Veillonella parvula is not independently cariogenic in the model but significantly worsens disease progression when coinfected with Streptococcus mutans.
The dual-species rodent group had greater caries progression and severity than single-species groups, while V. parvula alone did not differ significantly from the control. This is a rodent community-associated disease outcome. The separate adult plaque association does not establish the same causal effect in human adult severe caries.
+ Streptococcus mutans,
+
+ Veillonella parvula
+
+
@@ -783,6 +775,45 @@
(function() {
var intId = "interaction:0";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -967,11 +998,11 @@
processes.push("biofilm formation");
- var evidenceCount = 3;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Veillonella parvula Boost of Streptococcus mutans Glucosyltransferase-EPS Output",
+ label: "Veillonella-Associated gtf Expression and Mixed-Biofilm EPS",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -996,7 +1027,7 @@
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1009,7 +1040,7 @@
nodes.push({
id: intId,
- label: "Veillonella parvula Promotion of Streptococcus mutans Biofilm Virulence",
+ label: "Mixed-Biofilm and Stress-Response Phenotypes",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1018,23 +1049,26 @@
});
- var srcKey = "Veillonella parvula";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Streptococcus mutans";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Streptococcus mutans",
+
+ "Veillonella parvula"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1047,7 +1081,7 @@
nodes.push({
id: intId,
- label: "Pathobiont-Driven Adult Severe Caries Exacerbation",
+ label: "Rodent Coinfection Caries Outcome",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1056,17 +1090,20 @@
});
- var srcKey = "Veillonella parvula";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Streptococcus mutans";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Streptococcus mutans",
+
+ "Veillonella parvula"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/docs/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.html b/docs/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.html
index 3dbe924c9..54a2d3efe 100644
--- a/docs/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.html
+++ b/docs/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.html
@@ -554,17 +554,12 @@
-
-
Ecological Interactions
-
Bacillus subtilis BS3 converts residual ethanol in brewing wastewater to acetate via heterologous alcohol dehydrogenase and aldehyde dehydrogenase, removing an inhibitor of S. oneidensis extracellular electron transfer.
+
Bacillus subtilis BS3 converts residual ethanol in brewing wastewater to acetate via heterologous alcohol dehydrogenase and aldehyde dehydrogenase, removing an inhibitor of S. oneidensis extracellular electron transfer. This supports facilitation of SO3 electron transfer, but does not establish that BS3 is unaffected by SO3 as required for COMMENSALISM.
Source Taxon: Bacillus subtilis 168 BS3
@@ -611,7 +605,7 @@
BS3 ethanol detoxification of brewing wastewater
→ MtrC/OmcA and riboflavin NCM reduction
-
Removing ethanol relieves inhibition of the S. oneidensis EET machinery that reduces NCM for metal oxide leaching.
+
Ethanol removal relieves inhibition of Shewanella electron transfer and thereby supports NCM leaching in the authors' consortium model. The detoxification comparisons were conducted in predecessor strains; the final SO3-BS3 synthesis retains this function, without separately isolating its quantitative contribution from the other modifications.
Evidence
- Shewanella oneidensis SO3 catabolizes lactate from brewing wastewater and transfers electrons to NCM black mass either directly through outer-membrane cytochromes MtrC/OmcA or indirectly through riboflavin, reducing NCM metal oxides and releasing Li, Ni, Co, and Mn into solution.
+ Shewanella oneidensis SO3 catabolizes lactate from brewing wastewater and transfers electrons to NCM black mass either directly through outer-membrane cytochromes MtrC/OmcA or indirectly through riboflavin, reducing NCM metal oxides and releasing Li, Ni, Co, and Mn into solution. Final-consortium cytochrome perturbations and the reduced-riboflavin assay support the EET interpretation. The proposed direct and shuttle routes are not a quantitative partition of in-consortium electron flux.
@@ -716,6 +710,19 @@ Evidence
+
+
+
+ "confirming that the disruption of MtrC and OmcA significantly inhibited the EET process in strain SO3."
+
+
+
@@ -726,7 +733,7 @@
Evidence
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -763,6 +770,41 @@
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ What is the reciprocal fitness effect and relative contribution of the retained processes?
