org/licenses/by/4.0/."
+ crossref: /private/tmp/communitymech-batch110/shewanella-crossref.json
+ crossref_sha256: 1c9c86d88af3b5725083eadc39437ee8044436528596bd6b7dd70c8725901a92
+ crossref_license:
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+ timestamp: 1568851200000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0
+ - start:
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+ timestamp: 1568851200000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0
+ actual_read_scope:
+ - Primary texts independently retrieved via EuropePMC with exact Crossref DOI checks. Read spans:PHA abstract/background/Results/Discussion/Conclusions
+ and initial Methods lines1-114;DNT summary/main Results/Discussion/Methods/captions lines1-145;omics abstract/main
+ Results/Discussion/captions lines1-160;Shewanella abstract/main Results/Discussion/captions/initial Methods
+ lines1-128;nitrate abstract/introduction1-18 and coculture Results/Discussion/Conclusion55-94. Truncated spans
+ were reread; remaining Methods, supplementary files, figure pixels and raw datasets not audited.
+ - Halomonas independently retrieved primary abstract and whole committed abstract cache read. No PMCID;DOI landing
+ inaccessible,publisher403,author pagecitation only. Bounded title/DOI/OSTI search did not retrieve primary full
+ article. This is not global absence. LC1/complete organic inputs/isolated encapsulation mediation remain1860
+ and needs_research;not silently certified. Existing canonical taxonomy untouched.
+ - Other five cache content-type/section headers inspected,not whole caches. All graph/discussion quotations checked
+ against fresh primary and unchanged caches. Case/spacing/hyphen normalization accommodates XML/PDF rendering;matches
+ alone do not prove entailment. DNT oxidation/mineralization distinction comes from direct Results/Discussion,not
+ a removal-only assay. No source-cache changes.
+ bounded_fulltext_search:
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+ publisher: https://www.sciencedirect.com/science/article/abs/pii/S1096717617301763
+ author: https://faculty.engineering.asu.edu/taylorlweiss/publications/
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+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/dnt-primary.txt
+ cache_artifact: references_cache/PMID_32064751.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+ node: Heterotrophic PHA Accumulation
+ evidence_index: 0
+ reference: PMID:28814973
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/pha-primary.txt
+ cache_artifact: references_cache/PMID_28814973.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+ node: Heterotrophic PHA Accumulation
+ evidence_index: 1
+ reference: PMID:32523942
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/nitrate-primary.txt
+ cache_artifact: references_cache/PMID_32523942.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+ node: DNT Biotransformation with Photosynthetic Carbon Input
+ evidence_index: 0
+ reference: PMID:32064751
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/dnt-primary.txt
+ cache_artifact: references_cache/PMID_32064751.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+ node: DNT Biotransformation with Photosynthetic Carbon Input
+ evidence_index: 1
+ reference: PMID:32064751
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/dnt-primary.txt
+ cache_artifact: references_cache/PMID_32064751.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+ node: DNT Biotransformation with Photosynthetic Carbon Input
+ evidence_index: 2
+ reference: PMID:32064751
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/dnt-primary.txt
+ cache_artifact: references_cache/PMID_32064751.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+ node: Growth-Promoting Partner Feedback
+ evidence_index: 0
+ reference: PMID:38609451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/omics-primary.txt
+ cache_artifact: references_cache/PMID_38609451.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+ node: Growth-Promoting Partner Feedback
+ evidence_index: 1
+ reference: PMID:38609451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/omics-primary.txt
+ cache_artifact: references_cache/PMID_38609451.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+ node: Growth-Promoting Partner Feedback
+ evidence_index: 2
+ reference: PMID:38609451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/omics-primary.txt
+ cache_artifact: references_cache/PMID_38609451.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: Photosynthetic D-Lactate Cross-Feeding
+ evidence_index: 0
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: Photosynthetic D-Lactate Cross-Feeding
+ evidence_index: 1
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: Photosynthetic D-Lactate Cross-Feeding
+ evidence_index: 2
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: Shewanella Anode Electron Transfer
+ evidence_index: 0
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: Shewanella Anode Electron Transfer
+ evidence_index: 1
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: Shewanella Anode Electron Transfer
+ evidence_index: 2
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: Spatial-Temporal Separation for Compatibility
+ evidence_index: 0
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: Spatial-Temporal Separation for Compatibility
+ evidence_index: 1
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: Spatial-Temporal Separation for Compatibility
+ evidence_index: 2
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+discussion_snippet_checks:
+- record: Synechococcus_Halomonas_Light_Driven_PHB_Coculture
+ node: halomonas-strain-and-production-context
+ evidence_index: 0
+ reference: PMID:29061492
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/halomonas-abstract.txt
+ cache_artifact: references_cache/PMID_29061492.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture
+ node: pseudomonas-growth-feedback-mediator
+ evidence_index: 0
+ reference: PMID:38609451
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/omics-primary.txt
+ cache_artifact: references_cache/PMID_38609451.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+- record: Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium
+ node: shewanella-carbon-return-versus-electrode-output
+ evidence_index: 0
+ reference: PMID:31537786
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch110/shewanella-primary.txt
+ cache_artifact: references_cache/PMID_31537786.md
+ scope: Normalized literal match to fresh primary and unchanged cache; entailment reviewed separately.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Existing node scope/evidence repairs and qualification of identical existing directions. Missing
+ primary methods are an access/scope follow-up,not topology extension.
+limitations:
+- Fresh both-root baseline before primary reads:460 records,923 caches,56 existing warnings,zero structural defects.
+ Three full targets and ten nodes/six arrows reviewed. All topology retained; no new nodes/directions or Edison
+ spend.
+- Primary texts independently retrieved via EuropePMC with exact Crossref DOI checks. Read spans:PHA abstract/background/Results/Discussion/Conclusions
+ and initial Methods lines1-114;DNT summary/main Results/Discussion/Methods/captions lines1-145;omics abstract/main
+ Results/Discussion/captions lines1-160;Shewanella abstract/main Results/Discussion/captions/initial Methods lines1-128;nitrate
+ abstract/introduction1-18 and coculture Results/Discussion/Conclusion55-94. Truncated spans were reread; remaining
+ Methods, supplementary files, figure pixels and raw datasets not audited.
+- Halomonas independently retrieved primary abstract and whole committed abstract cache read. No PMCID;DOI landing
+ inaccessible,publisher403,author pagecitation only. Bounded title/DOI/OSTI search did not retrieve primary full
+ article. This is not global absence. LC1/complete organic inputs/isolated encapsulation mediation remain1860 and
+ needs_research;not silently certified. Existing canonical taxonomy untouched.
+- Other five cache content-type/section headers inspected,not whole caches. All graph/discussion quotations checked
+ against fresh primary and unchanged caches. Case/spacing/hyphen normalization accommodates XML/PDF rendering;matches
+ alone do not prove entailment. DNT oxidation/mineralization distinction comes from direct Results/Discussion,not
+ a removal-only assay. No source-cache changes.
+- Retain Halomonas feeding,PHB/persistence and alginate intervention;remove duplicate exchange/colonization typing
+ and unsupported organic-input exclusion. Keep alginate mechanism in text without asserting alginic-acid protonation.
+ Existing alginate-to-PHB direction stays HYPOTHESIZED/PARTIAL.
