- Niche partitioning
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -603,33 +598,19 @@
Ecological Interactions
-
Iron Oxidation by Leptospirillum
- CROSS_FEEDING
+
Proposed Leptospirillum Organic-Matter Supply
-
Leptospirillum ferriphilum oxidizes ferrous iron (Fe²⁺) to ferric iron (Fe³⁺) as its sole energy source, using the electrons to fix CO₂ through the Calvin-Benson-Bassham cycle. This obligate chemolithoautotroph oxidizes iron from pyrite and chalcopyrite mineral dissolution. The Fe³⁺ generated attacks sulfide minerals, perpetuating the iron redox cycle. During growth, Leptospirillum releases organic matter that can accumulate to toxic concentrations in pure culture. In co-culture with Ferroplasma, this organic matter is consumed, relieving organic-compound stress.
-
-
+
HYPOTHESIZED: L. ferriphilum growth supplies organic matter usable by F. acidiphilum. The inspected Merino abstract states this as the study hypothesis, not a quantified release flux or a resolved substrate identity. Retain the upstream supply context without asserting Calvin-Benson-Bassham fixation, mineral-specific dissolution, toxic accumulation thresholds or their relief in the exact pair.
HYPOTHESIZED: Organic matter released during Leptospirillum growth would provide substrate for Ferroplasma consumption. This is the source-stated supply hypothesis, not a traced partner-to-partner flux; reciprocal supernatant growth does not identify the transferred compound or prove the detoxification mechanism.
@@ -678,10 +642,10 @@
Evidence
PMID:27535541
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
-
"Ferroplasma acidiphilum and Leptospirillum ferriphilum are the dominant species in extremely acid environments and have great use in bioleaching applications"
+
"The hypothesis of this work is that F. acidiphilum uses the organic matter secreted by L. ferriphilum for growth"
@@ -691,11 +655,10 @@
Evidence
-
Organic Matter Consumption by Ferroplasma
+
Proposed Ferroplasma Organic-Matter Consumption
CROSS_FEEDING
-
Ferroplasma acidiphilum grows chemomixotrophically, consuming organic matter secreted by Leptospirillum ferriphilum while oxidizing ferrous iron for energy. F. acidiphilum uses the organic matter for carbon assimilation, maintaining low organic compound levels in the culture medium that prevents toxic effects on L. ferriphilum. This scavenging function is critical - in pure Leptospirillum cultures, organic matter accumulates and inhibits growth, but in co-culture, Ferroplasma maintains organic compounds below toxic thresholds. The archaeon can utilize diverse organic substrates including amino acids, organic acids, and cell debris. This creates a mutualistic relationship where Ferroplasma benefits from carbon supply while Leptospirillum benefits from detoxification.
-
+
HYPOTHESIZED: Organic matter supplied by L. ferriphilum contributes carbon to F. acidiphilum BRL-115 and its removal relieves inhibition of the bacterium. Reciprocal filtered-supernatant growth supports soluble partner effects, but the inspected abstract does not establish identified transferred substrates, assimilation flux or detoxification thresholds. BRL-115 chemomixotrophy and the 0.04% yeast-extract growth optimum are characterization results, not proof of the proposed mediator in mixed culture. CROSS_FEEDING denotes this proposed transfer, not established obligate syntrophy.
Soluble organic compounds contribute to the reciprocal filtered-medium growth response
-
-
-
-
Evidence
@@ -743,10 +692,10 @@
Evidence
PMID:27535541
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
-
"F. acidiphilum uses the organic matter secreted by L. ferriphilum for growth, maintaining low levels of organic compounds in the culture medium, preventing their toxic effects on L. ferriphilum"
+
"The hypothesis of this work is that F. acidiphilum uses the organic matter secreted by L. ferriphilum for growth"
@@ -769,20 +718,14 @@
Evidence
-
Iron Oxidation by Ferroplasma
- NICHE_PARTITIONING
+
Ferroplasma Iron-Metabolism Context
-
Ferroplasma acidiphilum oxidizes ferrous iron microaerophilically, complementing Leptospirillum's aerobic iron oxidation. F. acidiphilum obtains energy by oxidation of ferrous iron using oxygen as terminal electron acceptor, with a membrane-bound complex dedicated to this process. The archaeon can function at lower oxygen concentrations than Leptospirillum, filling microaerobic niches. Ferroplasma's cellular machinery is iron-protein-dominated, with high iron content reflecting specialization for iron metabolism. Both organisms oxidize Fe²⁺ to Fe³⁺, but occupy different physiological niches (aerobic vs. microaerobic, autotrophic vs. mixotrophic), reducing direct competition and enabling stable coexistence.
-
-
-
+
Ferroplasma iron metabolism is physiological context, not an observed niche-partitioning interaction. Ferrer studied strain Y(T), reporting ferrous-iron oxidation and iron-rich proteins; this is not BRL-115 in the Leptospirillum pair. Wilson compared isolated rusticyanins: the archaeal FaR had similar redox potential but slower electron transfer than AfR. These sources do not establish lower-oxygen complementarity, a pair-specific membrane complex, competition relief or stable coexistence. Protein electron-transfer properties do not measure consortium iron-oxidation flux.
"properties of the Type-1 copper protein rusticyanin from Acidithiobacillus ferrooxidans (AfR) were compared with those from an ancestral form of this enzyme (N0) and an archaeal enzyme identified in Ferroplasma acidiphilum (FaR)"
+
"While both N0 and FaR show redox potentials similar to that of AfR their electron transport rates were significantly slower."
@@ -840,7 +772,7 @@
Evidence
- SUPPORT (IN_VITRO)
-
"acidiphilum therefore has a currently unique iron-protein-dominated cellular machinery and biochemical phylogeny."
+
"F. acidiphilum strain Y(T) is a chemoautotroph"
@@ -850,11 +782,9 @@
Evidence
-
Filtered Medium Cross-Feeding
- MUTUALISM
+
Reciprocal Filtered-Medium Growth Response
-
Cell growth is favorably affected by the presence of filtered medium of the partner organism. The reciprocal supernatant response shows that the partnership involves soluble factors beyond direct cell contact.
-
+
In reciprocal assays, each organism grew favorably in filtered medium from its partner. This supports diffusible partner-associated growth effects without requiring direct cell contact in those assays, but does not identify the mediators, show equal reciprocal benefit in simultaneous coculture or prove obligatory syntrophy. Mixed-culture growth rates were used as input to flux-balance analysis; model behavior is not independent measurement of exchanged flux. Organic-matter consumption cannot be treated as the demonstrated cause of both reciprocal responses.
+ KNOWLEDGE_GAP
+ OPEN
+ Which soluble factors mediate the reciprocal growth response of BRL-115 and L. ferriphilum?
+
+
Only cited abstracts were inspected. The primary abstract explicitly frames carbon supply and detoxification as a hypothesis. Reciprocal filtered-medium responses do not identify molecules, quantify partner-resolved flux or establish toxic thresholds. Growth-rate inputs to FBA are not independent flux observations. Preserve only the HYPOTHESIZED supply-to-consumption arrow and remove its unsupported extension to both reciprocal assays. Y(T) iron-rich proteins and isolated FaR kinetics are separate systems, not oxygen-niche or pair-specific membrane-complex evidence. No new structure is added. Non-graph physiology, medium and syntrophy claims remain #1462.
E. coli glucose competition imposes F. betulina carbon stress
+
E. coli-Associated Glucose Depletion and F. betulina Stress
COMPETITION
-
When E. coli ATCC 25922 was added to 3-day F. betulina liquid MEB cultures, glucose fell to zero within 1 day after bacterial addition, F. betulina dry biomass dropped from about 60 mg in monoculture to 34 mg in coculture, and RNA-seq after 3 days of coculture showed broad F. betulina differential expression consistent with carbon depletion and metabolic stress.
+
PARTIAL: E. coli addition to established F. betulina liquid MEB cultures was followed by glucose depletion within one day, fungal biomass of 34 mg (reported as 44% lower), and stress-related fungal transcription after three days of coculture. These observations support nutrient competition as an interpretation, but the inspected selected primary excerpts do not describe selective glucose rescue establishing mediation. BGC expression indicates transcriptional response, not production or identification of an active secreted metabolite. Endpoint bacterial counts were not reduced in this liquid assay.
"The bacterial count on agar medium at the end of the experiment did not reveal any impact of the coculture on the bacterial growth."
+
+
+
@@ -627,9 +645,8 @@
Evidence
F. betulina distal inhibition of E. coli on malt extract agar
- COMPETITION
-
In malt extract agar confrontation plates, F. betulina CIRM-BRFM 860 formed a visible zone that inhibited E. coli ATCC 25922 growth at a distance from the fungal mycelium. LC-MS metabolomics of media plugs from the inhibition zone detected enriched Sumiki's-acid-derivative, calcium-diformate, and sulfuric-acid features, and the authors linked the zone to local medium acidification rather than to detectable piptamine production.
+
F. betulina inhibited distal E. coli growth on malt extract agar. Inhibition-zone UHPLC-HRMS features were putatively identified as a Sumiki's acid derivative, calcium diformate and sulfuric acid; these are not confirmed active compounds. HYPOTHESIZED: acid-associated local pH changes mediate inhibition. The inspected selected excerpts describe a pH gradient but no selective neutralization or defined-compound rescue establishing necessity. Piptamine was not detected under these conditions, not shown to be universally absent. This agar phenotype is distinct from liquid-culture stress transcription and unchanged endpoint bacterial counts.
"The features detected in the inhibition zone were putatively identified as a Sumiki's acid derivative, calcium diformate, and sulfuric acid."
+
+
+
@@ -671,6 +701,25 @@
Evidence
+
+
Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which mediators cause liquid fungal stress and separate agar bacterial inhibition?
+
+
Selected primary preprint excerpts support measured glucose depletion, fungal biomass loss and transcription in liquid, versus distal bacterial inhibition and putative acid features on agar. No selective glucose rescue or pH neutralization is described in those excerpts; the full paper was not re-read because the public PDF request returned HTTP 429, so this is not a claim of universal experimental absence. Piptamine nondetection is condition-specific; BGC induction is not active-product identification. Preserve two nodes and zero arrows rather than connect different assay regimes. Prior cache-support fixes #1169/#1170/#1171 and the natural-partner caveat removal #1173 remain intact.
+
+
Attaches to: ecological_interactions#E. coli-Associated Glucose Depletion and F. betulina Stress, ecological_interactions#F. betulina distal inhibition of E. coli on malt extract agar
+
+
+
+
+
+
+
@@ -934,11 +983,11 @@
Evidence
var processes = [];
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
- label: "E. coli glucose competition imposes F. betulina carbon stress",
+ label: "E. coli-Associated Glucose Depletion and F. betulina Stress",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -963,12 +1012,12 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
diff --git a/docs/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.html b/docs/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.html
index 38202434d..c14ab275b 100644
--- a/docs/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.html
+++ b/docs/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.html
@@ -620,6 +620,23 @@
Ecological Interactions
+
+
Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which observed phenotypes and proposed mechanisms belong in the four-species causal graph?
+
+
The openly available primary main body (PMID:42545019; PMC13595950) now supports source review beyond the abstract. The record still has no interaction nodes and remains needs_research under #1461. Day-10 vPCR persistence, total CFU, DNA-qPCR and protein fractions are distinct readouts. P. koreensis-containing bicultures alkalinize, and community pH recovers after acid perturbation, but total CFU does not resolve member-specific compositional resilience. Siderophore uptake, partner-resolved acid/pyruvate exchange, ammonia mediation and AI-2 coordination require hypothesis-qualified treatment, not inferred flux or selective causality from proteins alone. Predicted antimicrobial pathways produced no inhibition zones in the tested agar assay, not proof of universal absence. Nutrient-rich BHI and pH 9-10 are not physiological healthy-airway conditions. Challenge organisms are not members of the canonical four-species record. One-community Edison dry run completed; specific credit authorization requested and no provider job or spend made. Add no speculative nodes or arrows while research is pending. Source body, tables and captions read; figure images, supplements and raw data not inspected. Strain and model metadata remain #1463.
+
+
+
+
+
+
+
diff --git a/history/records/Ferroplasma_Leptospirillum_Syntrophy/2026-10-06T104340Z-codex-37b7f6.yaml b/history/records/Ferroplasma_Leptospirillum_Syntrophy/2026-10-06T104340Z-codex-37b7f6.yaml
new file mode 100644
index 000000000..650ebe487
--- /dev/null
+++ b/history/records/Ferroplasma_Leptospirillum_Syntrophy/2026-10-06T104340Z-codex-37b7f6.yaml
@@ -0,0 +1,29 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml
+ slug: Ferroplasma_Leptospirillum_Syntrophy
+session:
+ id: 2026-10-06T104340Z-codex-37b7f6
+ timestamp: '2026-10-06T10:43:40Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1459
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain proposed organic supply as intrinsic source context without an unsupported
+ carbon-fixation route.; Retain proposed consumption with hypothesis-qualified evidence,
+ without measured detoxification or the reciprocal-response arrow.; Retain iron-metabolism
+ context with explicit strain and isolated-protein limits, not niche partitioning.; Retain
+ reciprocal filtered-medium growth without assigned mediator or obligate mutualism.
+ details: Existing-graph repair or explicit unresolved expansion; no new causal structure.
+ reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml
diff --git a/history/records/Fomitopsis_Ecoli_Nutritional_Stress_Coculture/2026-10-06T104341Z-codex-a2b56f.yaml b/history/records/Fomitopsis_Ecoli_Nutritional_Stress_Coculture/2026-10-06T104341Z-codex-a2b56f.yaml
new file mode 100644
index 000000000..6a8529727
--- /dev/null
+++ b/history/records/Fomitopsis_Ecoli_Nutritional_Stress_Coculture/2026-10-06T104341Z-codex-a2b56f.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml
+ slug: Fomitopsis_Ecoli_Nutritional_Stress_Coculture
+session:
+ id: 2026-10-06T104341Z-codex-a2b56f
+ timestamp: '2026-10-06T10:43:41Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1460
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain liquid glucose depletion and fungal stress with PARTIAL nutrient-competition
+ mediation.; Retain observed distal agar inhibition with putative identities and HYPOTHESIZED
+ acid mediation; no cross-regime arrow.