+
+
Primary predecessor comparisons support ethanol removal, electron-transfer improvement and leaching. Final-consortium perturbations and riboflavin evidence support the retained reduction node. Neither benefit to SO3 nor greater leaching establishes neutral fitness of BS3 in the exact pair, so the optional COMMENSALISM type is removed without denying the supported facilitation. Direct-versus-shuttle flux and the isolated contribution of detoxification in the final consortium are not quantified by the cited comparisons. The existing scale-up discussion remains unchanged.
+
+
Attaches to: ecological_interactions#BS3 ethanol detoxification of brewing wastewater, ecological_interactions#MtrC/OmcA and riboflavin NCM reduction
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
confirming that the ethanol inhibition of the EET of the SO1‐BS1 consortium was significantly alleviated
+
Identifies the predecessor consortium used for the detoxification comparison.
+
+
+
+
@@ -1183,7 +1225,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "COMMENSALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1240,7 +1282,7 @@
Evidence
var processes = [];
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
diff --git a/history/records/SMutans_CAlbicans_ECC_Biofilm/2026-10-07T184553Z-codex-1564ae.yaml b/history/records/SMutans_CAlbicans_ECC_Biofilm/2026-10-07T184553Z-codex-1564ae.yaml
new file mode 100644
index 000000000..f1775a13f
--- /dev/null
+++ b/history/records/SMutans_CAlbicans_ECC_Biofilm/2026-10-07T184553Z-codex-1564ae.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml
+ slug: SMutans_CAlbicans_ECC_Biofilm
+session:
+ id: 2026-10-07T184553Z-codex-1564ae
+ timestamp: '2026-10-07T18:45:53Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1772
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain supported mutualism and a PARTIAL rodent-outcome direction.; Retain positive
+ Candida-to-S. mutans biofilm facilitation with the correct in-vitro source.; Retain the
+ positive rodent carriage/lesion outcome at community scope, not pairwise colonization.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
diff --git a/history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T184554Z-codex-0f7a08.yaml b/history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T184554Z-codex-0f7a08.yaml
new file mode 100644
index 000000000..af20b1ff2
--- /dev/null
+++ b/history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T184554Z-codex-0f7a08.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml
+ slug: SMutans_SSputigena_ECC_Pathobiont
+session:
+ id: 2026-10-07T184554Z-codex-0f7a08
+ timestamp: '2026-10-07T18:45:54Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1773
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain supported directional colonization facilitation and the existing structural
+ link, correcting modality.; Retain community structure and acidogenesis, with positive
+ perturbation evidence and PARTIAL in-vivo mediation.; Retain the rodent disease comparison
+ at two-member community scope.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
diff --git a/history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T185016Z-codex-9c291b.yaml b/history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T185016Z-codex-9c291b.yaml
new file mode 100644
index 000000000..73eda9355
--- /dev/null
+++ b/history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T185016Z-codex-9c291b.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml
+ slug: SMutans_SSputigena_ECC_Pathobiont
+session:
+ id: 2026-10-07T185016Z-codex-9c291b
+ timestamp: '2026-10-07T18:50:16Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1773
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ summary: Attach direct primary-result evidence to the retained Honeycomb Biofilm Acidogenesis
+ interpretation after adversarial diff review; no new node, direction, mechanism or protocol.
+ details: Additional evidence following history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T184554Z-codex-0f7a08.yaml.
+ The original history is preserved; this correction preceded final validation.