+- Pseudomonas preserves separate cscAB,cscRABY/nitrate-blind and EM173 implementations. PHA family not PHB;8.8-fold
+ endpoint not rate;DNT disappearance not complete mineralization. Conditional mutualism retains carbon supply/cyanobacterial
+ benefit,not heterotroph advantage over externally fed controls. Additional molecular exchange unresolved,not reverse
+ sucrose. General PHA term reused from same record.
+- Shewanella retains D-lactate contribution,not substrate exclusivity. Anode is abiotic recipient;positive cyanobacterial
+ growth is retained separately from hypothetical CO2-return mediation. Retain existing reverse direction using
+ source Fig1 proposal,not device-separation wording. Device modes and replenishment/LB context qualified. D-lactate
+ CHEBI16004 canonical label checked against EBI acid/base relation and focused term validation. No new engineering/cultivation/protocol
+ instructions.
+- Whole reviewed Azotobacter neighboring record and reusable Shewanella MR1 taxon record read as modeling context,not
+ evidence for targets. Reusable record is not linked automatically to the engineered derivative;no gene claims
+ copied. Ignored/hidden kb/taxa search found only that matching reusable taxon. Fresh all-state title/body dedup
+ matched1093,258,1851,1669,1606,1605,837,836,835;all wholebodies and related529 read. Local matching-path index
+ read,not every report;PRs/comments not exhaustive.
+- Only ecological_interactions,discussions,curation_history change. Preserve other457records,all923caches,non-graph
+ rawblocks and prior history/decisionfiles. Issues1857-1859 remainopen untilprotectedmainmerge;research1860 and
+ nongraph1861-1862 remainopen afterward. Self-review is not independent approval or full corpus completion. No
+ schema/validator/runtime change. Participantcensus updates must be measurement-based with unchanged connectivity/share
+ rules. Loader1703,DOIcase1091,cachepolicy949/1093 not certified. Denied/unanswered Edison scopes untouched.
+- Replace growth-rate excerpt with an exact passage shared by the primary XML and unchanged PDF cache; the initial
+ CLI rejected a PDF word-join artifact. Matched-control growth interpretation and graph topology are unchanged.
+ Issue#1858. Four append-only histories across three records; no prior history rewritten.
+- Local snippet auditor reports one exact known MISMATCH for the Pseudomonas discussion because it drops the PDF
+ fi ligature. Primary XML and unchanged cache match under independent NFKD normalization; CLI references pass.
+ Preserve the faithful quote and record the exact classification rather than claiming a clean snippet audit. Shared-auditor
+ follow-up1863 remains open; related257/596 and fresh all-state title/body dedup reviewed. Initial audit assertion
+ failure is retained; no shared validator change.
+records:
+- path: kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml
+ id: CommunityMech:000198
+ original_sha256: 5990528941355c726bbeca0d65db9327c4455a131cd32d14c5e39a9f50dce4b1
+ record_sha256: 6f80bc26157b469b40d247d9d8bdf08aacee7ce6009e53527820248179397b3c
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
+ scope: Whole record and every existing node/direction; graph repair, not whole-record certification.
+ summary: Retain abstract-supported sucrose feeding while exposing unresolved LC1/medium scope.; Retain PHB and
+ persistence as a community phenotype, not duplicate exchange or photosynthesis.; Retain alginate intervention
+ effects without colonization typing or proven PHB mediation.
+ node_decisions:
+ - node: Photosynthetic Sucrose Transfer To Halomonas
+ rationale: Retain abstract-supported sucrose feeding while exposing unresolved LC1/medium scope.
+ - node: Light-Driven Biopolymer Production
+ rationale: Retain PHB and persistence as a community phenotype, not duplicate exchange or photosynthesis.
+ - node: Alginate-Partitioned Coculture Stabilization
+ rationale: Retain alginate intervention effects without colonization typing or proven PHB mediation.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id001
+ source: Photosynthetic Sucrose Transfer To Halomonas
+ target: Light-Driven Biopolymer Production
+ description: 'Exported cyanobacterial sucrose is the photosynthetically derived organic carbon that H. boliviensis
+ consumes to support PHB accumulation without added external organic carbon.
+
+ '
+ - &id003
+ source: Alginate-Partitioned Coculture Stabilization
+ target: Light-Driven Biopolymer Production
+ description: Enhanced sucrose export and improved partitioned-coculture stability increase the reliability of
+ cyanobacterial sucrose delivery that supports Halomonas PHB accumulation.
+ edges_after:
+ - &id002
+ source: Photosynthetic Sucrose Transfer To Halomonas
+ target: Light-Driven Biopolymer Production
+ description: Photosynthetically supplied sucrose supports the PHB-producing Halomonas partner. This preserves
+ the source-supported carbon-to-product route without asserting that the abstract proves exclusion of every
+ external organic input or a quantitative carbon balance.
+ - &id004
+ source: Alginate-Partitioned Coculture Stabilization
+ target: Light-Driven Biopolymer Production
+ description: 'HYPOTHESIZED/PARTIAL: alginate-enhanced sucrose export and stability could sustain carbon delivery
+ to the PHB producer. The abstract reports these benefits and PHB production but does not separate their causal
+ contributions to productivity.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: Photosynthetically supplied sucrose supports the PHB-producing Halomonas partner. This preserves
+ the source-supported carbon-to-product route without asserting that the abstract proves exclusion of every
+ external organic input or a quantitative carbon balance.
+ - before: *id003
+ after: *id004
+ rationale: 'HYPOTHESIZED/PARTIAL: alginate-enhanced sucrose export and stability could sustain carbon delivery
+ to the PHB producer. The abstract reports these benefits and PHB production but does not separate their causal
+ contributions to productivity.'
+ removed_edge_decisions: []
+ references:
+ - PMID:29061492
+ issues:
+ - 1857
+ - 1860
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Synechococcus_Halomonas_Light_Driven_PHB_Coculture/2026-10-08T053619Z-codex-d68757.yaml
+- path: kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml
+ id: CommunityMech:000167
+ original_sha256: f923cbc0711714b969a4d0c5769186050048b7af3521a1dc2c7bc6d39e040bdb
+ record_sha256: 76fe4a6229c920128650e889592471c220a7a42283bc97c605c6d9615983cf8a
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
+ scope: Whole record and every existing node/direction; graph repair, not whole-record certification.
+ summary: Retain sucrose carbon support with separate production and DNT assay contexts.; Retain PHA phenotype
+ with correct polymer-family grounding and endpoint comparison.; Retain DNT transformation and PHA outcome without
+ inferring complete mineralization.; Preserve conditional growth partnership without reverse sucrose donation
+ or identified mediator.
+ node_decisions:
+ - node: Photosynthetic Sucrose Cross-Feeding
+ rationale: Retain sucrose carbon support with separate production and DNT assay contexts.
+ - node: Heterotrophic PHA Accumulation
+ rationale: Retain PHA phenotype with correct polymer-family grounding and endpoint comparison.
+ - node: DNT Biotransformation with Photosynthetic Carbon Input
+ rationale: Retain DNT transformation and PHA outcome without inferring complete mineralization.