+ details: Existing-graph repair or explicit unresolved expansion; no new causal structure.
+ reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml
diff --git a/history/records/FourSpecies_Aerobic_Lung_Microbiome_Model/2026-10-06T104341Z-codex-319aac.yaml b/history/records/FourSpecies_Aerobic_Lung_Microbiome_Model/2026-10-06T104341Z-codex-319aac.yaml
new file mode 100644
index 000000000..e68794f7b
--- /dev/null
+++ b/history/records/FourSpecies_Aerobic_Lung_Microbiome_Model/2026-10-06T104341Z-codex-319aac.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml
+ slug: FourSpecies_Aerobic_Lung_Microbiome_Model
+session:
+ id: 2026-10-06T104341Z-codex-319aac
+ timestamp: '2026-10-06T10:43:41Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1461
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - discussions
+ summary: Record full-text graph-expansion candidates and retain needs_research; no new nodes
+ or arrows pending the one-community research workflow
+ details: Existing-graph repair or explicit unresolved expansion; no new causal structure.
+ reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml
diff --git a/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml b/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml
index d92e6cd57..50cc73dd3 100644
--- a/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml
+++ b/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml
@@ -109,71 +109,44 @@ taxonomy:
made with the objective of determining its optimal growth conditions
explanation: Confirms synergistic growth with Leptospirillum
ecological_interactions:
-- name: Iron Oxidation by Leptospirillum
- description: 'Leptospirillum ferriphilum oxidizes ferrous iron (Fe²⁺) to ferric iron (Fe³⁺) as its sole
- energy source, using the electrons to fix CO₂ through the Calvin-Benson-Bassham cycle. This obligate
- chemolithoautotroph oxidizes iron from pyrite and chalcopyrite mineral dissolution. The Fe³⁺ generated
- attacks sulfide minerals, perpetuating the iron redox cycle. During growth, Leptospirillum releases
- organic matter that can accumulate to toxic concentrations in pure culture. In co-culture with
- Ferroplasma, this organic matter is consumed, relieving organic-compound stress.
-
- '
- scope: COMMUNITY_LEVEL
- interaction_type: CROSS_FEEDING
- participating_taxa:
- - preferred_term: Leptospirillum ferriphilum
- term:
- id: NCBITaxon:178606
- label: Leptospirillum ferriphilum
+- name: Proposed Leptospirillum Organic-Matter Supply
+ description: 'HYPOTHESIZED: L. ferriphilum growth supplies organic matter usable by F. acidiphilum. The inspected
+ Merino abstract states this as the study hypothesis, not a quantified release flux or a resolved substrate identity.
+ Retain the upstream supply context without asserting Calvin-Benson-Bassham fixation, mineral-specific dissolution,
+ toxic accumulation thresholds or their relief in the exact pair.'
+ scope: PAIRWISE
metabolites:
- - preferred_term: Fe(II)
- term:
- id: CHEBI:29033
- label: iron(2+)
- concentration: Substrate from mineral dissolution
- - preferred_term: Fe(III)
- term:
- id: CHEBI:29034
- label: iron(3+)
- concentration: Product of ferrous-iron oxidation
- preferred_term: organic molecular entity
term:
id: CHEBI:50860
label: organic molecular entity
- notes: Secreted organic matter consumed by Ferroplasma
- biological_processes:
- - preferred_term: iron ion transport
- term:
- id: GO:0006826
- label: iron ion transport
- - preferred_term: carbon fixation
- term:
- id: GO:0015977
- label: carbon fixation
+ notes: Generic proposed organic substrate class; no compound identity or release flux established by the inspected
+ abstract.
downstream:
- - target: Organic Matter Consumption by Ferroplasma
- description: Organic compounds secreted by Leptospirillum are consumed by Ferroplasma
+ - target: Proposed Ferroplasma Organic-Matter Consumption
+ description: 'HYPOTHESIZED: Organic matter released during Leptospirillum growth would provide substrate for
+ Ferroplasma consumption. This is the source-stated supply hypothesis, not a traced partner-to-partner flux;
+ reciprocal supernatant growth does not identify the transferred compound or prove the detoxification mechanism.'
evidence:
- reference: PMID:27535541
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: Ferroplasma acidiphilum and Leptospirillum ferriphilum are the dominant
- species in extremely acid environments and have great use in bioleaching
- applications
- explanation: Merino et al. 2016 frame L. ferriphilum and F. acidiphilum as the
- co-dominant bioleaching consortium, establishing L. ferriphilum's iron oxidation
- role in the syntrophy.
-- name: Organic Matter Consumption by Ferroplasma
- description: 'Ferroplasma acidiphilum grows chemomixotrophically, consuming organic matter secreted
- by Leptospirillum ferriphilum while oxidizing ferrous iron for energy. F. acidiphilum uses the organic
- matter for carbon assimilation, maintaining low organic compound levels in the culture medium that
- prevents toxic effects on L. ferriphilum. This scavenging function is critical - in pure Leptospirillum
- cultures, organic matter accumulates and inhibits growth, but in co-culture, Ferroplasma maintains
- organic compounds below toxic thresholds. The archaeon can utilize diverse organic substrates including
- amino acids, organic acids, and cell debris. This creates a mutualistic relationship where Ferroplasma
- benefits from carbon supply while Leptospirillum benefits from detoxification.
-
- '
+ snippet: The hypothesis of this work is that F. acidiphilum uses the organic matter secreted by L. ferriphilum
+ for growth
+ explanation: Preserves the explicit hypothesis qualifier rather than using co-occurrence as evidence of an exact
+ carbon-release pathway.
+ source_taxon:
+ preferred_term: Leptospirillum ferriphilum
+ term:
+ id: NCBITaxon:178606
+ label: Leptospirillum ferriphilum
+- name: Proposed Ferroplasma Organic-Matter Consumption
+ description: 'HYPOTHESIZED: Organic matter supplied by L. ferriphilum contributes carbon to F. acidiphilum BRL-115
+ and its removal relieves inhibition of the bacterium. Reciprocal filtered-supernatant growth supports soluble
+ partner effects, but the inspected abstract does not establish identified transferred substrates, assimilation
+ flux or detoxification thresholds. BRL-115 chemomixotrophy and the 0.04% yeast-extract growth optimum are characterization
+ results, not proof of the proposed mediator in mixed culture. CROSS_FEEDING denotes this proposed transfer,
+ not established obligate syntrophy.'
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -191,48 +164,31 @@ ecological_interactions:
term:
id: CHEBI:50860
label: organic molecular entity
- notes: Organic compounds from Leptospirillum secretion
- - preferred_term: Fe(II)
- term:
- id: CHEBI:29033
- label: iron(2+)
- notes: Also oxidized by Ferroplasma for energy
- downstream:
- - target: Filtered Medium Cross-Feeding
- description: Soluble organic compounds contribute to the reciprocal filtered-medium growth response
+ notes: Proposed Leptospirillum-derived organic matter; iron oxidation is not itself a transferred nutrient in
+ this arrow.
evidence:
- reference: PMID:27535541
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: F. acidiphilum uses the organic matter secreted by L. ferriphilum for
- growth, maintaining low levels of organic compounds in the culture medium,
- preventing their toxic effects on L. ferriphilum
- explanation: Merino et al. 2016 describe the syntrophic mechanism — F. acidiphilum
- consumes the organic matter secreted by L. ferriphilum, detoxifying the culture
- and preventing organic-compound toxicity on L. ferriphilum.
+ snippet: The hypothesis of this work is that F. acidiphilum uses the organic matter secreted by L. ferriphilum
+ for growth
+ explanation: The authors state a working hypothesis; positive supernatant responses do not uniquely establish
+ organic-carbon assimilation or detoxification.
- reference: PMID:27535541
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: acidiphilum, strain BRL-115 is a chemomixotrophic organism, and its growth is maximized with
- yeast extract at a concentration of 0.04% wt/vol
- explanation: Establishes mixotrophic metabolism
-- name: Iron Oxidation by Ferroplasma
- description: 'Ferroplasma acidiphilum oxidizes ferrous iron microaerophilically, complementing Leptospirillum''s
- aerobic iron oxidation. F. acidiphilum obtains energy by oxidation of ferrous iron using oxygen as
- terminal electron acceptor, with a membrane-bound complex dedicated to this process. The archaeon
- can function at lower oxygen concentrations than Leptospirillum, filling microaerobic niches. Ferroplasma''s
- cellular machinery is iron-protein-dominated, with high iron content reflecting specialization for
- iron metabolism. Both organisms oxidize Fe²⁺ to Fe³⁺, but occupy different physiological niches (aerobic
- vs. microaerobic, autotrophic vs. mixotrophic), reducing direct competition and enabling stable coexistence.
-
- '
- scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
- participating_taxa:
- - preferred_term: Ferroplasma acidiphilum
- term:
- id: NCBITaxon:74969
- label: Ferroplasma acidiphilum
+ snippet: acidiphilum, strain BRL-115 is a chemomixotrophic organism, and its growth is maximized with yeast
+ extract at a concentration of 0.04% wt/vol
+ explanation: Supports BRL-115 characterization, not a measured carbon transfer or the mixed culture's optimal
+ yeast-extract requirement.
+- name: Ferroplasma Iron-Metabolism Context
+ description: 'Ferroplasma iron metabolism is physiological context, not an observed niche-partitioning interaction.
+ Ferrer studied strain Y(T), reporting ferrous-iron oxidation and iron-rich proteins; this is not BRL-115 in
+ the Leptospirillum pair. Wilson compared isolated rusticyanins: the archaeal FaR had similar redox potential
+ but slower electron transfer than AfR. These sources do not establish lower-oxygen complementarity, a pair-specific
+ membrane complex, competition relief or stable coexistence. Protein electron-transfer properties do not measure
+ consortium iron-oxidation flux.'
+ scope: PAIRWISE
metabolites:
- preferred_term: Fe(II)
term:
@@ -242,35 +198,32 @@ ecological_interactions:
term:
id: CHEBI:29034
label: iron(3+)
- biological_processes:
- - preferred_term: iron ion transport
- term:
- id: GO:0006826
- label: iron ion transport
evidence:
- reference: PMID:38593609
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: properties of the Type-1 copper protein rusticyanin from Acidithiobacillus
- ferrooxidans (AfR) were compared with those from an ancestral form of this
- enzyme (N0) and an archaeal enzyme identified in Ferroplasma acidiphilum (FaR)
- explanation: Wilson et al. 2024 characterize the archaeal rusticyanin (FaR) from
- Ferroplasma acidiphilum, the type-1 copper protein driving iron-oxidation
- electron transfer — describes the Ferroplasma iron oxidation machinery.
+ snippet: While both N0 and FaR show redox potentials similar to that of AfR their electron transport rates were
+ significantly slower.
+ explanation: Isolated-protein comparison, not a demonstrated pathway in the BRL-115 coculture.
- reference: PMID:17203061
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: acidiphilum therefore has a currently unique iron-protein-dominated cellular machinery and
- biochemical phylogeny.
- explanation: Establishes iron-centric metabolism
-- name: Filtered Medium Cross-Feeding
- description: 'Cell growth is favorably affected by the presence of filtered medium of the partner organism.
- The reciprocal supernatant response shows that the partnership involves soluble factors beyond direct
- cell contact.
-
- '
+ snippet: F. acidiphilum strain Y(T) is a chemoautotroph
+ explanation: Strain-specific physiological context; do not transfer the Y(T) result to chemomixotrophic BRL-115
+ or infer oxygen partitioning.
+ source_taxon:
+ preferred_term: Ferroplasma acidiphilum
+ term:
+ id: NCBITaxon:74969
+ label: Ferroplasma acidiphilum
+- name: Reciprocal Filtered-Medium Growth Response
+ description: In reciprocal assays, each organism grew favorably in filtered medium from its partner. This supports
+ diffusible partner-associated growth effects without requiring direct cell contact in those assays, but does
+ not identify the mediators, show equal reciprocal benefit in simultaneous coculture or prove obligatory syntrophy.
+ Mixed-culture growth rates were used as input to flux-balance analysis; model behavior is not independent measurement
+ of exchanged flux. Organic-matter consumption cannot be treated as the demonstrated cause of both reciprocal
+ responses.
scope: COMMUNITY_LEVEL
- interaction_type: MUTUALISM
participating_taxa:
- preferred_term: Leptospirillum ferriphilum
term:
@@ -280,12 +233,6 @@ ecological_interactions:
term:
id: NCBITaxon:74969
label: Ferroplasma acidiphilum
- metabolites:
- - preferred_term: organic molecular entity
- term:
- id: CHEBI:50860
- label: organic molecular entity
- notes: Soluble factors in filtered medium
biological_processes:
- preferred_term: response to other organism
term:
@@ -295,10 +242,11 @@ ecological_interactions:
- reference: PMID:27535541
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: acidiphilum supernatant and vice versa, it was observed that in both cases cell growth is
- favorably affected by the presence of the filtered medium of the other microorganism, proving a
- synergistic interaction between these species
- explanation: Demonstrates soluble factor-mediated synergy
+ snippet: acidiphilum supernatant and vice versa, it was observed that in both cases cell growth is favorably
+ affected by the presence of the filtered medium of the other microorganism, proving a synergistic interaction
+ between these species
+ explanation: Supports the observed reciprocal filtered-medium response, not selective organic-detoxification
+ mediation or balanced mutualism in simultaneous coculture.
environmental_factors:
- name: Extreme Acidity
value: 0.7-2.5
@@ -571,3 +519,30 @@ growth_media:
explanation: Demonstrates syntrophic benefit of co-cultivation
culturemech_id: CultureMech:003277
culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:003277
+discussions:
+- discussion_id: ferroplasma_soluble_mediation_and_strain_scope
+ prompt: Which soluble factors mediate the reciprocal growth response of BRL-115 and L. ferriphilum?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Proposed Leptospirillum Organic-Matter Supply
+ - ecological_interactions#Proposed Ferroplasma Organic-Matter Consumption
+ - ecological_interactions#Ferroplasma Iron-Metabolism Context
+ - ecological_interactions#Reciprocal Filtered-Medium Growth Response
+ rationale: 'Only cited abstracts were inspected. The primary abstract explicitly frames carbon supply and detoxification
+ as a hypothesis. Reciprocal filtered-medium responses do not identify molecules, quantify partner-resolved flux
+ or establish toxic thresholds. Growth-rate inputs to FBA are not independent flux observations. Preserve only
+ the HYPOTHESIZED supply-to-consumption arrow and remove its unsupported extension to both reciprocal assays.