diff --git a/history/records/SMutans_VParvula_ASC_Biofilm/2026-10-07T184554Z-codex-a80c30.yaml b/history/records/SMutans_VParvula_ASC_Biofilm/2026-10-07T184554Z-codex-a80c30.yaml
new file mode 100644
index 000000000..7041f1e65
--- /dev/null
+++ b/history/records/SMutans_VParvula_ASC_Biofilm/2026-10-07T184554Z-codex-a80c30.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SMutans_VParvula_ASC_Biofilm.yaml
+ slug: SMutans_VParvula_ASC_Biofilm
+session:
+ id: 2026-10-07T184554Z-codex-a80c30
+ timestamp: '2026-10-07T18:45:54Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1774
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain measured expression and EPS, not direct enzyme activity or colonization.;
+ Retain in-vitro composite phenotypes at community scope with correct modality.; Retain
+ the positive rodent outcome, not proven human adult causation.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
diff --git a/history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T184554Z-codex-3515ec.yaml b/history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T184554Z-codex-3515ec.yaml
new file mode 100644
index 000000000..f36e76eb0
--- /dev/null
+++ b/history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T184554Z-codex-3515ec.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml
+ slug: SO3_BS3_Lithium_Battery_Bioleaching_Consortium
+session:
+ id: 2026-10-07T184554Z-codex-3515ec
+ timestamp: '2026-10-07T18:45:54Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1775
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain detoxification and its leaching direction without an unsupported neutral-partner
+ fitness claim.; Retain the primary EET interpretation while distinguishing perturbation
+ support from quantitative flux partition.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
diff --git a/history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T185016Z-codex-8bc7a6.yaml b/history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T185016Z-codex-8bc7a6.yaml
new file mode 100644
index 000000000..59ca64540
--- /dev/null
+++ b/history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T185016Z-codex-8bc7a6.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml
+ slug: SO3_BS3_Lithium_Battery_Bioleaching_Consortium
+session:
+ id: 2026-10-07T185016Z-codex-8bc7a6
+ timestamp: '2026-10-07T18:50:16Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1775
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ summary: Attach direct primary-result evidence to the retained MtrC/OmcA and riboflavin
+ NCM reduction interpretation after adversarial diff review; no new node, direction, mechanism
+ or protocol.
+ details: Additional evidence following history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T184554Z-codex-3515ec.yaml.
+ The original history is preserved; this correction preceded final validation.
diff --git a/kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml b/kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml
index 556ec1ba3..140c65b0b 100644
--- a/kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml
+++ b/kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml
@@ -82,10 +82,8 @@ taxonomy:
explanation: Establishes Candida albicans as the fungal member of the model.
ecological_interactions:
- name: Cross-Kingdom Biofilm Enhancement
- description: >-
- Coinoculation of Streptococcus mutans and Candida albicans enhances biofilm
- formation relative to either species alone in both in vitro and in vivo
- settings.
+ description: Coinoculation of Streptococcus mutans and Candida albicans enhances biofilm formation relative to
+ either species alone in both in vitro and in vivo settings.
interaction_type: MUTUALISM
scope: PAIRWISE
source_taxon:
@@ -104,21 +102,21 @@ ecological_interactions:
id: GO:0042710
label: biofilm formation
downstream:
- - target: Synergistic Caries Virulence
- description: The enhanced dual-species plaque biofilm is the infection state that
- drives higher microbial carriage and more aggressive carious lesions in vivo.
+ - target: Rodent Coinfection Carriage and Caries Outcome
+ description: 'PARTIAL: the mixed biofilm provides the proposed context for the greater disease severity in the
+ rodent model. Coinfection establishes an effect on carriage and lesions, but does not isolate biofilm quantity
+ as the necessary mediator of the lesion outcome or establish human disease causation.'
evidence:
- reference: PMID:24566629
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >-
- We showed that the ability of these organisms together to form biofilms
- is enhanced in vitro and in vivo.
+ snippet: We showed that the ability of these organisms together to form biofilms is enhanced in vitro and in
+ vivo.
explanation: Supports a mutually reinforcing cross-kingdom biofilm interaction.
- name: Candida-Driven EPS Amplification of Streptococcus mutans
- description: >-
- Candida albicans promotes an EPS-rich matrix and higher viable Streptococcus
- mutans abundance within cospecies plaque biofilms.
+ description: Candida albicans promotes an EPS-rich matrix and higher viable Streptococcus mutans abundance within
+ cospecies plaque biofilms. This observation is from the in-vitro biofilm comparison, not a direct measurement
+ of EPS mediation in animals.
interaction_type: COLONIZATION_FACILITATION
scope: PAIRWISE
source_taxon:
@@ -138,35 +136,20 @@ ecological_interactions:
label: biofilm formation
downstream:
- target: Cross-Kingdom Biofilm Enhancement
- description: Candida-driven exopolysaccharide accumulation increases the biomass
- and viable S. mutans burden of the cross-kingdom plaque biofilm.