+ - node: Growth-Promoting Partner Feedback
+ rationale: Preserve conditional growth partnership without reverse sucrose donation or identified mediator.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id005
+ source: Photosynthetic Sucrose Cross-Feeding
+ target: Heterotrophic PHA Accumulation
+ description: Secreted sucrose provides the carbon source for P. putida PHA biosynthesis.
+ - &id007
+ source: Photosynthetic Sucrose Cross-Feeding
+ target: DNT Biotransformation with Photosynthetic Carbon Input
+ description: Secreted sucrose supports active metabolism of engineered P. putida during pollutant transformation.
+ edges_after:
+ - &id006
+ source: Photosynthetic Sucrose Cross-Feeding
+ target: Heterotrophic PHA Accumulation
+ description: Cyanobacterial sucrose supplies carbon for P. putida PHA accumulation in the production assays.
+ Polymer accumulation depends on the tested strain and nitrogen regime; the nitrate-blind comparison measures
+ final accumulation, not a production-rate increase.
+ - &id008
+ source: Photosynthetic Sucrose Cross-Feeding
+ target: DNT Biotransformation with Photosynthetic Carbon Input
+ description: In the separate EM173-derived DNT implementation, sucrose from encapsulated cyanobacteria supports
+ heterotrophic growth and metabolism during DNT biotransformation. This does not equate pollutant disappearance
+ with complete mineralization.
+ retained_edge_decisions:
+ - before: *id005
+ after: *id006
+ rationale: Cyanobacterial sucrose supplies carbon for P. putida PHA accumulation in the production assays. Polymer
+ accumulation depends on the tested strain and nitrogen regime; the nitrate-blind comparison measures final
+ accumulation, not a production-rate increase.
+ - before: *id007
+ after: *id008
+ rationale: In the separate EM173-derived DNT implementation, sucrose from encapsulated cyanobacteria supports
+ heterotrophic growth and metabolism during DNT biotransformation. This does not equate pollutant disappearance
+ with complete mineralization.
+ removed_edge_decisions: []
+ references:
+ - PMID:28814973
+ - PMID:32064751
+ - PMID:32523942
+ - PMID:38609451
+ issues:
+ - 1858
+ - 1861
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 2
+ history_files:
+ - history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T053619Z-codex-9a9ab2.yaml
+ - history/records/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T054129Z-codex-d4dcce.yaml
+- path: kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml
+ id: CommunityMech:000211
+ original_sha256: bde403de6edb430affdf758c26fca337040374a2b9ae74aa7623acfb55b22c59
+ record_sha256: 826172b3e4ec14cb21b506f830175d55dc982b3ee809bc7811e9a29cb67e231c
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml
+ scope: Whole record and every existing node/direction; graph repair, not whole-record certification.
+ summary: Retain D-lactate supply and anode support without exclusive organic-input claims.; Correct anode recipient
+ and preserve source-proposed CO2 feedback as hypothetical.; Retain abiotic compatibility and duration with distinct
+ replenished-device context.
+ node_decisions:
+ - node: Photosynthetic D-Lactate Cross-Feeding
+ rationale: Retain D-lactate supply and anode support without exclusive organic-input claims.
+ - node: Shewanella Anode Electron Transfer
+ rationale: Correct anode recipient and preserve source-proposed CO2 feedback as hypothetical.
+ - node: Spatial-Temporal Separation for Compatibility
+ rationale: Retain abiotic compatibility and duration with distinct replenished-device context.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id009
+ source: Photosynthetic D-Lactate Cross-Feeding
+ target: Shewanella Anode Electron Transfer
+ description: 'Photosynthetically produced D-lactate is the engineered carrier oxidized by S. oneidensis as it
+ releases electrons to the anode.
+
+ '
+ - &id011
+ source: Shewanella Anode Electron Transfer
+ target: Photosynthetic D-Lactate Cross-Feeding
+ description: 'Physical and temporal separation prevents light- and oxygen-associated inhibition of S. oneidensis
+ while preserving D-lactate transfer from the engineered cyanobacterium.
+
+ '
+ edges_after:
+ - &id010
+ source: Photosynthetic D-Lactate Cross-Feeding
+ target: Shewanella Anode Electron Transfer
+ description: Photosynthetically produced D-lactate is oxidized by the engineered Shewanella partner, supporting
+ electron transfer to the anode. Lactate-free and axenic comparisons support its contribution, not exclusive
+ attribution of all current to D-lactate.
+ - &id012
+ source: Shewanella Anode Electron Transfer
+ target: Photosynthetic D-Lactate Cross-Feeding
+ description: 'HYPOTHESIZED/PARTIAL: the source schematic proposes that CO2 released during Shewanella oxidation
+ can be re-assimilated by cyanobacteria for D-lactate production. The reviewed main text does not demonstrate
+ this carbon-return flux or identify it as the cause of cyanobacterial growth benefit; electrons flow to the
+ anode, not the cyanobacterium.'
+ retained_edge_decisions:
+ - before: *id009
+ after: *id010
+ rationale: Photosynthetically produced D-lactate is oxidized by the engineered Shewanella partner, supporting
+ electron transfer to the anode. Lactate-free and axenic comparisons support its contribution, not exclusive
+ attribution of all current to D-lactate.
+ - before: *id011
+ after: *id012
+ rationale: 'HYPOTHESIZED/PARTIAL: the source schematic proposes that CO2 released during Shewanella oxidation
+ can be re-assimilated by cyanobacteria for D-lactate production. The reviewed main text does not demonstrate
+ this carbon-return flux or identify it as the cause of cyanobacterial growth benefit; electrons flow to the
+ anode, not the cyanobacterium.'