+ Y(T) iron-rich proteins and isolated FaR kinetics are separate systems, not oxygen-niche or pair-specific membrane-complex
+ evidence. No new structure is added. Non-graph physiology, medium and syntrophy claims remain #1462.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T10:43:39Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain proposed organic supply as intrinsic source context without an unsupported carbon-fixation route.;
+ Retain proposed consumption with hypothesis-qualified evidence, without measured detoxification or the reciprocal-response
+ arrow.; Retain iron-metabolism context with explicit strain and isolated-protein limits, not niche partitioning.;
+ Retain reciprocal filtered-medium growth without assigned mediator or obligate mutualism. Issue #1459; reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml b/kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml
index 09f7721d8..8d5a5b8ac 100644
--- a/kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml
+++ b/kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml
@@ -118,13 +118,13 @@ taxonomy:
Collection
explanation: Identifies the E. coli ATCC 25922 bacterial member.
ecological_interactions:
-- name: E. coli glucose competition imposes F. betulina carbon stress
- description: >-
- When E. coli ATCC 25922 was added to 3-day F. betulina liquid MEB cultures,
- glucose fell to zero within 1 day after bacterial addition, F. betulina dry
- biomass dropped from about 60 mg in monoculture to 34 mg in coculture, and
- RNA-seq after 3 days of coculture showed broad F. betulina differential
- expression consistent with carbon depletion and metabolic stress.
+- name: E. coli-Associated Glucose Depletion and F. betulina Stress
+ description: 'PARTIAL: E. coli addition to established F. betulina liquid MEB cultures was followed by glucose
+ depletion within one day, fungal biomass of 34 mg (reported as 44% lower), and stress-related fungal transcription
+ after three days of coculture. These observations support nutrient competition as an interpretation, but the
+ inspected selected primary excerpts do not describe selective glucose rescue establishing mediation. BGC expression
+ indicates transcriptional response, not production or identification of an active secreted metabolite. Endpoint
+ bacterial counts were not reduced in this liquid assay.'
interaction_type: COMPETITION
scope: PAIRWISE
source_taxon:
@@ -146,24 +146,28 @@ ecological_interactions:
- reference: doi:10.64898/2026.09.14.751415
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- the glucose concentration was reduced to zero within 1 day
- explanation: Supports rapid E. coli-associated glucose depletion in liquid coculture.
+ snippet: the glucose concentration was reduced to zero within 1 day
+ explanation: Measured glucose depletion after bacterial addition; the causal explanation remains PARTIAL without
+ a selective rescue described in the inspected excerpts.
- reference: doi:10.64898/2026.09.14.751415
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- the growth of F. betulina was reduced to 34 mg dry weight
- explanation: Supports the reduced F. betulina biomass in liquid coculture.
+ snippet: the growth of F. betulina was reduced to 34 mg dry weight
+ explanation: Measured fungal dry-biomass reduction, not a uniquely isolated glucose-mediated mechanism.
+ - reference: doi:10.64898/2026.09.14.751415
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The bacterial count on agar medium at the end of the experiment did not reveal any impact of the coculture
+ on the bacterial growth.
+ explanation: Counts from the liquid experiment distinguish its bacterial endpoint from the separate agar inhibition
+ phenotype.
- name: F. betulina distal inhibition of E. coli on malt extract agar
- description: >-
- In malt extract agar confrontation plates, F. betulina CIRM-BRFM 860 formed
- a visible zone that inhibited E. coli ATCC 25922 growth at a distance from
- the fungal mycelium. LC-MS metabolomics of media plugs from the inhibition
- zone detected enriched Sumiki's-acid-derivative, calcium-diformate, and
- sulfuric-acid features, and the authors linked the zone to local medium
- acidification rather than to detectable piptamine production.
- interaction_type: COMPETITION
+ description: 'F. betulina inhibited distal E. coli growth on malt extract agar. Inhibition-zone UHPLC-HRMS features
+ were putatively identified as a Sumiki''s acid derivative, calcium diformate and sulfuric acid; these are not
+ confirmed active compounds. HYPOTHESIZED: acid-associated local pH changes mediate inhibition. The inspected
+ selected excerpts describe a pH gradient but no selective neutralization or defined-compound rescue establishing
+ necessity. Piptamine was not detected under these conditions, not shown to be universally absent. This agar
+ phenotype is distinct from liquid-culture stress transcription and unchanged endpoint bacterial counts.'
scope: PAIRWISE
source_taxon:
preferred_term: Fomitopsis betulina CIRM-BRFM 860
@@ -179,10 +183,15 @@ ecological_interactions:
- reference: doi:10.64898/2026.09.14.751415
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- We observed a clear inhibition of the bacterial growth at distance from
- the mycelium
+ snippet: We observed a clear inhibition of the bacterial growth at distance from the mycelium
explanation: Supports distal inhibition of E. coli in the agar confrontation assay.
+ - reference: doi:10.64898/2026.09.14.751415
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: The features detected in the inhibition zone were putatively identified as a Sumiki's acid derivative,
+ calcium diformate, and sulfuric acid.
+ explanation: Preserves tentative metabolite identification; feature association does not establish the active
+ inhibitory molecule.
growth_media:
- name: malt extract broth liquid coculture
temperature: '30'
@@ -248,8 +257,31 @@ curation_history:
- timestamp: '2026-09-28T01:39:09Z'
curator: codex
action: CREATE_RECORD
- changes: >-
- Created a doi:10.64898/2026.09.14.751415-backed Fomitopsis betulina CIRM-BRFM
- 860 and Escherichia coli ATCC 25922 coculture record with agar inhibition
- and liquid glucose-competition evidence from the accessible bioRxiv PDF.
+ changes: Created a doi:10.64898/2026.09.14.751415-backed Fomitopsis betulina CIRM-BRFM 860 and Escherichia coli
+ ATCC 25922 coculture record with agar inhibition and liquid glucose-competition evidence from the accessible
+ bioRxiv PDF.
+ llm_assisted: true
+- timestamp: '2026-10-06T10:43:40Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain liquid glucose depletion and fungal stress with PARTIAL nutrient-competition mediation.; Retain
+ observed distal agar inhibition with putative identities and HYPOTHESIZED acid mediation; no cross-regime arrow.
+ Issue #1460; reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml'
llm_assisted: true
+discussions:
+- discussion_id: fomitopsis_regime_specific_mediators
+ prompt: Which mediators cause liquid fungal stress and separate agar bacterial inhibition?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#E. coli-Associated Glucose Depletion and F. betulina Stress
+ - ecological_interactions#F. betulina distal inhibition of E. coli on malt extract agar
+ rationale: 'Selected primary preprint excerpts support measured glucose depletion, fungal biomass loss and transcription
+ in liquid, versus distal bacterial inhibition and putative acid features on agar. No selective glucose rescue
+ or pH neutralization is described in those excerpts; the full paper was not re-read because the public PDF request
+ returned HTTP 429, so this is not a claim of universal experimental absence. Piptamine nondetection is condition-specific;
+ BGC induction is not active-product identification. Preserve two nodes and zero arrows rather than connect different
+ assay regimes. Prior cache-support fixes #1169/#1170/#1171 and the natural-partner caveat removal #1173 remain
+ intact.'
+ posed_by: codex
+ posed_date: '2026-10-06'
diff --git a/kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml b/kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml
index 8d71c4e17..cc0e0a435 100644
--- a/kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml
+++ b/kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml
@@ -154,11 +154,37 @@ curation_history:
- timestamp: '2026-09-24T13:24:51Z'
curator: codex
action: ADD_COMMUNITY_RECORD
- changes: Created CommunityMech:000432 for the PMID:42545019 four-species aerobic lung microbiome model, including species-level
- membership, 34°C BHI co-culture conditions, validation endpoints, and exact PubMed abstract evidence.
+ changes: Created CommunityMech:000432 for the PMID:42545019 four-species aerobic lung microbiome model, including
+ species-level membership, 34°C BHI co-culture conditions, validation endpoints, and exact PubMed abstract evidence.
llm_assisted: true
- timestamp: '2026-09-24T13:31:26Z'
curator: codex
action: FIX_EXTERNAL_RESOURCE_EVIDENCE
- changes: Tightened the DOI external-resource evidence to cite the exact PMID:42545019 DOI line rather than the article title.
+ changes: Tightened the DOI external-resource evidence to cite the exact PMID:42545019 DOI line rather than the
+ article title.
llm_assisted: true
+- timestamp: '2026-10-06T10:43:40Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Record full-text graph-expansion candidates and retain needs_research; no new nodes or arrows pending
+ the one-community research workflow Issue #1461; reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml'
+ llm_assisted: true
+discussions:
+- discussion_id: lung_full_text_causal_expansion
+ prompt: Which observed phenotypes and proposed mechanisms belong in the four-species causal graph?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: 'The openly available primary main body (PMID:42545019; PMC13595950) now supports source review beyond
+ the abstract. The record still has no interaction nodes and remains needs_research under #1461. Day-10 vPCR
+ persistence, total CFU, DNA-qPCR and protein fractions are distinct readouts. P. koreensis-containing bicultures
+ alkalinize, and community pH recovers after acid perturbation, but total CFU does not resolve member-specific
+ compositional resilience. Siderophore uptake, partner-resolved acid/pyruvate exchange, ammonia mediation and
+ AI-2 coordination require hypothesis-qualified treatment, not inferred flux or selective causality from proteins
+ alone. Predicted antimicrobial pathways produced no inhibition zones in the tested agar assay, not proof of
+ universal absence. Nutrient-rich BHI and pH 9-10 are not physiological healthy-airway conditions. Challenge
+ organisms are not members of the canonical four-species record. One-community Edison dry run completed; specific
+ credit authorization requested and no provider job or spend made. Add no speculative nodes or arrows while research
+ is pending. Source body, tables and captions read; figure images, supplements and raw data not inspected. Strain
+ and model metadata remain #1463.'
+ posed_by: codex
+ posed_date: '2026-10-06'
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch41.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch41.yaml
new file mode 100644
index 000000000..aad6e963b
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch41.yaml
@@ -0,0 +1,165 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: a09d6620fdcf4787f50b02f851c0b6e8c712c0f4
+scope:
+- kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml
+- kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml
+- kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch41.json
+findings:
+- issue: 1459
+ severity: P2
+ status: addressed_in_this_change
+ finding: 'Ferroplasma graph: distinguish filtered-medium benefit from proposed organic detoxification'
+ disposition: Existing-graph defect corrected; close only after protected main merge.
+- issue: 1460
+ severity: P2
+ status: addressed_in_this_change
+ finding: 'Fomitopsis graph: qualify mediator identity and keep agar inhibition separate from liquid
+ stress'
+ disposition: Existing-graph defect corrected; close only after protected main merge.
+- issue: 1461
+ severity: P2
+ status: open_graph_research
+ finding: 'Lung model graph: curate full-text interaction candidates through the one-community research
+ workflow'
+ disposition: Full primary main body now read, but zero-node graph remains needs_research. One-community
+ dry run only, specific authorization requested, no provider spend.
+- issue: 1462
+ severity: P2
+ status: open_nongraph_followup
+ finding: 'Ferroplasma metadata: reconcile unverified physiology, medium and syntrophy claims'
+ disposition: Non-graph fields preserved, not certified; remains open.
+- issue: 1463
+ severity: P2
+ status: open_nongraph_followup
+ finding: 'Lung model metadata: update abstract-era strain and model-limit annotations from full text'
+ disposition: Non-graph fields preserved, not certified; remains open.
+adversarial_checks:
+- Whole records and every existing graph node/arrow reviewed with explicit source-access limits. Six nodes
+ retained, one HYPOTHESIZED arrow retained and one unsupported arrow removed. Five renames, exact targets
+ and discussion anchors checked. No new causal structure.
+- Ferroplasma abstract explicitly says hypothesis. Restore that qualifier in evidence and descriptions.
+ Positive supernatant growth is not identified organic-carbon flux, detoxification thresholds, Calvin-cycle
+ fixation or obligate syntrophy. Keep source-only intrinsic context and remove unsupported process/category
+ annotations.
+- The retained organic-supply-to-consumption arrow is hypothetical substrate availability. Consumption
+ is not established mediation of both reciprocal supernatant assays, so its extension to the response
+ node is removed. Growth rates supplied to FBA are not independent exchange measurements.
+- Ferrer strain Y(T) and Wilson isolated rusticyanins are separate systems from BRL-115 with Leptospirillum.
+ Similar redox potential does not imply similar transfer rates. Do not infer lower-oxygen niches, pair-specific
+ membrane complexes, competition relief or stable coexistence. No retraction claim is made.
+- Fomitopsis liquid glucose depletion, 34 mg fungal biomass and stress-related transcription support a
+ PARTIAL competition interpretation. Inspected selected excerpts do not describe selective rescue, but
+ the full preprint was not accessed in this review, so absence from the entire study is not claimed.
+- Fomitopsis agar features are putative identities and acid mediation is HYPOTHESIZED. Piptamine nondetection
+ is condition-specific, and BGC expression is not active-product identification. Preserve observed distal
+ inhibition without unsupported resource-competition classification. Liquid bacterial endpoint counts
+ were unchanged; do not connect distinct assay regimes or restore historical prose-target arrows.
+- 'Closed Fomitopsis #1169/#1170/#1171 concern previously missing cache support and are not reopened or
+ duplicated. The expanded selected cache now supports the assay facts. Preserve #1173 natural-partner
+ caveat removal and the zero-arrow topology.'
+- 'Lung main body is now openly available and read, including tables/captions and Methods. The zero-node
+ graph is not certified complete: #1461 remains open and needs_research. One-community Edison dry run
+ retained verbatim with query hash; no API submission or credit spend, and no blanket authorization inferred
+ from an earlier unrelated job.'