+ description: Candida-driven exopolysaccharide accumulation increases the biomass and viable S. mutans burden
+ of the cross-kingdom plaque biofilm.
evidence:
- reference: PMID:24566629
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >-
- The presence of C. albicans augments the production of
- exopolysaccharides (EPS), such that cospecies biofilms accrue more
- biomass and harbor more viable S. mutans cells than single-species
- biofilms.
+ evidence_source: IN_VITRO
+ snippet: The presence of C. albicans augments the production of exopolysaccharides (EPS), such that cospecies
+ biofilms accrue more biomass and harbor more viable S. mutans cells than single-species biofilms.
explanation: Supports Candida-mediated enhancement of S. mutans colonization and matrix formation.
-- name: Synergistic Caries Virulence
- description: >-
- Coinfection with Streptococcus mutans and Candida albicans increases plaque
- infection burden and produces more aggressive carious lesions than either
- species alone.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Candida albicans
- term:
- id: NCBITaxon:5476
- label: Candida albicans
- target_taxon:
- preferred_term: Streptococcus mutans
- term:
- id: NCBITaxon:1309
- label: Streptococcus mutans
+- name: Rodent Coinfection Carriage and Caries Outcome
+ description: The dual-species rodent infection model showed increased plaque microbial carriage and more severe
+ carious lesions relative to the single-species groups. This is a community-associated host outcome, not itself
+ a directed colonization benefit to S. mutans or proof of the same causal effect in children.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biofilm formation
term:
@@ -176,18 +159,24 @@ ecological_interactions:
- reference: PMID:24566629
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >-
- Coinfected animals displayed higher levels of infection and microbial
- carriage within plaque biofilms than animals infected with either species
- alone.
+ snippet: Coinfected animals displayed higher levels of infection and microbial carriage within plaque biofilms
+ than animals infected with either species alone.
explanation: Documents increased pathogenic load during dual-species coinfection.
- reference: PMID:24566629
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >-
- Furthermore, coinfection synergistically enhanced biofilm virulence,
- leading to aggressive onset of the disease with rampant carious lesions.
+ snippet: Furthermore, coinfection synergistically enhanced biofilm virulence, leading to aggressive onset of
+ the disease with rampant carious lesions.
explanation: Documents amplified caries severity caused by the dual-species consortium.
+ participating_taxa:
+ - preferred_term: Streptococcus mutans
+ term:
+ id: NCBITaxon:1309
+ label: Streptococcus mutans
+ - preferred_term: Candida albicans
+ term:
+ id: NCBITaxon:5476
+ label: Candida albicans
related_ingredients:
- preferred_term: exopolysaccharide
chebi_term:
@@ -263,3 +252,33 @@ growth_media:
evidence_source: IN_VITRO
snippet: at 37°C under 5% CO2
explanation: Biofilms cultivated at 37 °C under 5% CO2 (capnophilic).
+discussions:
+- discussion_id: candida_graph_evidence_and_model_scope
+ prompt: How much of the rodent lesion effect is mediated by the measured biofilm changes?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: The fresh primary abstract and PubMed figure captions support reciprocal biofilm benefit, EPS-associated
+ accumulation and the rodent coinfection outcome. Those positive observations remain. The EPS assay is in vitro;
+ the rodent disease endpoint is distinct from recipient colonization. The existing disease arrow is retained
+ as PARTIAL mediation. EuropePMC full-text retrieval returned HTTP500, so complete main-text, supplement and
+ figure-pixel review is not claimed. Non-graph evidence labels remain separate follow-up work.
+ evidence:
+ - reference: PMID:24566629
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Our in vitro data also revealed that glucosyltransferase-derived EPS is a key mediator of cospecies
+ biofilm development
+ explanation: Supports in-vitro mediation of biofilm development, not isolated mediation of the rodent lesion
+ outcome.