+ removed_edge_decisions: []
+ references:
+ - PMID:31537786
+ issues:
+ - 1859
+ - 1862
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium/2026-10-08T053619Z-codex-a21481.yaml
+unresolved_validator_issues:
+- 1863
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index e79ad8db8..e686504f6 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -401,10 +401,10 @@ kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml
kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml CommunityMech:000207 a96409b502da3b96811a68db9d999ca493fd4ff455ae3e303ceb39a04538238a 3 2 96.7 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
kb/communities/Synechococcus_Bacillus_SPC.yaml CommunityMech:000065 a04fd02a2219aa3518ab4e4ac9bd35503d606b3b19d5332c0df65961f939fc4c 2 1 80.0 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
kb/communities/Synechococcus_Ecoli_SPC.yaml CommunityMech:000066 529766861de184236d78198a26eba1c964d999973a1230db145330bd875c3556 3 2 96.7 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
-kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml CommunityMech:000198 5990528941355c726bbeca0d65db9327c4455a131cd32d14c5e39a9f50dce4b1 3 2 100.0 pending
-kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml CommunityMech:000167 f923cbc0711714b969a4d0c5769186050048b7af3521a1dc2c7bc6d39e040bdb 4 2 100.0 pending
+kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml CommunityMech:000198 6f80bc26157b469b40d247d9d8bdf08aacee7ce6009e53527820248179397b3c 3 2 93.3 reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml needs_research
+kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml CommunityMech:000167 76fe4a6229c920128650e889592471c220a7a42283bc97c605c6d9615983cf8a 4 2 93.8 reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml reviewed
kb/communities/Synechococcus_Saccharomyces_SPC.yaml CommunityMech:000067 9c021f5bf08a2596743a140a3b14ca90e781d294234a09257a021324e8a20ac6 3 2 96.7 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
-kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml CommunityMech:000211 bde403de6edb430affdf758c26fca337040374a2b9ae74aa7623acfb55b22c59 3 2 100.0 pending
+kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml CommunityMech:000211 826172b3e4ec14cb21b506f830175d55dc982b3ee809bc7811e9a29cb67e231c 3 2 91.7 reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml reviewed
kb/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml CommunityMech:000363 0d0dd8d3ab938241d8e9f44d4aa1a9847058883cb5167c79aba7c5c5148392fa 2 1 85.0 pending
kb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml CommunityMech:000149 7824f8a6761528794f6d43efede940228e490a140dc57174a7c8ded5e6d7a208 3 2 100.0 pending
kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml CommunityMech:000130 a5d9d47e0a01cc492d9ad09971b02ece6c4292925e09d1919d00e29b8699492e 6 0 75.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index b16fd751e..7530e8bd1 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -7,9 +7,9 @@
"records_without_nodes": 10,
"records_without_edges": 185,
"review_status_counts": {
- "needs_research": 52,
- "pending": 58,
- "reviewed": 350
+ "needs_research": 53,
+ "pending": 55,
+ "reviewed": 352
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch110.json b/reports/causal_graph_review/validation-20261008-batch110.json
new file mode 100644
index 000000000..a527e8508
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch110.json
@@ -0,0 +1,1021 @@
+{
+ "base_commit": "9b429a9fa64f383ece90031645efbb8f913e111b",
+ "scope": [
+ "kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml",
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml",
+ "kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch110.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/focused.log",
+ "log_sha256": "a94c3c1c640b8791c2f5a9b3453c7d52b46a64d28d088d22f648edfad8fdf0e1",
+ "output_tail": "....... [100%]\n7 passed in 1.57s\n"
+ },
+ {
+ "check": "Synechococcus_Halomonas_Light_Driven_PHB_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Halomonas_Light_Driven_PHB_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Halomonas_Light_Driven_PHB_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch110/Synechococcus_Halomonas_Light_Driven_PHB_Coculture-strict.tsv",
+ "kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Halomonas_Light_Driven_PHB_Coculture-strict.log",
+ "log_sha256": "0f23d375041aaf7aaa548b1e3df56911bae1e86e072fe097682242ee1ee0953c",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch110/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-batch110/Synechococcus_Halomonas_Light_Driven_PHB_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Synechococcus_Halomonas_Light_Driven_PHB_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Halomonas_Light_Driven_PHB_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Synechococcus_Halomonas_Light_Driven_PHB_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Halomonas_Light_Driven_PHB_Coculture-references.log",
+ "log_sha256": "cea24a26f3510d86ba14abdb5bd4d7c02083789bc982170660dc4121af77b7f3",
+ "output_tail": "Validating kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_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/Synechococcus_Halomonas_Light_Driven_PHB_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": "Synechococcus_Halomonas_Light_Driven_PHB_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Halomonas_Light_Driven_PHB_Coculture-snippets.log",
+ "log_sha256": "32d5c17677a000100a0b22db07734e7af95b7e2b40f82a74ed21b581b1a6d4f5",
+ "output_tail": "# 20 evidence snippets scanned across 1 files\n MATCH 20\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": "Synechococcus_Halomonas_Light_Driven_PHB_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Halomonas_Light_Driven_PHB_Coculture-rank.log",
+ "log_sha256": "dd66187f40ea42f01dac10c1529278f659529667cc64eb5892dd1e7e10bedea4",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000198\",\n \"name\": \"Synechococcus-Halomonas Light-Driven PHB 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\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Synechococcus_Halomonas_Light_Driven_PHB_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/Synechococcus_Halomonas_Light_Driven_PHB_Coculture/2026-10-08T053619Z-codex-d68757.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Halomonas_Light_Driven_PHB_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch110/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-strict.tsv",
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-strict.log",
+ "log_sha256": "c101332d3039a12064b851465d8c968a4004617cbb5b6d61c258d4e188a2baa2",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch110/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-batch110/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-references.log",
+ "log_sha256": "97df34a412925c01b29526473014bf4cef63c9a275cae7028826f3586fa425fa",
+ "output_tail": "Validating kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_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/Synechococcus_Pseudomonas_PhotoPHA_DNT_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": "Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-snippets.log",
+ "log_sha256": "69ffcb4d170681e16d2b71a087ae7d8196340cac059281430f747dccb037db34",
+ "output_tail": "# 40 evidence snippets scanned across 1 files\n MATCH 37\n RENDERING 2\n ASSEMBLED 0\n WEAK 0\n MISMATCH 1\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\n\n# MISMATCH/WEAK detail\n [MISMATCH cov=0.0] kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml PMID:38609451\n attributing core metabolites to a specific co-culture partner is not p...\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 2 kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-rank.log",
+ "log_sha256": "e0e25a37dad8fbdca11ddc128101c7a049520a63ccaf4d904d9fd9a47e6fcb00",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000167\",\n \"name\": \"Synechococcus-Pseudomonas Phototrophic PHA and DNT Coculture\",\n \"score\": 93.8,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 10,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Synechococcus_Pseudomonas_PhotoPHA_DNT_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/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T053619Z-codex-9a9ab2.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Pseudomonas_PhotoPHA_DNT_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/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture/2026-10-08T054129Z-codex-d4dcce.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-history-1.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch110/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-strict.tsv",
+ "kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-strict.log",
+ "log_sha256": "76c21720392558fef8cafb9b5264f87df3331fb77e5e5a3d017acb161882d717",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch110/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-batch110/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-references.log",
+ "log_sha256": "efce2e3303b1b292434d1c8a484cee72c4807a405a04ef9d9d92c363a6c4784e",
+ "output_tail": "Validating kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_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/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_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": "Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-snippets.log",
+ "log_sha256": "d140f70efe6e700027157f436bdd4c6df0c8482291a6b6572b52329d433a2cb8",
+ "output_tail": "# 37 evidence snippets scanned across 1 files\n MATCH 37\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": "Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-rank.log",
+ "log_sha256": "c653f7cb5587a659d9d5c87d306014fe611a1a000733746d35d6136b6f52accf",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000211\",\n \"name\": \"Synechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\",\n \"score\": 91.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 9,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Synechococcus_Shewanella_Dlactate_Biophotovoltaic_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/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium/2026-10-08T053619Z-codex-a21481.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium-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-batch110/verification/inventory.log",
+ "log_sha256": "1c5ae9ab5470b7db8c8df3748dfaa7a02291452f6d08b94709cfc16bb305f318",