+- Lung vPCR persistence, total CFU, DNA-qPCR and protein-abundance fractions are distinct evidence. pH
+ recovery is functional, not member-resolved compositional resilience. Siderophore uptake, partner-resolved
+ acid/pyruvate exchange, ammonia mediation and AI-2 coordination remain proposed mechanisms. Agar nondetection
+ is not universal antimicrobial absence. Challenge organisms are not the four canonical members.
+- 'No protocol expansion, taxonomy replacement or full-text cache addition. Canonical taxon IDs/groundings,
+ historical events and all non-graph raw blocks preserved. #1462/#1463 remain open. User workspace files
+ untouched; edits isolated in the batch worktree.'
+- 457 other records and 920 reference-cache files unchanged. Participant registry stays at 187 with unchanged
+ connectivity census/numeric bounds. All 33 baseline warnings exactly preserved and zero structural defects;
+ no links invented to suppress warnings.
+- Repeat rendering deterministic and every published description checked by HTML parser across all 456
+ pages. Eight new tests and the full combined regression suite pass on the recorded tested bytes. No
+ browser screenshot review claimed.
+- Reference validator 0.1.7 exits 0 with zero effective checks; explicitly a no-op. Snippet MATCH is textual,
+ not scientific validation. Actual output tails/digests and pre-paper baseline retained. The ancestry-only
+ restack is documented without falsifying the original baseline commit. Initial dry-run helper failure
+ disclosed.
+- 'Source access differs: Ferroplasma abstracts, Fomitopsis selected preprint excerpts with HTTP 429 on
+ full PDF, lung primary main body. No figure images, equation rendering, separate supplements or raw
+ data reviewed. No rate-control bypass.'
+- Deduplication covered 778 all-state issue titles/bodies and ignored/hidden-inclusive local files; all
+ seven matched bodies read, not every comment or PR review. This is source-based self-adversarial review,
+ not independent approval, protected merge or full-corpus completion.
+verification:
+ combined_regressions: 431 passed in 170.84s (0:02:50)
+ new_regression_tests: 8
+ schema_strict_terms_history: passed; actual outputs and digests retained
+ snippet_counts_by_record:
+ kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml:
+ MATCH: 19
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml:
+ MATCH: 12
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml:
+ MATCH: 11
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ network: Zero errors; 33 baseline warnings exactly preserved, none added.
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml: 4f0a70fa0459dfeeb6c9871c54f2440b9067a4ee5037d80808c4c4be7a07dda6
+ tests/test_causal_review_batch41.py: a3c82a3f9d08b650d708ddc8217c1a6842e06f61f154b9511a2e0ea02503306f
+ kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml: 08e60d74c495dfee5ec77a2a8ed63da4da51b1ebe1adb527350591d0e5b6340b
+ kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml: e23f7534b2c596261fdb8f6a69225c64ee0fcc4b10b95eb27bfccc7a48e2b0fe
+ kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml: e6123414e5fb18492837dd471cc7a12496821032306fdb6a6fba9b938e7908fb
+ post_commit_docs_current: Separate publication gate; not asserted in pre-commit record.
+ protected_ci_and_merge: Eligible exact-head checks and protected queue still required.
+participant_census:
+ connectivity_before:
+ community_level_only: 263
+ credited_solely_by_the_rule: 1219
+ mixed: 124
+ records: 460
+ taxa: 1494
+ with_community_level: 387
+ connectivity_after:
+ community_level_only: 263
+ credited_solely_by_the_rule: 1219
+ mixed: 124
+ records: 460
+ taxa: 1494
+ with_community_level: 387
+ exact_change: No registry or numeric-bound changes; 187 registered records. Ferroplasma already registered,
+ Fomitopsis remains pairwise and lung has no graph. Canonical taxonomy preserved.
+ numeric_bounds_changed: false
+corpus:
+ records: 460
+ nodes: 1469
+ edges: 687
+ review_status_counts:
+ needs_research: 10
+ pending: 288
+ reviewed: 162
+limitations:
+- Ferroplasma cited abstracts only; full primary body, figure images and supplements not reviewed.
+- Fomitopsis selected preprint excerpts only. Full PDF returned HTTP 429; no bypass. Missing selective
+ interventions are not claimed absent from the entire paper.
+- Lung public main body, tables and captions read; no figure images, equation rendering, separate supplements
+ or raw data. Its zero-node graph remains needs_research, not complete.
+- All six existing nodes retained, one arrow retained and one removed. No new structure or provider spend.
+ Five node renames and corresponding targets updated.
+- 'Canonical taxonomy, prior history, original source caches and non-graph raw blocks preserved, not certified.
+ Non-graph followups #1462/#1463 remain open.'
+- Self-adversarial review is not independent approval, protected merge or full-corpus completion. Snippet
+ matching is textual, not scientific validation.
+- Reference validator 0.1.7 performs zero checks for this schema; disclose the no-op.
diff --git a/reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml b/reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml
new file mode 100644
index 000000000..31a796979
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml
@@ -0,0 +1,432 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: a09d6620fdcf4787f50b02f851c0b6e8c712c0f4
+baseline_commit: 8e610ca6652c7906952a7c031a81f31669b8ce26
+base_tree: 7eb3104eab79453a36cfe9fcf4f97fcb39463df4
+baseline_ancestry_change:
+ reason: Batch17 protected merge followed by whole-tree and own-patch identical restacking of batch40. Pre-paper
+ baseline remains at its original commit, not falsely relabeled.
+ old_head: 8e610ca6652c7906952a7c031a81f31669b8ce26
+ new_head: a09d6620fdcf4787f50b02f851c0b6e8c712c0f4
+ tree: 7eb3104eab79453a36cfe9fcf4f97fcb39463df4
+ own_patch_sha256: 904b08cf9b6f51a9316c58f9e0646828b48be52e1e3e1500022e79a245b50433
+issues:
+- 1459
+- 1460
+open_nongraph_followups:
+- 1462
+- 1463
+open_graph_research:
+- 1461
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 778
+ ignored_hidden_local_search: true
+ relevant_bodies_read:
+ - 1358
+ - 1356
+ - 1173
+ - 1171
+ - 1170
+ - 1169
+ - 1080
+ limitations: Not all issue comments or PR reviews inspected.
+reference_cache_original_hashes:
+ references_cache/PMID_27535541.txt: daf84c5d47a7e43c14d877dffdd3f915f959793d05b5e58bf5504dbd7c029376
+ references_cache/PMID_38593609.txt: d9157d19a4fd3aab74f09030815069dfa49bb578bca4eed21ab5e3f32cf3faf4
+ references_cache/PMID_17203061.md: 03332901b51fc4cb4547930876daca95b8c9ed7a7dc9c5d4c73b363e61945e97
+ references_cache/PMID_16104851.md: a6c91bc5c233bfcd4251bdecb1bf52ee2974307f69b6a168cc65bf6034c2ac96
+ references_cache/doi_10.64898_2026.09.14.751415.md: d5b36843ad6590134754e521d90380dea8218199c3229ab16c65ea083ad00dd0
+ references_cache/PMID_42545019.txt: 424d343f911617346d8954da92daca3f23ab0e110ab1094a3d9419123df077ef
+edison:
+ status: dry_run_only_awaiting_specific_lung_job_authorization
+ provider_job_submitted: false
+ provider_credits_spent: false
+ community: CommunityMech:000432
+ query_chars: 7671
+ query_sha256: 89ec04708989286f0f04e4f2a5da3ea60e8fc9a949144e75f46b2d590d3b2a3b
+ dryrun_meta_sha256: fdfa04bacd6346433e07158347117cbe684dd31abc35373dd0c772a817f1c97b
+ dryrun_meta:
+ slug: FourSpecies_Aerobic_Lung_Microbiome_Model
+ community_path: kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml
+ community_id: CommunityMech:000432
+ job: LITERATURE
+ job_id: job-futurehouse-paperqa3
+ label: causal
+ template_path: templates/community_causal_graph_research.md
+ template_vars:
+ community_name: Four-Species Aerobic Lung Microbiome Model
+ community_id: CommunityMech:000432
+ community_file: FourSpecies_Aerobic_Lung_Microbiome_Model.yaml
+ community_slug: FourSpecies_Aerobic_Lung_Microbiome_Model
+ community_category: OTHER
+ ecological_state: ENGINEERED
+ community_origin: SYNTHETIC
+ description: A simplified artificial lung microbiome model assembled as an aerobic four-species co-culture
+ of Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei. The model was maintained
+ for 10 days at 34°C in brain heart infusion medium and validated with qPCR, viability PCR, conventional
+ microbiology, and metaproteomics to provide a controlled platform for lung microbiome interaction and pulmonary-drug
+ studies.
+ source_summary: ''
+ environment_summary: laboratory environment | ENVO:01001405 | The curated entity is an in vitro aerobic BHI
+ co-culture constructed to model the human lung microbiome, rather than a sampled airway community.
+ taxonomy_summary: Pseudomonas koreensis | Rothia aeria | Neisseria cinerea | Streptococcus downei
+ interaction_summary: ''
+ environmental_factor_summary: Incubation temperature - 34 - The four-species BHI co-culture was incubated
+ at 34°C during 10-day stability testing.
+ growth_media_summary: Brain heart infusion medium - P. koreensis, R. aeria, N. cinerea, and S. downei were
+ co-cultured in brain heart infusion medium as a simplified artificial lung microbiome model.
+ dataset_summary: DOI - Four-species aerobic lung microbiome model - doi:10.1128/msystems.00491-26 - https://doi.org/10.1128/msystems.00491-26
+ | PubMed - Four-species aerobic lung microbiome model - PMID:42545019 - https://pubmed.ncbi.nlm.nih.gov/42545019/
+ evidence_summary: 'PMID:42545019: we developed a simplified artificial lung microbiome model composed of four
+ representative bacterial species (Supports the source''s objective of making a simplified artificial lung
+ microbiome model.) | PMID:42545019: We successfully established a stable 10-day co-culture at 34°C using
+ brain heart infusion medium (Supports the 10-day BHI co-culture implementation and incubation temperature.)
+ | PMID:42545019: Integrated bioinformatic analyses revealed a variety of potential microbe-microbe interactions,
+ which were supported by metaproteomic analysis using mass spectrometry. (Supports metaproteomics as an interaction-supporting
+ endpoint while not asserting individual pairwise edges.) | PMID:42545019: Pseudomonas koreensis, Rothia
+ aeria, Neisseria cinerea, and Streptococcus downei (Names Pseudomonas koreensis as a species in the four-member
+ artificial lung microbiome model.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea,
+ and Streptococcus downei (Names Rothia aeria as a species in the four-member artificial lung microbiome
+ model.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei
+ (Names Neisseria cinerea as a species in the four-member artificial lung microbiome model.) | PMID:42545019:
+ Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Streptococcus downei
+ as a species in the four-member artificial lung microbiome model.) | PMID:42545019: stable 10-day co-culture
+ at 34°C using brain heart infusion medium (Supports the 34°C incubation temperature.) | PMID:42545019: We
+ successfully established a stable 10-day co-culture at 34°C using brain heart infusion medium (Names BHI
+ medium and the 10-day, 34°C co-culture condition.) | PMID:42545019: DOI: 10.1128/msystems.00491-26 (Supports
+ the DOI identifier for the mSystems article reporting the four-species aerobic lung microbiome model.) |
+ PMID:42545019: Establishment of an in vitro aerobic bacterial community as a model of the human lung microbiome
+ (Links the PubMed record to the curated lung microbiome model study.)'