+ attaches_to:
+ - ecological_interactions#Cross-Kingdom Biofilm Enhancement
+ - ecological_interactions#Candida-Driven EPS Amplification of Streptococcus mutans
+ - ecological_interactions#Rodent Coinfection Carriage and Caries Outcome
+curation_history:
+- timestamp: '2026-10-07T18:45:52Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain supported mutualism and a PARTIAL rodent-outcome direction.; Retain positive Candida-to-S. mutans
+ biofilm facilitation with the correct in-vitro source.; Retain the positive rodent carriage/lesion outcome at
+ community scope, not pairwise colonization. Issue#1772; reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
+ llm_assisted: true
diff --git a/kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml b/kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml
index 4c31d840b..8ba42ce9e 100644
--- a/kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml
+++ b/kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml
@@ -96,9 +96,9 @@ taxonomy:
explanation: Establishes Selenomonas sputigena as the pathobiont evaluated in the model.
ecological_interactions:
- name: Streptococcal Exoglucan Entrapment of Selenomonas sputigena
- description: >-
- Streptococcus mutans exoglucans trap Selenomonas sputigena, suppress its
- motility, and create a structured mixed-species biofilm.
+ description: Streptococcus mutans exoglucans trap Selenomonas sputigena, suppress its motility, and create a structured
+ mixed-species biofilm. The primary in-vitro surface-colonization comparison supports S. mutans-to-S. sputigena
+ facilitation; it does not establish the reverse direction from acid output alone.
interaction_type: COLONIZATION_FACILITATION
scope: PAIRWISE
source_taxon:
@@ -123,38 +123,22 @@ ecological_interactions:
label: biofilm formation
downstream:
- target: Honeycomb Biofilm Acidogenesis
- description: Exoglucan entrapment immobilizes and supports S. sputigena in
- the mixed biofilm, leading to a honeycomb-like superstructure around S.
- mutans that enhances acidogenesis.
+ description: Exoglucan entrapment immobilizes and supports S. sputigena in the mixed biofilm, leading to a honeycomb-like
+ superstructure around S. mutans that enhances acidogenesis.
evidence:
- reference: PMID:37217495
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >-
- We show that S. sputigena, a flagellated anaerobe with previously unknown
- role in supragingival biofilm, becomes trapped in streptococcal
- exoglucans, loses motility but actively proliferates to build a
- honeycomb-like multicellular-superstructure encapsulating S. mutans,
- enhancing acidogenesis.
+ evidence_source: IN_VITRO
+ snippet: We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm,
+ becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like
+ multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis.
explanation: Documents matrix-mediated trapping and structured coassembly with S. mutans.
- name: Honeycomb Biofilm Acidogenesis
- description: >-
- Entrapped Selenomonas sputigena actively proliferates into a
- honeycomb-like multicellular superstructure that encapsulates
- Streptococcus mutans and enhances acidogenesis in the mixed-species
- biofilm.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Selenomonas sputigena
- term:
- id: NCBITaxon:69823
- label: Selenomonas sputigena
- target_taxon:
- preferred_term: Streptococcus mutans
- term:
- id: NCBITaxon:1309
- label: Streptococcus mutans
+ description: Entrapped Selenomonas sputigena actively proliferates into a honeycomb-like multicellular superstructure
+ that encapsulates Streptococcus mutans and enhances acidogenesis in the mixed-species biofilm. This is a mixed-biofilm
+ structure and metabolic outcome, not a measurement of S. mutans establishment. Primary matrix-disruption results
+ support the structural contribution to localized acidity.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: glucan
term:
@@ -166,38 +150,39 @@ ecological_interactions:
id: GO:0042710
label: biofilm formation
downstream:
- - target: Pathobiont-Enhanced Cariogenicity
- description: The structured S. mutans-S. sputigena biofilm intensifies
- acidogenesis, providing the local virulence context for the extensive
- enamel lesions observed during coinfection.
+ - target: Rodent Coinfection Caries Outcome
+ description: 'PARTIAL: the structured acidic biofilm is the proposed mediator of the rodent lesion outcome.
+ The primary in-vitro disruption and ex-vivo enamel results support the structure-to-damage interpretation,
+ while the rodent coinfection comparison does not independently isolate that mediator in vivo.'
evidence:
- reference: PMID:37217495
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >-
- We show that S. sputigena, a flagellated anaerobe with previously unknown
- role in supragingival biofilm, becomes trapped in streptococcal
- exoglucans, loses motility but actively proliferates to build a
- honeycomb-like multicellular-superstructure encapsulating S. mutans,
- enhancing acidogenesis.