+ "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\": 1381,\n \"edges\": 544,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 185,\n \"review_status_counts\": {\n \"needs_research\": 53,\n \"pending\": 55,\n \"reviewed\": 352\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-batch110/verification/network.log",
+ "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+ "output_tail": " \"total_genomes\": 17191,\n \"is_reclassified\": false,\n \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n },\n \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"mexZ\"\n },\n \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n \"evidence\": [\n {\n \"reference\": \"PMID:42153623\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/just-network-json.log",
+ "log_sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/rank-all.log",
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/private/tmp/communitymech-causal-batch110/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch110/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch110/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch110/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-batch110/verification/render-repeat.log",
+ "log_sha256": "98b574c28e441c7b7a71ebffa821acd7c3c8de5ec99a7a18c99aa237ee7826a6",
+ "output_tail": "unitymech-causal-batch110/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch110/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch110/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch110/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch110/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-batch109')),('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-batch110/verification/connectivity-survey.log",
+ "log_sha256": "35d6d544116cbffa602de56c96ced2f67496f682c91c58253222ca3c2bf16b3a",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 407, \"mixed\": 132, \"community_level_only\": 275, \"taxa\": 1552, \"credited_solely_by_the_rule\": 1270}, \"current\": {\"records\": 460, \"with_community_level\": 408, \"mixed\": 133, \"community_level_only\": 275, \"taxa\": 1554, \"credited_solely_by_the_rule\": 1270}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_batch107.py",
+ "tests/test_causal_review_batch108.py",
+ "tests/test_causal_review_batch109.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch110.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/regressions.log",
+ "log_sha256": "e67b35901e338580882dfbcc063fc13891e82ebc9fce6e57e290df73887e3c34",
+ "output_tail": "........................................................................ [ 7%]\n........................................................................ [ 14%]\n........................................................................ [ 21%]\n........................................................................ [ 28%]\n........................................................................ [ 36%]\n........................................................................ [ 43%]\n........................................................................ [ 50%]\n........................................................................ [ 57%]\n........................................................................ [ 65%]\n........................................................................ [ 72%]\n........................................................................ [ 79%]\n........................................................................ [ 86%]\n........................................................................ [ 94%]\n.......................................................... [100%]\n994 passed in 335.27s (0:05:35)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/just-lint.log",
+ "log_sha256": "171ad9e2a967476aaa69947b5e7c378f5670561e9075992e0339478e758fc936",
+ "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n363 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n"
+ },
+ {
+ "check": "mypy-explicit-runtime",
+ "command": [
+ "/private/tmp/communitymech-batch100/lint-env/bin/mypy",
+ "--no-incremental",
+ "--python-executable",
+ "/private/tmp/communitymech-batch100/lint-env/bin/python",
+ "src/"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/mypy-explicit-runtime.log",
+ "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875",
+ "output_tail": "Success: no issues found in 49 source files\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/audit-snippets-all.log",
+ "log_sha256": "14f750af7fac4bec6ae3fba574251ebf8d1781a98179637898957bf99ed771f6",
+ "output_tail": "# 8998 evidence snippets scanned across 460 files\n MATCH 8858\n RENDERING 23\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Fresh both-root baseline before primary reads:460 records,923 caches,56 existing warnings,zero structural defects. Three full targets and ten nodes/six arrows reviewed. All topology retained; no new nodes/directions or Edison spend.",
+ "Primary texts independently retrieved via EuropePMC with exact Crossref DOI checks. Read spans:PHA abstract/background/Results/Discussion/Conclusions and initial Methods lines1-114;DNT summary/main Results/Discussion/Methods/captions lines1-145;omics abstract/main Results/Discussion/captions lines1-160;Shewanella abstract/main Results/Discussion/captions/initial Methods lines1-128;nitrate abstract/introduction1-18 and coculture Results/Discussion/Conclusion55-94. Truncated spans were reread; remaining Methods, supplementary files, figure pixels and raw datasets not audited.",
+ "Halomonas independently retrieved primary abstract and whole committed abstract cache read. No PMCID;DOI landing inaccessible,publisher403,author pagecitation only. Bounded title/DOI/OSTI search did not retrieve primary full article. This is not global absence. LC1/complete organic inputs/isolated encapsulation mediation remain1860 and needs_research;not silently certified. Existing canonical taxonomy untouched.",
+ "Other five cache content-type/section headers inspected,not whole caches. All graph/discussion quotations checked against fresh primary and unchanged caches. Case/spacing/hyphen normalization accommodates XML/PDF rendering;matches alone do not prove entailment. DNT oxidation/mineralization distinction comes from direct Results/Discussion,not a removal-only assay. No source-cache changes.",
+ "Retain Halomonas feeding,PHB/persistence and alginate intervention;remove duplicate exchange/colonization typing and unsupported organic-input exclusion. Keep alginate mechanism in text without asserting alginic-acid protonation. Existing alginate-to-PHB direction stays HYPOTHESIZED/PARTIAL.",
+ "Pseudomonas preserves separate cscAB,cscRABY/nitrate-blind and EM173 implementations. PHA family not PHB;8.8-fold endpoint not rate;DNT disappearance not complete mineralization. Conditional mutualism retains carbon supply/cyanobacterial benefit,not heterotroph advantage over externally fed controls. Additional molecular exchange unresolved,not reverse sucrose. General PHA term reused from same record.",
+ "Shewanella retains D-lactate contribution,not substrate exclusivity. Anode is abiotic recipient;positive cyanobacterial growth is retained separately from hypothetical CO2-return mediation. Retain existing reverse direction using source Fig1 proposal,not device-separation wording. Device modes and replenishment/LB context qualified. D-lactate CHEBI16004 canonical label checked against EBI acid/base relation and focused term validation. No new engineering/cultivation/protocol instructions.",
+ "Whole reviewed Azotobacter neighboring record and reusable Shewanella MR1 taxon record read as modeling context,not evidence for targets. Reusable record is not linked automatically to the engineered derivative;no gene claims copied. Ignored/hidden kb/taxa search found only that matching reusable taxon. Fresh all-state title/body dedup matched1093,258,1851,1669,1606,1605,837,836,835;all wholebodies and related529 read. Local matching-path index read,not every report;PRs/comments not exhaustive.",
+ "Only ecological_interactions,discussions,curation_history change. Preserve other457records,all923caches,non-graph rawblocks and prior history/decisionfiles. Issues1857-1859 remainopen untilprotectedmainmerge;research1860 and nongraph1861-1862 remainopen afterward. Self-review is not independent approval or full corpus completion. No schema/validator/runtime change. Participantcensus updates must be measurement-based with unchanged connectivity/share rules. Loader1703,DOIcase1091,cachepolicy949/1093 not certified. Denied/unanswered Edison scopes untouched.",
+ "Replace growth-rate excerpt with an exact passage shared by the primary XML and unchanged PDF cache; the initial CLI rejected a PDF word-join artifact. Matched-control growth interpretation and graph topology are unchanged. Issue#1858. Four append-only histories across three records; no prior history rewritten.",
+ "Local snippet auditor reports one exact known MISMATCH for the Pseudomonas discussion because it drops the PDF fi ligature. Primary XML and unchanged cache match under independent NFKD normalization; CLI references pass. Preserve the faithful quote and record the exact classification rather than claiming a clean snippet audit. Shared-auditor follow-up1863 remains open; related257/596 and fresh all-state title/body dedup reviewed. Initial audit assertion failure is retained; no shared validator change."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml": {
+ "MATCH": 20,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml": {
+ "MATCH": 37,
+ "RENDERING": 2,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 1,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml": {
+ "MATCH": 37,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "known_snippet_audit_false_positive": {
+ "issue": 1863,
+ "path": "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml.discussions[0].evidence[0]",
+ "reference": "PMID:38609451",
+ "snippet": "attributing core metabolites to a specific co-culture partner is not possible",
+ "reported_class": "MISMATCH",
+ "reported_coverage": 0.0,
+ "independent_normalization": "NFKD/case/whitespace/punctuation contiguous match",
+ "source_sha256": {
+ "/private/tmp/communitymech-causal-batch110/references_cache/PMID_38609451.md": "823040c434fe5d39a55b9b7efe43ee277021dd2f22c979c71cd40142d6025b96",
+ "/private/tmp/communitymech-batch110/omics-primary.txt": "d0297a40f3662014578949cac1f4e8434449b29db9f5887642006be0088bb8c8"
+ },
+ "disposition": "Explicit single-quote exception for PDF fi ligature stripped by auditor. Primary and cache checked; CLI references pass. Initial audit assertion stopped validation; shared auditor and canonical quote unchanged. Follow-up1863 remains open."