+ query_chars: 7671
+ query: "# Microbial Community Causal-Graph Research Template\n\n## Target Community\n- **Community name:** Four-Species\
+ \ Aerobic Lung Microbiome Model\n- **Community id:** CommunityMech:000432\n- **Community file:** FourSpecies_Aerobic_Lung_Microbiome_Model.yaml\n\
+ - **Community category:** OTHER\n- **Ecological state:** ENGINEERED\n- **Community origin:** SYNTHETIC\n-\
+ \ **Environment:** laboratory environment | ENVO:01001405 | The curated entity is an in vitro aerobic BHI\
+ \ co-culture constructed to model the human lung microbiome, rather than a sampled airway community.\n- **Description:**\
+ \ A simplified artificial lung microbiome model assembled as an aerobic four-species co-culture of Pseudomonas\
+ \ koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei. The model was maintained for 10 days\
+ \ at 34°C in brain heart infusion medium and validated with qPCR, viability PCR, conventional microbiology,\
+ \ and metaproteomics to provide a controlled platform for lung microbiome interaction and pulmonary-drug studies.\n\
+ \n## Existing Record Context\n- **Taxa:** Pseudomonas koreensis | Rothia aeria | Neisseria cinerea | Streptococcus\
+ \ downei\n- **Known ecological interactions:** \n- **Environmental factors:** Incubation temperature - 34\
+ \ - The four-species BHI co-culture was incubated at 34°C during 10-day stability testing.\n- **Growth media\
+ \ / culture conditions:** Brain heart infusion medium - P. koreensis, R. aeria, N. cinerea, and S. downei\
+ \ were co-cultured in brain heart infusion medium as a simplified artificial lung microbiome model.\n- **Associated\
+ \ datasets / resources:** DOI - Four-species aerobic lung microbiome model - doi:10.1128/msystems.00491-26\
+ \ - https://doi.org/10.1128/msystems.00491-26 | PubMed - Four-species aerobic lung microbiome model - PMID:42545019\
+ \ - https://pubmed.ncbi.nlm.nih.gov/42545019/\n- **Existing evidence:** PMID:42545019: we developed a simplified\
+ \ artificial lung microbiome model composed of four representative bacterial species (Supports the source's\
+ \ objective of making a simplified artificial lung microbiome model.) | PMID:42545019: We successfully established\
+ \ a stable 10-day co-culture at 34°C using brain heart infusion medium (Supports the 10-day BHI co-culture\
+ \ implementation and incubation temperature.) | PMID:42545019: Integrated bioinformatic analyses revealed\
+ \ a variety of potential microbe-microbe interactions, which were supported by metaproteomic analysis using\
+ \ mass spectrometry. (Supports metaproteomics as an interaction-supporting endpoint while not asserting individual\
+ \ pairwise edges.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus\
+ \ downei (Names Pseudomonas koreensis as a species in the four-member artificial lung microbiome model.) |\
+ \ PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Rothia\
+ \ aeria as a species in the four-member artificial lung microbiome model.) | PMID:42545019: Pseudomonas koreensis,\
+ \ Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Neisseria cinerea as a species in the four-member\
+ \ artificial lung microbiome model.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea,\
+ \ and Streptococcus downei (Names Streptococcus downei as a species in the four-member artificial lung microbiome\
+ \ model.) | PMID:42545019: stable 10-day co-culture at 34°C using brain heart infusion medium (Supports the\
+ \ 34°C incubation temperature.) | PMID:42545019: We successfully established a stable 10-day co-culture at\
+ \ 34°C using brain heart infusion medium (Names BHI medium and the 10-day, 34°C co-culture condition.) | PMID:42545019:\
+ \ DOI: 10.1128/msystems.00491-26 (Supports the DOI identifier for the mSystems article reporting the four-species\
+ \ aerobic lung microbiome model.) | PMID:42545019: Establishment of an in vitro aerobic bacterial community\
+ \ as a model of the human lung microbiome (Links the PubMed record to the curated lung microbiome model study.)\n\
+ \n## Research Objective\n\nBuild a source-backed **causal interaction graph** for the microbial community\n\
+ **Four-Species Aerobic Lung Microbiome Model**, suitable for the `ecological_interactions` block of\n`kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml`.\
+ \ The graph's **nodes are mechanistic\ninteractions** and its **directed edges are causal links** (\"interaction\
+ \ A\nenables / drives / suppresses interaction B\"). Extract only relationships the\nprimary literature supports;\
+ \ do not infer edges that are not stated or directly\nimplied by an experiment.\n\n## Required Findings\n\n\
+ ### 1. Interaction nodes (the vertices)\n\nFor each mechanistic interaction, report as a table row:\n\n- **name**\
+ \ — a short, unique interaction name (used as the node id and as the\n `target` of any causal edge that points\
+ \ to it).\n- **interaction_type** — one of: MUTUALISM, COMMENSALISM, CROSS_FEEDING,\n COMPETITION, PREDATION,\
+ \ SYNTROPHY, NICHE_PARTITIONING, STRAIN_COMPETITION,\n COLONIZATION_FACILITATION (or state \"OTHER: \"\
+ \ if none fit).\n- **scope** — PAIRWISE (organism→organism) or COMMUNITY_LEVEL (emergent /\n abiotically\
+ \ driven, e.g. electrolysis-supplied H2). PAIRWISE **must** name a\n source taxon.\n- **source_taxon → target_taxon**\
+ \ — the directed pair (who acts on whom). Give\n NCBITaxon CURIEs + labels where resolvable.\n- **metabolites\
+ \ / biological_processes** — the exchanged compound(s) (CHEBI) and\n process(es) (GO) that mediate the interaction.\n\
+ - **direction / sign** — does the source **increase (+)** or **decrease (−)** the\n target's growth/activity?\
+ \ State it explicitly.\n- **evidence** — a short **verbatim** snippet + its reference (PMID/DOI).\n\n### 2.\
+ \ Causal edges (the arcs)\n\nThis is the graph structure. For every ordered pair of nodes where the\nliterature\
+ \ supports a causal link, report a row:\n\n- **from** — upstream interaction name (a node from §1).\n- **to**\
+ \ — downstream interaction name (a node from §1).\n- **causal link** — one sentence: *how* the upstream interaction\
+ \ causes /\n enables / is required for / suppresses the downstream one (e.g. \"H2 produced\n by the syntrophic\
+ \ oxidation lowers pH2 enough for the acetogen to grow, which\n in turn supplies acetate to the methanogen\"\
+ ).\n- **evidence** — verbatim snippet + reference for the causal claim specifically\n (not just for the two\
+ \ endpoints existing).\n\nPrefer chains that a paper demonstrates by perturbation (knockout, substrate\nremoval,\
+ \ inhibitor, co-culture vs mono-culture), and say which experiment shows\neach edge. Flag any edge that is\
+ \ hypothesized rather than demonstrated.\n\n### 3. Grounding\n\n- CURIEs where available: NCBITaxon (taxa),\
+ \ CHEBI (metabolites), GO (processes),\n ENVO (environment), PMID / DOI (evidence).\n- Do not invent taxa,\
+ \ ontology ids, snippets, accession ids, or citations. If a\n node or edge lacks a citable source, omit it\
+ \ or mark it UNVERIFIED.\n\n## Output Format\n\nReturn a curation-focused report with:\n\n1. **Scope summary**\
+ \ — the consortium and the top-level function the causal graph\n explains (1–3 sentences).\n2. **Node table**\
+ \ — the interaction nodes (§1 columns).\n3. **Edge table** — the directed causal edges (§2 columns: from,\
+ \ to, causal\n link, evidence).\n4. **Adjacency / DOT sketch** — a compact `from -> to` edge list (or Graphviz\
+ \ DOT\n snippet) so the graph can be eyeballed; annotate edges with + / − sign.\n5. **Gaps & controversies**\
+ \ — edges the literature disputes, or plausible edges\n with no direct evidence (candidates for a `Discussion`/knowledge-gap\
+ \ note).\n6. **References** — every PMID/DOI cited, once.\n\nEach biological claim (node and edge) must carry\
+ \ a verbatim snippet and a\nreference. This report is reviewed by a curator before anything is written to\n\
+ `kb/communities/`.\n"
+ submitted_at: '2026-10-06T10:38:06.050699+00:00'
+ status: dry-run
+ query_sha256: 89ec04708989286f0f04e4f2a5da3ea60e8fc9a949144e75f46b2d590d3b2a3b
+ limitations: SDK emitted a remote cost-map fetch warning and used its local fallback; no provider job was submitted
+ and no price estimate was supplied. Other record repairs require no new structure.
+limitations:
+- Ferroplasma cited abstracts only; full primary body, figure images and supplements not reviewed.
+- Fomitopsis selected preprint excerpts only. Full PDF returned HTTP 429; no bypass. Missing selective interventions
+ are not claimed absent from the entire paper.
+- Lung public main body, tables and captions read; no figure images, equation rendering, separate supplements or
+ raw data. Its zero-node graph remains needs_research, not complete.
+- All six existing nodes retained, one arrow retained and one removed. No new structure or provider spend. Five
+ node renames and corresponding targets updated.
+- 'Canonical taxonomy, prior history, original source caches and non-graph raw blocks preserved, not certified.
+ Non-graph followups #1462/#1463 remain open.'
+- Self-adversarial review is not independent approval, protected merge or full-corpus completion. Snippet matching
+ is textual, not scientific validation.
+- Reference validator 0.1.7 performs zero checks for this schema; disclose the no-op.
+records:
+- path: kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml
+ id: CommunityMech:000027
+ original_sha256: f357e3ec553f3c8ff1448687f6bf1ab557d2aa72e9e011162ce4b583bdb9a7e7
+ record_sha256: 08e60d74c495dfee5ec77a2a8ed63da4da51b1ebe1adb527350591d0e5b6340b
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml
+ scope: Whole record and all existing nodes/arrows assessed; source-access limits explicit. Non-graph fields preserved,
+ not certified.
+ summary: Retain proposed organic supply as intrinsic source context without an unsupported carbon-fixation route.;
+ Retain proposed consumption with hypothesis-qualified evidence, without measured detoxification or the reciprocal-response
+ arrow.; Retain iron-metabolism context with explicit strain and isolated-protein limits, not niche partitioning.;
+ Retain reciprocal filtered-medium growth without assigned mediator or obligate mutualism.
+ renamed_nodes:
+ Iron Oxidation by Leptospirillum: Proposed Leptospirillum Organic-Matter Supply
+ Organic Matter Consumption by Ferroplasma: Proposed Ferroplasma Organic-Matter Consumption
+ Iron Oxidation by Ferroplasma: Ferroplasma Iron-Metabolism Context
+ Filtered Medium Cross-Feeding: Reciprocal Filtered-Medium Growth Response
+ node_decisions:
+ - node: Proposed Leptospirillum Organic-Matter Supply
+ rationale: Retain proposed organic supply as intrinsic source context without an unsupported carbon-fixation
+ route.
+ - node: Proposed Ferroplasma Organic-Matter Consumption
+ rationale: Retain proposed consumption with hypothesis-qualified evidence, without measured detoxification or
+ the reciprocal-response arrow.
+ - node: Ferroplasma Iron-Metabolism Context
+ rationale: Retain iron-metabolism context with explicit strain and isolated-protein limits, not niche partitioning.
+ - node: Reciprocal Filtered-Medium Growth Response
+ rationale: Retain reciprocal filtered-medium growth without assigned mediator or obligate mutualism.
+ removed_node_decisions: []
+ edges_before:
+ - source: Iron Oxidation by Leptospirillum
+ target: Organic Matter Consumption by Ferroplasma
+ description: Organic compounds secreted by Leptospirillum are consumed by Ferroplasma
+ - source: Organic Matter Consumption by Ferroplasma
+ target: Filtered Medium Cross-Feeding
+ description: Soluble organic compounds contribute to the reciprocal filtered-medium growth response
+ edges_after:
+ - source: Proposed Leptospirillum Organic-Matter Supply
+ target: Proposed Ferroplasma Organic-Matter Consumption
+ description: 'HYPOTHESIZED: Organic matter released during Leptospirillum growth would provide substrate for
+ Ferroplasma consumption. This is the source-stated supply hypothesis, not a traced partner-to-partner flux;
+ reciprocal supernatant growth does not identify the transferred compound or prove the detoxification mechanism.'
+ retained_edge_decisions:
+ - source: Proposed Leptospirillum Organic-Matter Supply
+ target: Proposed Ferroplasma Organic-Matter Consumption
+ rationale: 'HYPOTHESIZED: Organic matter released during Leptospirillum growth would provide substrate for Ferroplasma
+ consumption. This is the source-stated supply hypothesis, not a traced partner-to-partner flux; reciprocal
+ supernatant growth does not identify the transferred compound or prove the detoxification mechanism.'
+ removed_edge_decisions:
+ - source: Organic Matter Consumption by Ferroplasma
+ target: Filtered Medium Cross-Feeding
+ rationale: Organic-matter consumption is a proposed mechanism and not established mediation of both reciprocal
+ filtered-medium responses; assays do not identify the same causal route.
+ references:
+ - PMID:27535541
+ - PMID:38593609
+ - PMID:17203061
+ - PMID:16104851
+ issues:
+ - 1459
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Ferroplasma_Leptospirillum_Syntrophy/2026-10-06T104340Z-codex-37b7f6.yaml
+ source_review:
+ PMID:27535541:
+ cache: references_cache/PMID_27535541.txt
+ url: https://aiche.onlinelibrary.wiley.com/doi/10.1002/btpr.2340
+ scope: Complete cached primary abstract and public publisher abstract read; full-body URL inaccessible. No
+ primary body, figures or supplements reviewed.
+ PMID:38593609:
+ cache: references_cache/PMID_38593609.txt
+ url: https://doi.org/10.1016/j.jinorgbio.2024.112539
+ scope: Complete cached primary abstract read, not full body, figures or supplements.
+ PMID:17203061:
+ cache: references_cache/PMID_17203061.md
+ url: https://doi.org/10.1038/nature05362
+ scope: Complete cached primary abstract read, not full body, figures or supplements. Y(T), not BRL-115.
+ PMID:16104851:
+ cache: references_cache/PMID_16104851.md
+ url: https://doi.org/10.1111/j.1462-2920.2005.00861.x
+ scope: Complete cached review abstract read as ecological context, not exact-pair primary evidence.
+- path: kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml
+ id: CommunityMech:000457
+ original_sha256: 7626c8ddd2ae88e323ebf2ae6058a19ff70e0a17d647b7b5f941be91def3af78
+ record_sha256: e23f7534b2c596261fdb8f6a69225c64ee0fcc4b10b95eb27bfccc7a48e2b0fe
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml
+ scope: Whole record and all existing nodes/arrows assessed; source-access limits explicit. Non-graph fields preserved,
+ not certified.
+ summary: Retain liquid glucose depletion and fungal stress with PARTIAL nutrient-competition mediation.; Retain
+ observed distal agar inhibition with putative identities and HYPOTHESIZED acid mediation; no cross-regime arrow.
+ renamed_nodes:
+ E. coli glucose competition imposes F. betulina carbon stress: E. coli-Associated Glucose Depletion and F. betulina
+ Stress
+ node_decisions:
+ - node: E. coli-Associated Glucose Depletion and F. betulina Stress
+ rationale: Retain liquid glucose depletion and fungal stress with PARTIAL nutrient-competition mediation.
+ - node: F. betulina distal inhibition of E. coli on malt extract agar
+ rationale: Retain observed distal agar inhibition with putative identities and HYPOTHESIZED acid mediation;
+ no cross-regime arrow.
+ removed_node_decisions: []
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - doi:10.64898/2026.09.14.751415
+ issues:
+ - 1460
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Fomitopsis_Ecoli_Nutritional_Stress_Coculture/2026-10-06T104341Z-codex-a2b56f.yaml
+ source_review:
+ doi:10.64898/2026.09.14.751415:
+ cache: references_cache/doi_10.64898_2026.09.14.751415.md
+ url: https://www.biorxiv.org/content/10.64898/2026.09.14.751415v1.full.pdf
+ scope: Complete selected_full_text cache read. Primary preprint, not peer-reviewed. PDF request returned HTTP
+ 429; no bypass, full-paper or figure-image review claimed. No separate supplements reviewed.
+- path: kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml
+ id: CommunityMech:000432
+ original_sha256: 01531be768a6ce1f2a546d2ee5ee9ca8e134bcc08a77eb7d6cf47e3eafe0c29f
+ record_sha256: e6123414e5fb18492837dd471cc7a12496821032306fdb6a6fba9b938e7908fb
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml
+ scope: Whole record and all existing nodes/arrows assessed; source-access limits explicit. Non-graph fields preserved,
+ not certified.