- explanation: Documents S. sputigena proliferation and S. mutans encapsulation
- as the mixed-biofilm architecture that heightens acidogenesis.
-- name: Pathobiont-Enhanced Cariogenicity
- description: >-
- Selenomonas sputigena is non-cariogenic alone but markedly worsens enamel
- lesion formation when coinfected with Streptococcus mutans.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Selenomonas sputigena
- term:
- id: NCBITaxon:69823
- label: Selenomonas sputigena
- target_taxon:
- preferred_term: Streptococcus mutans
+ evidence_source: IN_VITRO
+ snippet: We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm,
+ becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like
+ multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis.
+ explanation: Documents S. sputigena proliferation and S. mutans encapsulation as the mixed-biofilm architecture
+ that heightens acidogenesis.
+ - reference: PMID:37217495
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The data suggest that the interspecies spatial structuring between S. sputigena and S. mutans is required
+ to create a virulent acidic microenvironment.
+ explanation: Direct primary result supporting the retained structural interpretation; not isolated in-vivo mediation.
+ participating_taxa:
+ - preferred_term: Streptococcus mutans
term:
id: NCBITaxon:1309
label: Streptococcus mutans
+ - preferred_term: Selenomonas sputigena
+ term:
+ id: NCBITaxon:69823
+ label: Selenomonas sputigena
+- name: Rodent Coinfection Caries Outcome
+ description: In the reported rodent model, S. sputigena alone did not cause more caries than the control, whereas
+ dual-species coinfection increased lesion severity. This community-associated host outcome does not itself demonstrate
+ a colonization benefit to S. mutans or establish human causal direction.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biological process involved in interspecies interaction between organisms
term:
@@ -207,11 +192,18 @@ ecological_interactions:
- reference: PMID:37217495
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >-
- While incapable of causing caries on its own, when co-infected with S.
- mutans, S. sputigena causes extensive tooth enamel lesions and
- exacerbates disease severity in vivo.
+ snippet: While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes
+ extensive tooth enamel lesions and exacerbates disease severity in vivo.
explanation: Supports S. sputigena as a pathobiont that heightens S. mutans virulence.
+ participating_taxa:
+ - preferred_term: Streptococcus mutans
+ term:
+ id: NCBITaxon:1309
+ label: Streptococcus mutans
+ - preferred_term: Selenomonas sputigena
+ term:
+ id: NCBITaxon:69823
+ label: Selenomonas sputigena
related_ingredients:
- preferred_term: glucan
chebi_term:
@@ -286,3 +278,38 @@ cultivation_setup:
snippet: a saliva-coated hydroxyapatite disc (2.7 ± 0.2 cm2; Clarkson Chromatography
Products) was placed in a vertical position to mimic the tooth-enamel surfaces
of human teeth
+discussions:
+- discussion_id: selenomonas_graph_evidence_and_model_scope
+ prompt: How directly does the model establish mediation of disease in humans?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: Primary results support S. mutans-assisted S. sputigena colonization, matrix-dependent structure and
+ local acidity, ex-vivo enamel damage, and greater rodent disease under coinfection. Retain this experimental
+ evidence and both directions; only the in-vivo mediation bridge is PARTIAL. Do not turn the reverse acidogenesis
+ effect into a colonization-facilitation label. Human discovery data are cross-sectional. Exact molecular details
+ remain unresolved; no new mechanisms or experimental procedures are added.
+ evidence:
+ - reference: PMID:37217495
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: the cross-sectional nature of our human observational data, which limits the samples’ inferential potential
+ regarding temporality and causality
+ explanation: The primary discussion explicitly limits human causal inference.
+ attaches_to:
+ - ecological_interactions#Streptococcal Exoglucan Entrapment of Selenomonas sputigena
+ - ecological_interactions#Honeycomb Biofilm Acidogenesis
+ - ecological_interactions#Rodent Coinfection Caries Outcome
+curation_history:
+- timestamp: '2026-10-07T18:45:53Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain supported directional colonization facilitation and the existing structural link, correcting modality.;
+ Retain community structure and acidogenesis, with positive perturbation evidence and PARTIAL in-vivo mediation.;
+ Retain the rodent disease comparison at two-member community scope. Issue#1773; reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
+ llm_assisted: true
+- timestamp: '2026-10-07T18:50:15Z'
+ curator: codex
+ action: FIX_ADVERSARIAL_REVIEW_FINDINGS
+ changes: Attach direct primary-result evidence to the retained Honeycomb Biofilm Acidogenesis interpretation after
+ adversarial diff review; no new node, direction, mechanism or protocol. Issue#1773.