+ },
+ "unchanged_record_files": 457,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 54,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [],
+ "repair_scope": "Existing node scope/evidence repairs and qualification of identical existing directions. Missing primary methods are an access/scope follow-up,not topology extension."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch110/baseline.json": "2d61587c414ad3b2ef5fbdc650b81772d471574f15c35d8c7dbd57e56d2a30ea",
+ "/private/tmp/communitymech-batch110/dedup-local-current.txt": "c9c9f9d438450928edc05384a25f765678d8d2fd4b0b4408b4f97255469ed3ac",
+ "/private/tmp/communitymech-batch110/dnt-abstract.txt": "b6e9c4ab7cace0d0ef29b1726ff8eb4942244cd125cbe3987ab41fc44ddbf6d4",
+ "/private/tmp/communitymech-batch110/dnt-crossref.json": "184149be5823a9e4b1684a0344adc74340023f4ad9eba9219844a28a79a36390",
+ "/private/tmp/communitymech-batch110/dnt-metadata.json": "154834ded50858b67c2514387282426a85286464d0c2a04947b040b54a6c94ad",
+ "/private/tmp/communitymech-batch110/dnt-primary.txt": "8f3f442f6892761829ce27b43766cd9d6f331d9b039bab5d33771b3c29bac51c",
+ "/private/tmp/communitymech-batch110/dnt-primary.xml": "a4a8e42b6f8c85c62947ec7106147082bf4446093e9fdedfcb52491282e7fcc0",
+ "/private/tmp/communitymech-batch110/halomonas-abstract.txt": "b868eefc2a9142bca52838ec23dee3ce50915b0fc12f30b0b754528b6d7d73b5",
+ "/private/tmp/communitymech-batch110/halomonas-crossref.json": "824b0951ae3ae72cf654ac78fb28b94af1d63a5d9dfac6ca4204ed07c7cc20b9",
+ "/private/tmp/communitymech-batch110/halomonas-metadata.json": "3ee4bb9699d6787306348303002e5ebcad8a59f7744fbac5e57fab2cd0801e70",
+ "/private/tmp/communitymech-batch110/issue-dedup-current.json": "af05eaaf59a0ec9ad8b34670607630bcd09768d9060c7dde985cde0307b5c28b",
+ "/private/tmp/communitymech-batch110/nitrate-abstract.txt": "4fa0999fb18f1d0d07a32121ba889901aad4baf4a0da27ecc61df1b7e965b635",
+ "/private/tmp/communitymech-batch110/nitrate-crossref.json": "e9ec5824fbe0eed19243b6d8d89df2590ecde066c7498fe610ed1401f03cc154",
+ "/private/tmp/communitymech-batch110/nitrate-metadata.json": "e1c5908d99176ffb94d88ead705b3fd7c3ddfef07e703fae224bed6b352e46f9",
+ "/private/tmp/communitymech-batch110/nitrate-primary.txt": "fe01a626b490ac32bef31fb500fb27f502407bb0ea7237c103fff3061d3f5de0",
+ "/private/tmp/communitymech-batch110/nitrate-primary.xml": "6e2fdb0a75a40423c0a89b1eb10b0ec69d3567fd007edfea1cc5802bfb934b79",
+ "/private/tmp/communitymech-batch110/omics-abstract.txt": "02ad6aa0500370c45c0aa822ea952b0eebc888f1b9ee2a088eeaffd1bf8328c7",
+ "/private/tmp/communitymech-batch110/omics-crossref.json": "04f8ba720123113007e4ba9cad89797f79eed0a20224c2212b2abe37a280009a",
+ "/private/tmp/communitymech-batch110/omics-metadata.json": "fa14cbdc872eac703ec9c78220fb37acc42932d0525a075ca5b2441455096726",
+ "/private/tmp/communitymech-batch110/omics-primary.txt": "d0297a40f3662014578949cac1f4e8434449b29db9f5887642006be0088bb8c8",
+ "/private/tmp/communitymech-batch110/omics-primary.xml": "c4d0c5a3b1d591c01d646680533feb9120f4c3c50a70c59eb3aca6c58ece3401",
+ "/private/tmp/communitymech-batch110/pha-abstract.txt": "b7a325beb7d96b8ad94d2f08157ce49e5beaa9698964b70c3b239f58ca8338d3",
+ "/private/tmp/communitymech-batch110/pha-crossref.json": "b1b3dabd9c57a01f06985c9d8300b07dafbd4970a9c6ba5f2efe8d8910a354d0",
+ "/private/tmp/communitymech-batch110/pha-metadata.json": "c0a71d945741a7d3e2fcac0e70eeeaf73b377e7a40efaa94a4479fad8e058f1b",
+ "/private/tmp/communitymech-batch110/pha-primary.txt": "1de61ab6b36360fd4d1c1a4a740e20ec2cf803b066a670062f42a0df943f4db9",
+ "/private/tmp/communitymech-batch110/pha-primary.xml": "433ffdbbe24ed62e1207c6dc608638e84fef6a792317c065d20d07d628cf322d",
+ "/private/tmp/communitymech-batch110/primary-manifest.json": "559dd1bccc435efd5fbc16269bffe9474d3651ed392e5e2502751f30ca2ddb88",
+ "/private/tmp/communitymech-batch110/shewanella-abstract.txt": "a70dd2377d0e8341a94290c489b5c9144d670e6da089d22a822170409c8781c3",
+ "/private/tmp/communitymech-batch110/shewanella-crossref.json": "1c9c86d88af3b5725083eadc39437ee8044436528596bd6b7dd70c8725901a92",
+ "/private/tmp/communitymech-batch110/shewanella-metadata.json": "986590bf3b94aaca2023e4f4e4253a141f37daf5b6a69eb579c4fdb866838e0c",
+ "/private/tmp/communitymech-batch110/shewanella-primary.txt": "a63997f2d187c4d97b1651a4526ab8b76b3ee414f33230d57cd9d8f25e4da05a",
+ "/private/tmp/communitymech-batch110/shewanella-primary.xml": "52316f1590836be781beaba85238f8839d064f350ac3c953135a8855213e0f2c",
+ "references_cache/PMID_28814973.md": "da984c3054b65503caafc9f14bbf8b7e3c21ac37e27c9c221e699bddce208c9f",
+ "references_cache/PMID_29061492.md": "816c373f1144f53cf27397b175ac17afa2626e8f6be92758c6018ef6fbff4b7f",
+ "references_cache/PMID_31537786.md": "b4a1d5a9a6128ef63ba1b4874b108e80e27f328b3475c5d23f2a6b199012abe2",
+ "references_cache/PMID_32064751.md": "4cc298d58f67b2de7f325e4c7aaa0edf6dd596e56900810568e45efc84e71d14",
+ "references_cache/PMID_32523942.md": "fc6e99f24598a3a29782df3d5a6ca8b16642b728b301b312f92eaee9f4f39f50",
+ "references_cache/PMID_38609451.md": "823040c434fe5d39a55b9b7efe43ee277021dd2f22c979c71cd40142d6025b96"
+ },
+ "immutable_prior_history_and_decision_files": 840,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 24,
+ "new_discussion_quotations": 3,
+ "fresh_primary_literal_matches": 27,
+ "all_cached_literal_matches": 27,
+ "retained_nodes": 10,
+ "removed_nodes": 0,
+ "retained_arrows": 6,
+ "removed_arrows": 0,
+ "new_nodes_or_directions": 0,
+ "scope": "All reviewed quotations match fresh primary text and unchanged caches;source entailment separately reviewed. Primary abstract and bounded main-text/caption spans documented in ledger;no raw-data,figure-pixel or supplement certification."