+ summary: Record full-text graph-expansion candidates and retain needs_research; no new nodes or arrows pending
+ the one-community research workflow
+ renamed_nodes: {}
+ node_decisions: []
+ removed_node_decisions: []
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42545019
+ issues:
+ - 1461
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ curation_events_added: 1
+ history_files:
+ - history/records/FourSpecies_Aerobic_Lung_Microbiome_Model/2026-10-06T104341Z-codex-319aac.yaml
+ source_review:
+ PMID:42545019:
+ cache: references_cache/PMID_42545019.txt
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13595950/fullTextXML
+ scope: Complete cached abstract plus public primary main body through Methods, tables and captions read. CC
+ BY 4.0. No figure images, separate supplements, equation rendering or raw data reviewed. Full text remains
+ temporary; original cache unchanged.
+ receipt:
+ source_url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13595950/fullTextXML
+ ids:
+ - pub-id-type: pmcid
+ value: PMC13595950
+ - pub-id-type: pmcaid
+ value: '13595950'
+ - pub-id-type: pmcaiid
+ value: '13595950'
+ - pub-id-type: pmid
+ value: '42545019'
+ - pub-id-type: doi
+ value: 10.1128/msystems.00491-26
+ licenses:
+ - This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International
+ license.
+ source_sha256: d26528baa780d0c4344ae24938862ad9d52a0d6143e490e9bcd10f9b03d73c5d
+ body_sha256: fa0e0fa01df6faca9298c7deeebea886ddf2b6bde8b5b8e0acbd3635987e4dd1
+ blocks: 138
+ body_bytes: 66654
+ sections:
+ - INTRODUCTION
+ - RESULTS AND DISCUSSION
+ - Composition of the microbial consortium
+ - Understanding the growth behavior of mono- and co-cultures
+ - Co-culture demonstrates beneficial interactions and viability shifts
+ - Pronounced pH elevation in co-culture indicates interplay of acid-base metabolic processes
+ - Co-culture shows robust resilience to acid perturbation and community expansion
+ - Comparative genomics identifies shared and unique pathways in the microbial consortium
+ - Validation of genome-based metabolic modeling by proteomics
+ - Predicted antimicrobial pathways in P. koreensis do not manifest in co-culture
+ - N. cinerea may exemplify metabolic complementarity through exploitation of siderophores
+ - Metabolic cross-feeding may explain alkalinization of the consortium
+ - Conclusion
+ - MATERIALS AND METHODS
+ - Maintenance of bacterial cultures
+ - Growth curves
+ - Inoculation of the co-culture
+ - Primer design
+ - gDNA extraction and qPCR
+ - Viability PCR
+ - Metaproteomic sample preparation
+ - LC-MS/MS analysis
+ - Data processing and functional annotation
+ - Modified agar diffusion test
+ - pH trajectories
+ - Acid perturbation
+ - Comparative genomics
+ - Bioinformatic investigation of siderophore receptors
+ - Statistical analysis
+ - ACKNOWLEDGMENTS
+ - Contributor Information
+ - DATA AVAILABILITY
+ - SUPPLEMENTAL MATERIAL
+ - msystems.00491-26-s0001.docx
+ - msystems.00491-26-s0002.xlsx
+ - msystems.00491-26-s0003.docx
+ - msystems.00491-26-s0004.xlsx
+ - msystems.00491-26-s0005.xlsx
+ - msystems.00491-26-s0006.docx
+ - msystems.00491-26-s0007.docx
+ - msystems.00491-26-s0008.docx
+ - msystems.00491-26-s0009.docx
+ - REFERENCES
+ - Associated Data
+ - Supplementary Materials
+ - msystems.00491-26-s0001.docx
+ - msystems.00491-26-s0002.xlsx
+ - msystems.00491-26-s0003.docx
+ - msystems.00491-26-s0004.xlsx
+ - msystems.00491-26-s0005.xlsx
+ - msystems.00491-26-s0006.docx
+ - msystems.00491-26-s0007.docx
+ - msystems.00491-26-s0008.docx
+ - msystems.00491-26-s0009.docx
+ - Data Availability Statement
+ unresolved_graph_structure: 'No current nodes/arrows. Source-backed candidate phenotypes and qualified mechanisms
+ await one-community research and curation under #1461; the discussion is not a completed graph.'
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 85445004b..c6ccebe33 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -170,9 +170,9 @@ kb/communities/Eucalyptus_Nursery_FiveStrain_Inoculant_SynCom.yaml CommunityMech
kb/communities/Euglena_Chlorella_Microalgal_Biorefinery_Coculture.yaml CommunityMech:000325 4d5cdc403a12e77b46efdff937eebb29fd0e3b71418a497ea69287ac0a8d0bfc 4 1 78.8 reports/causal_graph_review/decisions/20261006-three-records-batch38.yaml reviewed
kb/communities/Ewaste_Bioleaching_Consortium.yaml CommunityMech:000026 e55cc485b57d871ad1a431bd2de7ea20588cde4e61029b769e095b1380499965 3 3 90.0 reports/causal_graph_review/decisions/20261006-three-records-batch39.yaml reviewed
kb/communities/FOS_Lactobacillus_MinimalCore_GutLiver_SynCom.yaml CommunityMech:000466 0ca3ae19e967be3786f5495c5633b088efc2afd4dbe18c322eb2a3a6447d29ef 3 0 63.3 reports/causal_graph_review/decisions/20261006-three-records-batch39.yaml needs_research
-kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml CommunityMech:000027 f357e3ec553f3c8ff1448687f6bf1ab557d2aa72e9e011162ce4b583bdb9a7e7 4 2 100.0 pending
-kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml CommunityMech:000457 7626c8ddd2ae88e323ebf2ae6058a19ff70e0a17d647b7b5f941be91def3af78 2 0 67.5 pending
-kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml CommunityMech:000432 01531be768a6ce1f2a546d2ee5ee9ca8e134bcc08a77eb7d6cf47e3eafe0c29f 0 0 0.0 pending
+kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml CommunityMech:000027 08e60d74c495dfee5ec77a2a8ed63da4da51b1ebe1adb527350591d0e5b6340b 4 1 82.5 reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml reviewed
+kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml CommunityMech:000457 e23f7534b2c596261fdb8f6a69225c64ee0fcc4b10b95eb27bfccc7a48e2b0fe 2 0 62.5 reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml reviewed
+kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml CommunityMech:000432 e6123414e5fb18492837dd471cc7a12496821032306fdb6a6fba9b938e7908fb 0 0 0.0 reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml needs_research
kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml CommunityMech:000449 c6b8a0d748ce7750e0435947e3a0b781a6d2387bca3dc85dcafbdee7c2059737 2 0 60.0 pending
kb/communities/GENIA_NineMember_MultiPollutant_Bioremediation_SynCom.yaml CommunityMech:000352 1daada660d8dad257e3a5b04d861665bb03bd631c598322ebdea22ff452fac3f 3 2 98.3 pending
kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml CommunityMech:000091 f7791cb413836f0ac9e8b7624d661cad0a1e31ef5bee4d58b38b6b8506a62da9 3 0 75.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 62a1e1025..fc4271c67 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -3,13 +3,13 @@
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
"nodes": 1469,
- "edges": 688,
+ "edges": 687,
"records_without_nodes": 8,
"records_without_edges": 146,
"review_status_counts": {
- "needs_research": 9,
- "pending": 291,
- "reviewed": 160
+ "needs_research": 10,
+ "pending": 288,
+ "reviewed": 162
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261006-batch41.json b/reports/causal_graph_review/validation-20261006-batch41.json
new file mode 100644
index 000000000..14c7d5498
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch41.json
@@ -0,0 +1,805 @@
+{
+ "base_commit": "a09d6620fdcf4787f50b02f851c0b6e8c712c0f4",
+ "scope": [
+ "kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml",
+ "kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml",
+ "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Ferroplasma_Leptospirillum_Syntrophy-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Ferroplasma_Leptospirillum_Syntrophy-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Ferroplasma_Leptospirillum_Syntrophy-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch41/Ferroplasma_Leptospirillum_Syntrophy-strict.tsv",
+ "kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Ferroplasma_Leptospirillum_Syntrophy-strict.log",
+ "log_sha256": "372165fd064606e653a2bec5870bb2f983631a236fdff926609b392b80ac9b1f",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch41/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-batch41/Ferroplasma_Leptospirillum_Syntrophy-strict.tsv\n"
+ },
+ {
+ "check": "Ferroplasma_Leptospirillum_Syntrophy-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Ferroplasma_Leptospirillum_Syntrophy-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Ferroplasma_Leptospirillum_Syntrophy-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Ferroplasma_Leptospirillum_Syntrophy-references.log",
+ "log_sha256": "74503ffa847eb00611e59df0dd3889761fce9f43ec164defc8614b293f9623da",
+ "output_tail": "Validating kb/communities/Ferroplasma_Leptospirillum_Syntrophy.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/Ferroplasma_Leptospirillum_Syntrophy.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": "Ferroplasma_Leptospirillum_Syntrophy-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Ferroplasma_Leptospirillum_Syntrophy-snippets.log",
+ "log_sha256": "8084678f5cf248d78dd90bd74538a6320ef0dcc9940ae3e5b5f759e13588ade6",
+ "output_tail": "# 19 evidence snippets scanned across 1 files\n MATCH 19\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": "Ferroplasma_Leptospirillum_Syntrophy-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Ferroplasma_Leptospirillum_Syntrophy-rank.log",
+ "log_sha256": "12223c6075271a01192469f6545fe0bdcd026d6e8b70a88d2ed3c965be24c031",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000027\",\n \"name\": \"Ferroplasma-Leptospirillum Iron-Cycling Syntrophy\",\n \"score\": 82.5,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Ferroplasma_Leptospirillum_Syntrophy-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Ferroplasma_Leptospirillum_Syntrophy/2026-10-06T104340Z-codex-37b7f6.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Ferroplasma_Leptospirillum_Syntrophy-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Fomitopsis_Ecoli_Nutritional_Stress_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Fomitopsis_Ecoli_Nutritional_Stress_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Fomitopsis_Ecoli_Nutritional_Stress_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch41/Fomitopsis_Ecoli_Nutritional_Stress_Coculture-strict.tsv",
+ "kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Fomitopsis_Ecoli_Nutritional_Stress_Coculture-strict.log",
+ "log_sha256": "fe5917df37cf14a84930777a74bf165aa265019564b13fc80cecfd23b24eb48b",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch41/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-batch41/Fomitopsis_Ecoli_Nutritional_Stress_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Fomitopsis_Ecoli_Nutritional_Stress_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Fomitopsis_Ecoli_Nutritional_Stress_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Fomitopsis_Ecoli_Nutritional_Stress_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Fomitopsis_Ecoli_Nutritional_Stress_Coculture-references.log",
+ "log_sha256": "39f382bbae52a39b66ff6c0157d89f03718ce2de4b5a5ae2a499f2cdb3ca13b3",
+ "output_tail": "Validating kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_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/Fomitopsis_Ecoli_Nutritional_Stress_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": "Fomitopsis_Ecoli_Nutritional_Stress_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Fomitopsis_Ecoli_Nutritional_Stress_Coculture-snippets.log",
+ "log_sha256": "389f1d2b093a1648cf407d53853e429a283f80eed2628a1a14cf1f38649ca780",
+ "output_tail": "# 12 evidence snippets scanned across 1 files\n MATCH 12\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": "Fomitopsis_Ecoli_Nutritional_Stress_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Fomitopsis_Ecoli_Nutritional_Stress_Coculture-rank.log",
+ "log_sha256": "6f43d6ce5af9120c8a2abd153fcc1f8162b3924787f466550d599d71b234ddcf",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000457\",\n \"name\": \"Fomitopsis-E. coli Nutritional-Stress Coculture\",\n \"score\": 62.5,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Fomitopsis_Ecoli_Nutritional_Stress_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/Fomitopsis_Ecoli_Nutritional_Stress_Coculture/2026-10-06T104341Z-codex-a2b56f.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/Fomitopsis_Ecoli_Nutritional_Stress_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "FourSpecies_Aerobic_Lung_Microbiome_Model-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/FourSpecies_Aerobic_Lung_Microbiome_Model-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "FourSpecies_Aerobic_Lung_Microbiome_Model-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch41/FourSpecies_Aerobic_Lung_Microbiome_Model-strict.tsv",
+ "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/FourSpecies_Aerobic_Lung_Microbiome_Model-strict.log",
+ "log_sha256": "0de55742846319a21e02b459b87218884ce713265f06cba520f24c74a301d377",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch41/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-batch41/FourSpecies_Aerobic_Lung_Microbiome_Model-strict.tsv\n"
+ },
+ {
+ "check": "FourSpecies_Aerobic_Lung_Microbiome_Model-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/FourSpecies_Aerobic_Lung_Microbiome_Model-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "FourSpecies_Aerobic_Lung_Microbiome_Model-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/FourSpecies_Aerobic_Lung_Microbiome_Model-references.log",
+ "log_sha256": "753eebc1b771a32c11a7829b1657e0e88d32f43ae34df0914527038d116d01f7",
+ "output_tail": "Validating kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.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/FourSpecies_Aerobic_Lung_Microbiome_Model.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": "FourSpecies_Aerobic_Lung_Microbiome_Model-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/FourSpecies_Aerobic_Lung_Microbiome_Model-snippets.log",
+ "log_sha256": "aec1f2712a64b5cd549f668dd69d5e1ab54d6d5693d8f53bbce26317b755b383",
+ "output_tail": "# 11 evidence snippets scanned across 1 files\n MATCH 11\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": "FourSpecies_Aerobic_Lung_Microbiome_Model-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/FourSpecies_Aerobic_Lung_Microbiome_Model-rank.log",
+ "log_sha256": "bca5d28f5febaba6030c12c381ecffadb09a3bbeb638cc6562a069f8150e8402",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000432\",\n \"name\": \"Four-Species Aerobic Lung Microbiome Model\",\n \"score\": 0.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 0,\n \"disconnected_taxa\": 4,\n \"ecological_interactions\": 0,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 0,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"ecological_interactions\"\n ],\n \"path\": \"kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "FourSpecies_Aerobic_Lung_Microbiome_Model-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/FourSpecies_Aerobic_Lung_Microbiome_Model/2026-10-06T104341Z-codex-319aac.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/FourSpecies_Aerobic_Lung_Microbiome_Model-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-batch41/inventory.log",
+ "log_sha256": "48d805df3d27bef0f3383afd0038784e432473b34be3dd7df89d483bb9371c8e",
+ "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\": 1469,\n \"edges\": 687,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 146,\n \"review_status_counts\": {\n \"needs_research\": 10,\n \"pending\": 288,\n \"reviewed\": 162\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-batch41/network.log",
+ "log_sha256": "c035fe6ed0bbf90371ab58d6557716c51eea79ac628e204173d70075f9efaa26",
+ "output_tail": "{\n \"preferred_term\": \"Legionella MAGs\",\n \"term\": {\n \"id\": \"NCBITaxon:445\",\n \"label\": \"Legionella\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n },\n \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n \"evidence\": [\n {\n \"reference\": \"PMID:41457319\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"COMPUTATIONAL\",\n \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n }\n ]\n },\n \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
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+ "command": [
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SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "communitymech.render"
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+ "log_sha256": "9bdbf9a1bdd77788aadae5b0b0db801255f088c58054486e86ebadfd52578fcc",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 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Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch41/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch41/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch41/docs/index.html\n"
+ },
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+ "log": "/private/tmp/communitymech-batch41/render-repeat.log",
+ "log_sha256": "9bdbf9a1bdd77788aadae5b0b0db801255f088c58054486e86ebadfd52578fcc",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch41/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch41/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch41/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch41/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path(\"tests/test_community_level_connectivity_credit.py\")[\"_survey\"](),sort_keys=True))"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/connectivity-survey.log",
+ "log_sha256": "fb47676e0ec6945737e5aeeba11192e7b8ff073a9e93ce8809972a4316c7c565",
+ "output_tail": "{\"community_level_only\": 263, \"credited_solely_by_the_rule\": 1219, \"mixed\": 124, \"records\": 460, \"taxa\": 1494, \"with_community_level\": 387}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/regressions.log",
+ "log_sha256": "97b1daa298c21ec5a8bb5dcc9ded2c3be34ba52f5595c4b71cde108d93d9687f",
+ "output_tail": "........................................................................ [ 16%]\n........................................................................ [ 33%]\n........................................................................ [ 50%]\n........................................................................ [ 66%]\n........................................................................ [ 83%]\n....................................................................... [100%]\n431 passed in 170.84s (0:02:50)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch41.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/black.log",
+ "log_sha256": "1a56c7cd8457fd05d978cfbd139d7bfd86e86acaa9b57668e718ef8bccc0cf48",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n1 file would be left unchanged.\n"
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch41.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch41/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Ferroplasma cited abstracts only; full primary body, figure images and supplements not reviewed.",
+ "Fomitopsis selected preprint excerpts only. Full PDF returned HTTP 429; no bypass. Missing selective interventions are not claimed absent from the entire paper.",
+ "Lung public main body, tables and captions read; no figure images, equation rendering, separate supplements or raw data. Its zero-node graph remains needs_research, not complete.",
+ "All six existing nodes retained, one arrow retained and one removed. No new structure or provider spend. Five node renames and corresponding targets updated.",
+ "Canonical taxonomy, prior history, original source caches and non-graph raw blocks preserved, not certified. Non-graph followups #1462/#1463 remain open.",
+ "Self-adversarial review is not independent approval, protected merge or full-corpus completion. Snippet matching is textual, not scientific validation.",
+ "Reference validator 0.1.7 performs zero checks for this schema; disclose the no-op.",
+ "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate.",
+ "All three reference-validator commands exit 0 with Total checks: 0. This is a no-op, not evidence validation. Independent snippet matching and primary-source review are separate."