+ llm_assisted: true
diff --git a/kb/communities/SMutans_VParvula_ASC_Biofilm.yaml b/kb/communities/SMutans_VParvula_ASC_Biofilm.yaml
index e7075e131..0afe43c96 100644
--- a/kb/communities/SMutans_VParvula_ASC_Biofilm.yaml
+++ b/kb/communities/SMutans_VParvula_ASC_Biofilm.yaml
@@ -96,13 +96,10 @@ taxonomy:
parvula.
explanation: Establishes Veillonella parvula as the adult severe caries-associated pathobiont.
ecological_interactions:
-- name: Veillonella parvula Boost of Streptococcus mutans Glucosyltransferase-EPS Output
- description: >-
- Veillonella parvula coculture increases Streptococcus mutans gtfB, gtfC,
- and gtfD expression and raises the EPS/bacteria ratio in sucrose-grown
- dual-species biofilms, increasing the extracellular matrix component of the
- mixed biofilm.
- interaction_type: COLONIZATION_FACILITATION
+- name: Veillonella-Associated gtf Expression and Mixed-Biofilm EPS
+ description: The primary in-vitro comparison reports increased S. mutans gtf transcript levels and a higher EPS-to-bacteria
+ fluorescence ratio in the mixed biofilm. These observations do not independently measure catalytic enzyme activity,
+ species-resolved cell numbers or the necessity of this expression change for the other phenotypes.
scope: PAIRWISE
source_taxon:
preferred_term: Veillonella parvula
@@ -129,83 +126,59 @@ ecological_interactions:
id: GO:0042710
label: biofilm formation
downstream:
- - target: Veillonella parvula Promotion of Streptococcus mutans Biofilm Virulence
- description: Increased S. mutans glucosyltransferase expression and EPS
- production strengthen the sucrose-grown mixed biofilm matrix that V.
- parvula makes denser and more viable.
+ - target: Mixed-Biofilm and Stress-Response Phenotypes
+ description: 'PARTIAL: increased EPS is proposed to contribute to the observed mixed-biofilm phenotype. The
+ expression and imaging comparisons do not independently isolate the expression-to-phenotype mediator or establish
+ its contribution to the separate stress-response assays.'
evidence:
- - reference: PMID:39345197
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: >-
- V. parvula enhances the glucosyltransferase activities of S. mutans and
- boosts S. mutans to produce more EPS
- explanation: Supports Veillonella-driven induction of S. mutans
- glucosyltransferase activity and EPS production.
- reference: PMID:39345197
supports: SUPPORT
evidence_source: IN_VITRO
snippet: gtfb, gtfc, and gtfd in dual-strains biofilm dramatically increased
- explanation: Supports the measured increase in S. mutans gtf expression in
- dual-species biofilms.
+ explanation: Supports the measured increase in S. mutans gtf expression in dual-species biofilms.
- reference: PMID:39345197
supports: SUPPORT
evidence_source: IN_VITRO
snippet: increased the EPS/bacteria ratio
- explanation: Supports a higher EPS load in S. mutans/V. parvula mixed
- biofilms than in S. mutans biofilms.
-- name: Veillonella parvula Promotion of Streptococcus mutans Biofilm Virulence
- description: >-
- Veillonella parvula promotes mature Streptococcus mutans biofilm formation
- and increases stress tolerance and virulence traits in the dual-species
- consortium.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Veillonella parvula
- term:
- id: NCBITaxon:29466
- label: Veillonella parvula
- target_taxon:
- preferred_term: Streptococcus mutans
- term:
- id: NCBITaxon:1309
- label: Streptococcus mutans
+ explanation: Supports a higher EPS load in S. mutans/V. parvula mixed biofilms than in S. mutans biofilms.