+ },
+ "network_delta": {
+ "existing_findings_preserved": 56,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "Ten nodes and six existing directions retained. All56existing warnings unchanged;zero structural defects. Halomonas needs research1860;non-graph follow-ups1861-1862."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1367,
+ "arrows": 536
+ },
+ "render_scope": "Deterministic rendering and exact HTML-description parser,not screenshots;postcommit docs-current separately required.",
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 407,
+ "mixed": 132,
+ "community_level_only": 275,
+ "taxa": 1552,
+ "credited_solely_by_the_rule": 1270
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 408,
+ "mixed": 133,
+ "community_level_only": 275,
+ "taxa": 1554,
+ "credited_solely_by_the_rule": 1270
+ }
+ },
+ "delta": {
+ "records": 0,
+ "with_community_level": 1,
+ "mixed": 1,
+ "community_level_only": 0,
+ "taxa": 2,
+ "credited_solely_by_the_rule": 0
+ },
+ "interpretation": "Shewanella electrode output and device intervention gain community-level identity-only scope. One additional mixed-scope record and two taxa in survey;zero new solely-credited taxa. Exact census and observational bounds updated;connectivity and share rules unchanged."
+ },
+ "lint_limitation": "Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.",
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies unchanged. Not a complete embedding runtime."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 8998,
+ "categories": {
+ "MATCH": 8858,
+ "RENDERING": 23,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 40,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1381,
+ "edges": 544,
+ "records_without_nodes": 10,
+ "records_without_edges": 185,
+ "review_status_counts": {
+ "needs_research": 53,
+ "pending": 55,
+ "reviewed": 352
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml": "814876819500a172c6d4423086c5299d62b15e9915c1f96ed66fdaaf3367fb2e",
+ "tests/test_causal_review_batch110.py": "39b08c28d3140ebbd608ca57317d51e1302d36d8a5474c186873d918858f3b69",
+ "tests/test_causal_review_batch109.py": "2b244b24479edf6025412c2a42459e92151d4602a20f571fef8fade9769d92d5",
+ "tests/test_participating_taxa.py": "f70e3c12c1c295edda98a5b9c60f0b791213a49b060be96071409fe0164188bc",
+ "tests/test_community_level_connectivity_credit.py": "4d13eaa74d04b6730e5e88c5aba5df1c2bc9aeea4597084274c48b9df9cd5247",
+ "reports/causal_graph_review/cache-provenance-20261008-batch110.json": "7fb379fd4c081d4251b9f6599018a5db9a2fdab31ccdf852957b06cc4107dbac",
+ "kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml": "6f80bc26157b469b40d247d9d8bdf08aacee7ce6009e53527820248179397b3c",
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml": "76fe4a6229c920128650e889592471c220a7a42283bc97c605c6d9615983cf8a",
+ "kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml": "826172b3e4ec14cb21b506f830175d55dc982b3ee809bc7811e9a29cb67e231c"
+ },
+ "pre_research_baseline": {
+ "base_commit": "9b429a9fa64f383ece90031645efbb8f913e111b",
+ "base_tree": "5b3c9f4f87ad147d839e896d6388695107f9fed3",
+ "research_worktree": "/private/tmp/communitymech-causal-batch109",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch110/baseline-rank.log",
+ "sha256": "3669224d4b68a7cd7ff60470a202349374718f510bd081240ba14d207774ac34"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch110/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch110/baseline-network.log",
+ "sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch110/baseline-downstream.log",
+ "sha256": "8dc90bae4c1c8ad571e1ba7c4715676ed10d07aaaec083ed647d393f51fbfbed"
+ }
+ ],
+ "baseline_sha256": "2d61587c414ad3b2ef5fbdc650b81772d471574f15c35d8c7dbd57e56d2a30ea"
+ },
+ "reference_validator_caveat": "Three full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.",
+ "status": "verified_existing_graph_repairs_with_source_access_limits",
+ "initial_failed_attempt": {
+ "artifact": "/private/tmp/communitymech-batch110/validation-attempt1.json",
+ "sha256": "9e7c4bf7ac745ae0463afc6a1183360eb6df042af6ef52819c5df5ad53393b4b",
+ "failed_check": {
+ "check": "Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch110/verification-attempt1/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture-references.log",
+ "log_sha256": "cd0ab1221ff4111d88fd313d59beee8da5682f9860f1c1f3149d37461385a475",
+ "output_tail": "Validating kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (1):\n [ERROR] Text part not found as substring: 'they did not differ within the same experiment'\n Location: ecological_interactions[3].evidence[2].snippet\n Reference: PMID:38609451\n\nValidation Summary:\n Total checks: 1\n Issues found: 1\n",
+ "explained_output_tail": "Validating kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (1):\n [ERROR] Text part not found as substring: 'they did not differ within the same experiment'\n Location: ecological_interactions[3].evidence[2].snippet\n Reference: PMID:38609451\n\nValidation Summary:\n Total checks: 1\n Issues found: 1\n"
+ },
+ "disposition": "PDF word join rejected the initial excerpt; replaced with another literal passage from the same primary paragraph, appended correction history, reran every gate. Caches and scientific interpretation unchanged."