+ ],
+ "snippet_counts_by_record": {
+ "kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml": {
+ "MATCH": 19,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml": {
+ "MATCH": 12,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml": {
+ "MATCH": 11,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 39,
+ "unchanged_record_files": 457,
+ "unchanged_cache_files": 920,
+ "network_delta": {
+ "existing_findings_preserved": 33,
+ "new_disconnected": 0,
+ "added_findings": {},
+ "rationale": "All baseline warnings exactly preserved; no invented graph links to suppress warnings."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1455,
+ "arrows": 679
+ },
+ "participant_census": {
+ "connectivity_before": {
+ "community_level_only": 263,
+ "credited_solely_by_the_rule": 1219,
+ "mixed": 124,
+ "records": 460,
+ "taxa": 1494,
+ "with_community_level": 387
+ },
+ "connectivity_after": {
+ "community_level_only": 263,
+ "credited_solely_by_the_rule": 1219,
+ "mixed": 124,
+ "records": 460,
+ "taxa": 1494,
+ "with_community_level": 387
+ },
+ "exact_change": "No registry or numeric-bound changes; 187 registered records. Ferroplasma already registered, Fomitopsis remains pairwise and lung has no graph. Canonical taxonomy preserved.",
+ "numeric_bounds_changed": false
+ },
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1469,
+ "edges": 687,
+ "records_without_nodes": 8,
+ "records_without_edges": 146,
+ "review_status_counts": {
+ "needs_research": 10,
+ "pending": 288,
+ "reviewed": 162
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml": "4f0a70fa0459dfeeb6c9871c54f2440b9067a4ee5037d80808c4c4be7a07dda6",
+ "tests/test_causal_review_batch41.py": "a3c82a3f9d08b650d708ddc8217c1a6842e06f61f154b9511a2e0ea02503306f",
+ "kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml": "08e60d74c495dfee5ec77a2a8ed63da4da51b1ebe1adb527350591d0e5b6340b",
+ "kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml": "e23f7534b2c596261fdb8f6a69225c64ee0fcc4b10b95eb27bfccc7a48e2b0fe",
+ "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml": "e6123414e5fb18492837dd471cc7a12496821032306fdb6a6fba9b938e7908fb"
+ },
+ "status": "verified_two_completed_reviews_and_one_research_pending_gap",
+ "reference_validator_effective_checks": 0,
+ "reference_validator_caveat": "All three reference-validator commands exit 0 with Total checks: 0. This is a no-op, not evidence validation. Independent snippet matching and primary-source review are separate.",
+ "pre_research_baseline": {
+ "base_commit": "8e610ca6652c7906952a7c031a81f31669b8ce26",
+ "base_tree": "7eb3104eab79453a36cfe9fcf4f97fcb39463df4",
+ "research_worktree": "/private/tmp/communitymech-causal-batch40",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch41/baseline-rank.log",
+ "sha256": "c5f1ec88361e4cbf9b56af5f2e1bce6e6033f9192248ed8078601d50b07b1358",
+ "output_tail": "nol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch41/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch41/baseline-network.log",
+ "sha256": "c035fe6ed0bbf90371ab58d6557716c51eea79ac628e204173d70075f9efaa26",
+ "output_tail": " 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"
+ },
+ {
+ "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-batch41/baseline-downstream.log",
+ "sha256": "87cf474d8a4834c03a7e25e2f3bf977b814bdd7020a05cff98836f39471dcb6a",
+ "output_tail": "stream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:339: downstream:\nkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml:150: downstream:\nkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml:181: downstream:\nkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml:215: downstream:\nkb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml:100: downstream:\nkb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml:139: downstream:\nkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:223: downstream:\nkb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml:159: downstream:\nkb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml:200: downstream:\nkb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:285: downstream:\nkb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:324: downstream:\nkb/communities/PMI_Variovorax_Thermotolerance_Collection.yaml:330: downstream:\nkb/communities/GOM_Oil_Degrading_Consortium.yaml:119: downstream:\nkb/communities/GOM_Oil_Degrading_Consortium.yaml:160: downstream:\nkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml:247: downstream:\nkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml:344: downstream:\nkb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml:153: downstream:\nkb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml:200: downstream:\nkb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml:142: downstream:\nkb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml:189: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:138: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:182: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:232: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:268: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:315: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:199: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:267: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:65: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:98: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:131: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:155: downstream:\nkb/communities/Synechococcus_Bacillus_SPC.yaml:120: downstream:\nkb/communities/Synechococcus_Bacillus_SPC.yaml:152: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:157: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:203: downstream:\nkb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml:336: downstream:\n"
+ }
+ ]
+ },
+ "baseline_ancestry_change": {
+ "reason": "Batch17 protected merge followed by whole-tree and own-patch identical restacking of batch40. Pre-paper baseline remains at its original commit, not falsely relabeled.",
+ "old_head": "8e610ca6652c7906952a7c031a81f31669b8ce26",
+ "new_head": "a09d6620fdcf4787f50b02f851c0b6e8c712c0f4",
+ "tree": "7eb3104eab79453a36cfe9fcf4f97fcb39463df4",
+ "own_patch_sha256": "904b08cf9b6f51a9316c58f9e0646828b48be52e1e3e1500022e79a245b50433"
+ },
+ "preflight_correction": "Initial mutator dry run raised KeyError: ecological_interactions on the intentionally empty lung record before any repository writes. The batch helper was corrected to return empty edge lists for an absent block. Repeated dry run passed, then guarded writes completed. No initial success is claimed.",
+ "edison_dryrun": {
+ "status": "dry_run_only_awaiting_specific_lung_job_authorization",
+ "provider_job_submitted": false,
+ "provider_credits_spent": false,
+ "community": "CommunityMech:000432",
+ "query_chars": 7671,
+ "query_sha256": "89ec04708989286f0f04e4f2a5da3ea60e8fc9a949144e75f46b2d590d3b2a3b",
+ "dryrun_meta_sha256": "fdfa04bacd6346433e07158347117cbe684dd31abc35373dd0c772a817f1c97b",
+ "dryrun_meta": {
+ "slug": "FourSpecies_Aerobic_Lung_Microbiome_Model",
+ "community_path": "kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml",
+ "community_id": "CommunityMech:000432",
+ "job": "LITERATURE",
+ "job_id": "job-futurehouse-paperqa3",
+ "label": "causal",
+ "template_path": "templates/community_causal_graph_research.md",
+ "template_vars": {
+ "community_name": "Four-Species Aerobic Lung Microbiome Model",
+ "community_id": "CommunityMech:000432",
+ "community_file": "FourSpecies_Aerobic_Lung_Microbiome_Model.yaml",
+ "community_slug": "FourSpecies_Aerobic_Lung_Microbiome_Model",
+ "community_category": "OTHER",
+ "ecological_state": "ENGINEERED",
+ "community_origin": "SYNTHETIC",
+ "description": "A simplified artificial lung microbiome model assembled as an aerobic four-species co-culture of Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei. The model was maintained for 10 days at 34\u00b0C in brain heart infusion medium and validated with qPCR, viability PCR, conventional microbiology, and metaproteomics to provide a controlled platform for lung microbiome interaction and pulmonary-drug studies.",
+ "source_summary": "",
+ "environment_summary": "laboratory environment | ENVO:01001405 | The curated entity is an in vitro aerobic BHI co-culture constructed to model the human lung microbiome, rather than a sampled airway community.",
+ "taxonomy_summary": "Pseudomonas koreensis | Rothia aeria | Neisseria cinerea | Streptococcus downei",
+ "interaction_summary": "",
+ "environmental_factor_summary": "Incubation temperature - 34 - The four-species BHI co-culture was incubated at 34\u00b0C during 10-day stability testing.",
+ "growth_media_summary": "Brain heart infusion medium - P. koreensis, R. aeria, N. cinerea, and S. downei were co-cultured in brain heart infusion medium as a simplified artificial lung microbiome model.",
+ "dataset_summary": "DOI - Four-species aerobic lung microbiome model - doi:10.1128/msystems.00491-26 - https://doi.org/10.1128/msystems.00491-26 | PubMed - Four-species aerobic lung microbiome model - PMID:42545019 - https://pubmed.ncbi.nlm.nih.gov/42545019/",
+ "evidence_summary": "PMID:42545019: we developed a simplified artificial lung microbiome model composed of four representative bacterial species (Supports the source's objective of making a simplified artificial lung microbiome model.) | PMID:42545019: We successfully established a stable 10-day co-culture at 34\u00b0C using brain heart infusion medium (Supports the 10-day BHI co-culture implementation and incubation temperature.) | PMID:42545019: Integrated bioinformatic analyses revealed a variety of potential microbe-microbe interactions, which were supported by metaproteomic analysis using mass spectrometry. (Supports metaproteomics as an interaction-supporting endpoint while not asserting individual pairwise edges.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Pseudomonas koreensis as a species in the four-member artificial lung microbiome model.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Rothia aeria as a species in the four-member artificial lung microbiome model.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Neisseria cinerea as a species in the four-member artificial lung microbiome model.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Streptococcus downei as a species in the four-member artificial lung microbiome model.) | PMID:42545019: stable 10-day co-culture at 34\u00b0C using brain heart infusion medium (Supports the 34\u00b0C incubation temperature.) | PMID:42545019: We successfully established a stable 10-day co-culture at 34\u00b0C using brain heart infusion medium (Names BHI medium and the 10-day, 34\u00b0C co-culture condition.) | PMID:42545019: DOI: 10.1128/msystems.00491-26 (Supports the DOI identifier for the mSystems article reporting the four-species aerobic lung microbiome model.) | PMID:42545019: Establishment of an in vitro aerobic bacterial community as a model of the human lung microbiome (Links the PubMed record to the curated lung microbiome model study.)"
+ },
+ "query_chars": 7671,
+ "query": "# Microbial Community Causal-Graph Research Template\n\n## Target Community\n- **Community name:** Four-Species Aerobic Lung Microbiome Model\n- **Community id:** CommunityMech:000432\n- **Community file:** FourSpecies_Aerobic_Lung_Microbiome_Model.yaml\n- **Community category:** OTHER\n- **Ecological state:** ENGINEERED\n- **Community origin:** SYNTHETIC\n- **Environment:** laboratory environment | ENVO:01001405 | The curated entity is an in vitro aerobic BHI co-culture constructed to model the human lung microbiome, rather than a sampled airway community.\n- **Description:** A simplified artificial lung microbiome model assembled as an aerobic four-species co-culture of Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei. The model was maintained for 10 days at 34\u00b0C in brain heart infusion medium and validated with qPCR, viability PCR, conventional microbiology, and metaproteomics to provide a controlled platform for lung microbiome interaction and pulmonary-drug studies.\n\n## Existing Record Context\n- **Taxa:** Pseudomonas koreensis | Rothia aeria | Neisseria cinerea | Streptococcus downei\n- **Known ecological interactions:** \n- **Environmental factors:** Incubation temperature - 34 - The four-species BHI co-culture was incubated at 34\u00b0C during 10-day stability testing.\n- **Growth media / culture conditions:** Brain heart infusion medium - P. koreensis, R. aeria, N. cinerea, and S. downei were co-cultured in brain heart infusion medium as a simplified artificial lung microbiome model.\n- **Associated datasets / resources:** DOI - Four-species aerobic lung microbiome model - doi:10.1128/msystems.00491-26 - https://doi.org/10.1128/msystems.00491-26 | PubMed - Four-species aerobic lung microbiome model - PMID:42545019 - https://pubmed.ncbi.nlm.nih.gov/42545019/\n- **Existing evidence:** PMID:42545019: we developed a simplified artificial lung microbiome model composed of four representative bacterial species (Supports the source's objective of making a simplified artificial lung microbiome model.) | PMID:42545019: We successfully established a stable 10-day co-culture at 34\u00b0C using brain heart infusion medium (Supports the 10-day BHI co-culture implementation and incubation temperature.) | PMID:42545019: Integrated bioinformatic analyses revealed a variety of potential microbe-microbe interactions, which were supported by metaproteomic analysis using mass spectrometry. (Supports metaproteomics as an interaction-supporting endpoint while not asserting individual pairwise edges.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Pseudomonas koreensis as a species in the four-member artificial lung microbiome model.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Rothia aeria as a species in the four-member artificial lung microbiome model.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Neisseria cinerea as a species in the four-member artificial lung microbiome model.) | PMID:42545019: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei (Names Streptococcus downei as a species in the four-member artificial lung microbiome model.) | PMID:42545019: stable 10-day co-culture at 34\u00b0C using brain heart infusion medium (Supports the 34\u00b0C incubation temperature.) | PMID:42545019: We successfully established a stable 10-day co-culture at 34\u00b0C using brain heart infusion medium (Names BHI medium and the 10-day, 34\u00b0C co-culture condition.) | PMID:42545019: DOI: 10.1128/msystems.00491-26 (Supports the DOI identifier for the mSystems article reporting the four-species aerobic lung microbiome model.) | PMID:42545019: Establishment of an in vitro aerobic bacterial community as a model of the human lung microbiome (Links the PubMed record to the curated lung microbiome model study.)\n\n## Research Objective\n\nBuild a source-backed **causal interaction graph** for the microbial community\n**Four-Species Aerobic Lung Microbiome Model**, suitable for the `ecological_interactions` block of\n`kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml`. The graph's **nodes are mechanistic\ninteractions** and its **directed edges are causal links** (\"interaction A\nenables / drives / suppresses interaction B\"). Extract only relationships the\nprimary literature supports; do not infer edges that are not stated or directly\nimplied by an experiment.\n\n## Required Findings\n\n### 1. Interaction nodes (the vertices)\n\nFor each mechanistic interaction, report as a table row:\n\n- **name** \u2014 a short, unique interaction name (used as the node id and as the\n `target` of any causal edge that points to it).\n- **interaction_type** \u2014 one of: MUTUALISM, COMMENSALISM, CROSS_FEEDING,\n COMPETITION, PREDATION, SYNTROPHY, NICHE_PARTITIONING, STRAIN_COMPETITION,\n COLONIZATION_FACILITATION (or state \"OTHER: \" if none fit).\n- **scope** \u2014 PAIRWISE (organism\u2192organism) or COMMUNITY_LEVEL (emergent /\n abiotically driven, e.g. electrolysis-supplied H2). PAIRWISE **must** name a\n source taxon.\n- **source_taxon \u2192 target_taxon** \u2014 the directed pair (who acts on whom). Give\n NCBITaxon CURIEs + labels where resolvable.\n- **metabolites / biological_processes** \u2014 the exchanged compound(s) (CHEBI) and\n process(es) (GO) that mediate the interaction.\n- **direction / sign** \u2014 does the source **increase (+)** or **decrease (\u2212)** the\n target's growth/activity? State it explicitly.\n- **evidence** \u2014 a short **verbatim** snippet + its reference (PMID/DOI).\n\n### 2. Causal edges (the arcs)\n\nThis is the graph structure. For every ordered pair of nodes where the\nliterature supports a causal link, report a row:\n\n- **from** \u2014 upstream interaction name (a node from \u00a71).\n- **to** \u2014 downstream interaction name (a node from \u00a71).\n- **causal link** \u2014 one sentence: *how* the upstream interaction causes /\n enables / is required for / suppresses the downstream one (e.g. \"H2 produced\n by the syntrophic oxidation lowers pH2 enough for the acetogen to grow, which\n in turn supplies acetate to the methanogen\").\n- **evidence** \u2014 verbatim snippet + reference for the causal claim specifically\n (not just for the two endpoints existing).\n\nPrefer chains that a paper demonstrates by perturbation (knockout, substrate\nremoval, inhibitor, co-culture vs mono-culture), and say which experiment shows\neach edge. Flag any edge that is hypothesized rather than demonstrated.\n\n### 3. Grounding\n\n- CURIEs where available: NCBITaxon (taxa), CHEBI (metabolites), GO (processes),\n ENVO (environment), PMID / DOI (evidence).\n- Do not invent taxa, ontology ids, snippets, accession ids, or citations. If a\n node or edge lacks a citable source, omit it or mark it UNVERIFIED.\n\n## Output Format\n\nReturn a curation-focused report with:\n\n1. **Scope summary** \u2014 the consortium and the top-level function the causal graph\n explains (1\u20133 sentences).\n2. **Node table** \u2014 the interaction nodes (\u00a71 columns).\n3. **Edge table** \u2014 the directed causal edges (\u00a72 columns: from, to, causal\n link, evidence).\n4. **Adjacency / DOT sketch** \u2014 a compact `from -> to` edge list (or Graphviz DOT\n snippet) so the graph can be eyeballed; annotate edges with + / \u2212 sign.\n5. **Gaps & controversies** \u2014 edges the literature disputes, or plausible edges\n with no direct evidence (candidates for a `Discussion`/knowledge-gap note).\n6. **References** \u2014 every PMID/DOI cited, once.\n\nEach biological claim (node and edge) must carry a verbatim snippet and a\nreference. This report is reviewed by a curator before anything is written to\n`kb/communities/`.\n",
+ "submitted_at": "2026-10-06T10:38:06.050699+00:00",
+ "status": "dry-run",
+ "query_sha256": "89ec04708989286f0f04e4f2a5da3ea60e8fc9a949144e75f46b2d590d3b2a3b"
+ },
+ "limitations": "SDK emitted a remote cost-map fetch warning and used its local fallback; no provider job was submitted and no price estimate was supplied. Other record repairs require no new structure."
+ }
+}
diff --git a/tests/test_causal_review_batch41.py b/tests/test_causal_review_batch41.py
new file mode 100644
index 000000000..132ab4642
--- /dev/null
+++ b/tests/test_causal_review_batch41.py
@@ -0,0 +1,157 @@
+"""Keep hypothesis strength, assay scope and research completeness explicit."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ return ledger, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in ledger["records"]]
+
+
+def test_ferroplasma_retains_hypothesis_not_demonstrated_detoxification():
+ _, docs = records()
+ supply, consumption, _, response = docs[0]["ecological_interactions"]
+ for node in [supply, consumption]:
+ assert node["description"].startswith("HYPOTHESIZED:")
+ assert node["evidence"][0]["supports"] == "PARTIAL"
+ assert node["evidence"][0]["snippet"].startswith("The hypothesis of this work")
+ assert supply["downstream"][0]["target"] == consumption["name"]
+ assert supply["downstream"][0]["description"].startswith("HYPOTHESIZED:")
+ assert "downstream" not in consumption
+ assert "not independent measurement" in response["description"]
+ assert "interaction_type" not in response and "metabolites" not in response
+
+
+def test_ferroplasma_intrinsic_context_has_no_false_niche_or_transport():
+ _, docs = records()
+ supply, consumption, iron, _ = docs[0]["ecological_interactions"]
+ for node in [supply, iron]:
+ assert node["scope"] == "PAIRWISE"
+ assert "source_taxon" in node
+ assert all(
+ key not in node
+ for key in [
+ "target_taxon",
+ "participating_taxa",
+ "interaction_type",
+ "biological_processes",
+ ]
+ )
+ assert "Y(T)" in iron["description"] and "not BRL-115" in iron["description"]
+ assert "slower electron transfer" in iron["description"]
+ assert "do not establish lower-oxygen complementarity" in iron["description"]
+ assert [t["term"]["id"] for t in consumption["metabolites"]] == ["CHEBI:50860"]
+
+
+def test_fomitopsis_liquid_observation_is_not_selective_mediation():
+ _, docs = records()
+ liquid = docs[1]["ecological_interactions"][0]
+ assert "Associated" in liquid["name"]
+ assert liquid["description"].startswith("PARTIAL:")
+ assert liquid["interaction_type"] == "COMPETITION"
+ assert "34 mg (reported as 44% lower)" in liquid["description"]
+ assert "do not describe selective glucose rescue" in liquid["description"]
+ assert "not production or identification" in liquid["description"]
+ assert "Endpoint bacterial counts were not reduced" in liquid["description"]
+ assert all("downstream" not in n for n in docs[1]["ecological_interactions"])
+
+
+def test_fomitopsis_agar_identity_and_acid_mediation_remain_qualified():
+ _, docs = records()
+ agar = docs[1]["ecological_interactions"][1]
+ assert "interaction_type" not in agar
+ assert "putatively identified" in agar["description"]
+ assert "HYPOTHESIZED:" in agar["description"]
+ assert "not shown to be universally absent" in agar["description"]
+ assert "distinct from liquid-culture stress" in agar["description"]
+ assert agar["evidence"][-1]["supports"] == "PARTIAL"
+ assert (
+ "not a claim of universal experimental absence" in docs[1]["discussions"][-1]["rationale"]
+ )
+
+
+def test_lung_missing_graph_is_not_certified_complete():
+ ledger, docs = records()
+ row = ledger["records"][2]
+ assert row["status"] == "needs_research"
+ assert "ecological_interactions" not in docs[2]
+ assert row["node_decisions"] == row["edges_after"] == []
+ assert ledger["open_graph_research"] == [1461]
+ assert len(docs[2]["taxonomy"]) == 4
+ gap = docs[2]["discussions"][-1]
+ assert gap["kind"] == "KNOWLEDGE_GAP" and gap["status"] == "OPEN"
+ assert "attaches_to" not in gap
+ for boundary in [
+ "total CFU does not resolve member-specific compositional resilience",
+ "hypothesis-qualified treatment",
+ "not physiological healthy-airway conditions",
+ "Challenge organisms are not members",
+ ]:
+ assert boundary in gap["rationale"]
+
+
+def test_batch41_edison_dryrun_and_source_limits_are_auditable():
+ ledger, _ = records()
+ edison = ledger["edison"]
+ assert edison["community"] == "CommunityMech:000432"
+ assert edison["provider_job_submitted"] is edison["provider_credits_spent"] is False
+ meta = edison["dryrun_meta"]
+ assert meta["status"] == "dry-run" and meta["query_chars"] == 7671
+ assert hashlib.sha256(meta["query"].encode()).hexdigest() == edison["query_sha256"]
+ ferro, fomitopsis, lung = [r["source_review"] for r in ledger["records"]]
+ assert "abstract" in ferro["PMID:27535541"]["scope"]
+ assert "HTTP 429" in next(iter(fomitopsis.values()))["scope"]
+ assert "preprint" in next(iter(fomitopsis.values()))["scope"]
+ primary = lung["PMID:42545019"]
+ assert (
+ primary["receipt"]["source_sha256"]
+ == "d26528baa780d0c4344ae24938862ad9d52a0d6143e490e9bcd10f9b03d73c5d"
+ )
+ assert "No figure images" in primary["scope"]
+ for path, expected in ledger["reference_cache_original_hashes"].items():
+ assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == expected
+
+
+def test_batch41_dispositions_participants_and_append_only_history():
+ ledger, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1459, 1460]
+ assert ledger["open_nongraph_followups"] == [1462, 1463]
+ assert sum(len(r["node_decisions"]) for r in ledger["records"]) == 6
+ assert sum(len(r["retained_edge_decisions"]) for r in ledger["records"]) == 1
+ assert sum(len(r["removed_edge_decisions"]) for r in ledger["records"]) == 1
+ assert sum(len(r["renamed_nodes"]) for r in ledger["records"]) == 5
+ for row, doc in zip(ledger["records"], docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert len(row["history_files"]) == 1 and (ROOT / row["history_files"][0]).is_file()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ canonical = {t["taxon_term"]["term"]["id"]: t["taxon_term"] for t in doc["taxonomy"]}
+ names = {n["name"] for n in doc.get("ecological_interactions", [])}
+ for node in doc.get("ecological_interactions", []):
+ participants = node.get("participating_taxa", [])
+ participants += [node[k] for k in ["source_taxon", "target_taxon"] if k in node]
+ for term in participants:
+ assert term["term"] == canonical[term["term"]["id"]]["term"]
+ assert all(
+ e["target"] in names and e["target"] != node["name"]
+ for e in node.get("downstream", [])
+ )
+ assert all(
+ a.split("#", 1)[1] in names for a in doc["discussions"][-1].get("attaches_to", [])
+ )
+
+
+def test_batch41_preserves_pre_paper_baseline_across_ancestry_change():
+ ledger, _ = records()
+ ancestry = ledger["baseline_ancestry_change"]
+ assert ledger["baseline_commit"] == ancestry["old_head"]
+ assert ledger["base_commit"] == ancestry["new_head"]
+ assert ledger["base_commit"] != ledger["baseline_commit"]
+ assert ledger["base_tree"] == ancestry["tree"]
+ assert ledger["issue_deduplication"]["ignored_hidden_local_search"] is True