+ },
+ "total_recorded_gate_outputs": 35
+}
diff --git a/tests/test_causal_review_batch109.py b/tests/test_causal_review_batch109.py
index 227442f37..355ab574e 100644
--- a/tests/test_causal_review_batch109.py
+++ b/tests/test_causal_review_batch109.py
@@ -176,14 +176,15 @@ def test_hashes_histories_and_canonical_identity_only_scope_are_explicit():
def test_measured_scope_change_adds_no_solely_credited_taxa():
+ # Batch110 adds one mixed-scope record; the solely-credited count is unchanged.
survey = runpy.run_path(str(ROOT / "tests/test_community_level_connectivity_credit.py"))[
"_survey"
]()
assert survey == {
"records": 460,
- "with_community_level": 407,
- "mixed": 132,
+ "with_community_level": 408,
+ "mixed": 133,
"community_level_only": 275,
- "taxa": 1552,
+ "taxa": 1554,
"credited_solely_by_the_rule": 1270,
}
diff --git a/tests/test_causal_review_batch110.py b/tests/test_causal_review_batch110.py
new file mode 100644
index 000000000..47692e6e4
--- /dev/null
+++ b/tests/test_causal_review_batch110.py
@@ -0,0 +1,129 @@
+"""Preserve production evidence without polymer, recipient or mediation overclaims."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-three-records-batch110.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_halomonas_preserves_outcomes_without_certifying_lc1_or_mediation():
+ _, rows, docs = records()
+ carbon, product, partition = docs[0]["ecological_interactions"]
+ assert rows[0]["status"] == "needs_research" and 1860 in rows[0]["issues"]
+ assert carbon["interaction_type"] == "CROSS_FEEDING"
+ assert "strain-specific attribution" in carbon["description"]
+ assert "31%" in product["description"] and "five months" in product["description"]
+ assert product["scope"] == "COMMUNITY_LEVEL" and "interaction_type" not in product
+ assert "biological_processes" not in product
+ assert "interaction_type" not in partition
+ assert partition["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+
+
+def test_pha_is_not_phb_or_a_rate_comparison():
+ _, _, docs = records()
+ product = docs[1]["ecological_interactions"][1]
+ assert "interaction_type" not in product and "source_taxon" not in product
+ assert product["metabolites"][1]["term"] == {
+ "id": "CHEBI:78037",
+ "label": "polyhydroxyalkanoate",
+ }
+ assert "not a measured rate increase" in product["description"]
+ assert "most abundant monomer" in product["evidence"][0]["snippet"]
+ assert "snapshot at the end" in product["evidence"][1]["snippet"]
+
+
+def test_dnt_removal_does_not_prove_complete_mineralization():
+ _, _, docs = records()
+ dnt = docs[1]["ecological_interactions"][2]
+ assert "interaction_type" not in dnt and "source_taxon" not in dnt
+ assert "adsorption and reductive" in dnt["description"]
+ assert "Complete mineralization was not directly established" in dnt["description"]
+ assert any("could not precisely quantitate" in e["snippet"] for e in dnt["evidence"])
+
+
+def test_growth_feedback_preserves_positive_context_without_reverse_sucrose():
+ _, _, docs = records()
+ feedback = docs[1]["ecological_interactions"][3]
+ assert feedback["interaction_type"] == "MUTUALISM"
+ assert "conditional carbon-supported partnership" in feedback["description"]
+ assert "matched external-sucrose controls" in feedback["description"]
+ assert "metabolites" not in feedback
+ assert feedback["evidence"][1]["supports"] == "PARTIAL"
+ assert "PARTIAL" in feedback["description"]
+
+
+def test_anode_is_not_a_cyanobacterial_recipient_and_carbon_return_is_hypothetical():
+ _, _, docs = records()
+ carbon, anode, separation = docs[2]["ecological_interactions"]
+ assert carbon["metabolites"][0]["term"] == {
+ "id": "CHEBI:16004",
+ "label": "(R)-lactate",
+ }
+ assert "not the exclusive organic input" in carbon["description"]
+ assert "source_taxon" not in anode and "target_taxon" not in anode
+ assert anode["scope"] == "COMMUNITY_LEVEL" and "interaction_type" not in anode
+ assert len(anode["participating_taxa"]) == 1
+ assert anode["participating_taxa"][0]["term"]["id"] == "NCBITaxon:211586"
+ assert anode["downstream"][0]["target"] == carbon["name"]
+ assert anode["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+ assert "CO2" in anode["downstream"][0]["description"]
+ assert anode["evidence"][1]["supports"] == "PARTIAL"
+ assert "enhanced the growth" in anode["evidence"][2]["snippet"]
+ assert "interaction_type" not in separation
+ assert "continuous medium replenishment" in separation["description"]
+ assert "LB supplementation" in separation["description"]
+
+
+def test_all_existing_topology_and_source_access_limits_are_recorded():
+ ledger, rows, docs = records()
+ assert ledger["reviewed_counts"] == {
+ "retained_nodes": 10,
+ "removed_nodes": 0,
+ "retained_arrows": 6,
+ "removed_arrows": 0,
+ "renamed_nodes": 0,
+ "graph_quotations": 24,
+ "discussion_quotations": 3,
+ }
+ assert [r["status"] for r in rows] == ["needs_research", "reviewed", "reviewed"]
+ assert ledger["unresolved_research_issues"] == [1860]
+ assert ledger["unresolved_non_graph_issues"] == [1861, 1862]
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ for r, d in zip(rows, docs, strict=True):
+ assert [(e["source"], e["target"]) for e in r["edges_before"]] == [
+ (e["source"], e["target"]) for e in r["edges_after"]
+ ]
+ assert len(r["node_decisions"]) == len(d["ecological_interactions"])
+
+
+def test_hashes_history_and_identity_only_participants_are_explicit():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert set(row["allowed_changed_fields"]) == {
+ "ecological_interactions",
+ "discussions",
+ "curation_history",
+ }
+ expected_events = 2 if row["id"] == "CommunityMech:000167" else 1
+ assert row["curation_events_added"] == len(row["history_files"]) == expected_events
+ assert all((ROOT / p).exists() for p in row["history_files"])
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ canonical = [
+ {k: t["taxon_term"][k] for k in ["preferred_term", "term"]} for t in doc["taxonomy"]
+ ]
+ for n in doc["ecological_interactions"]:
+ assert all(
+ t in canonical and set(t) == {"preferred_term", "term"}
+ for t in n.get("participating_taxa", [])
+ )
diff --git a/tests/test_community_level_connectivity_credit.py b/tests/test_community_level_connectivity_credit.py
index 261287157..79b30bc9a 100644
--- a/tests/test_community_level_connectivity_credit.py
+++ b/tests/test_community_level_connectivity_credit.py
@@ -106,8 +106,8 @@ def test_most_records_carry_a_community_level_interaction(survey):
# Census: 399 -> 402; exactly named participants, no extra solely-credited taxa.
# #1786 re-scopes Atacama's six-member subset as a community profile (402 -> 403).
# #1799 separates the Shewanella current endpoint from reverse cross-feeding (403 -> 404).
- # #1851-#1854 separate four phenotype endpoints (403 -> 407); no new solely-credited taxa.
- assert 130 <= survey["with_community_level"] <= 407, survey
+ # #1859 adds a scoped electrode process (407 -> 408); no new solely-credited taxa.
+ assert 130 <= survey["with_community_level"] <= 408, survey
def test_the_mixed_records_are_where_the_coarseness_bites(survey):
@@ -124,7 +124,7 @@ def test_the_mixed_records_are_where_the_coarseness_bites(survey):
"""
# #1772-#1774 change the mixed-record census from 125 to 128.
# #1851-#1854 add four mixed-scope records; batch109 pins the exact measured census.
- assert 35 <= survey["mixed"] <= 132, survey
+ assert 35 <= survey["mixed"] <= 133, survey
assert survey["mixed"] + survey["community_level_only"] == survey["with_community_level"]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 23966d9b9..c4e24c7d3 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -426,6 +426,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml",
"Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml",
"Synechococcus_Saccharomyces_SPC.yaml",
+ "Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml",
"Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml",
"Syntrophobacter_Methanobacterium_Syntrophy.yaml",
"Syntrophobacter_Methanospirillum_Syntrophy.yaml",