+- name: Mixed-Biofilm and Stress-Response Phenotypes
+ description: The in-vitro study reports denser mixed biofilms and improved S. mutans survival in separate stress-response
+ assays. These positive observations remain, while mixed-community biomass and fluorescence do not separately
+ resolve the abundance of each species. The composite phenotype is not itself a directed colonization measurement.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biofilm formation
term:
id: GO:0042710
label: biofilm formation
downstream:
- - target: Pathobiont-Driven Adult Severe Caries Exacerbation
- description: Veillonella-driven mature biofilm formation and stress tolerance
- set up the dual-species biofilm virulence measured as worsened rodent caries.
+ - target: Rodent Coinfection Caries Outcome
+ description: 'PARTIAL: the in-vitro phenotypes are proposed contributors to the greater rodent disease outcome.
+ The coinfection experiment supports the overall disease effect, but does not independently identify which
+ phenotype mediates it or prove a causal effect in adults.'
evidence:
- reference: PMID:39345197
supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: >-
- In vitro experiments found that V. parvula can effectively promote S.
- mutans mature biofilm formation with enhanced acid resistance, hydrogen
- peroxide detoxicity, and biofilm virulence.
- explanation: Supports Veillonella-driven enhancement of S. mutans virulence traits.
-- name: Pathobiont-Driven Adult Severe Caries Exacerbation
- description: >-
- Veillonella parvula is not independently cariogenic in the model but
- significantly worsens disease progression when coinfected with
- Streptococcus mutans.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Veillonella parvula
- term:
- id: NCBITaxon:29466
- label: Veillonella parvula
- target_taxon:
- preferred_term: Streptococcus mutans
+ evidence_source: IN_VITRO
+ snippet: In vitro experiments found that V. parvula can effectively promote S. mutans mature biofilm formation
+ with enhanced acid resistance, hydrogen peroxide detoxicity, and biofilm virulence.
+ explanation: Supports the reported in-vitro phenotypes, not an animal experiment or a species-resolved abundance
+ measurement.
+ participating_taxa:
+ - preferred_term: Streptococcus mutans
term:
id: NCBITaxon:1309
label: Streptococcus mutans
+ - preferred_term: Veillonella parvula
+ term:
+ id: NCBITaxon:29466
+ label: Veillonella parvula
+- name: Rodent Coinfection Caries Outcome
+ description: The dual-species rodent group had greater caries progression and severity than single-species groups,
+ while V. parvula alone did not differ significantly from the control. This is a rodent community-associated
+ disease outcome. The separate adult plaque association does not establish the same causal effect in human adult
+ severe caries.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biofilm formation
term:
@@ -215,12 +188,20 @@ ecological_interactions:
- reference: PMID:39345197
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: >-
- Rodent model experiments revealed that V. parvula was incapable of
- causing disease on its own, but it significantly heightened the biofilm
- virulence of S. mutans when being co-infected and augmented the
- progression, quantity, and severity of dental caries.
- explanation: Supports Veillonella parvula as a synergistic pathobiont in adult severe caries.
+ snippet: Rodent model experiments revealed that V. parvula was incapable of causing disease on its own, but
+ it significantly heightened the biofilm virulence of S. mutans when being co-infected and augmented the progression,
+ quantity, and severity of dental caries.
+ explanation: Supports the rodent coinfection outcome, not a human causal estimate or recipient colonization
+ benefit.
+ participating_taxa:
+ - preferred_term: Streptococcus mutans
+ term:
+ id: NCBITaxon:1309
+ label: Streptococcus mutans
+ - preferred_term: Veillonella parvula
+ term:
+ id: NCBITaxon:29466
+ label: Veillonella parvula
related_ingredients:
- preferred_term: hydrogen peroxide
chebi_term:
@@ -296,3 +277,32 @@ cultivation_setup:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: For the biofilm studies, 1% sucrose was added to the BHI broth
+discussions:
+- discussion_id: veillonella_graph_evidence_and_model_scope
+ prompt: Which measured in-vitro phenotype mediates the rodent disease effect?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: Results and discussion distinguish transcript abundance, mixed-biofilm imaging, stress-response assays
+ and the rodent endpoint. A results heading says activity, but the accompanying measurements do not independently
+ quantify enzyme catalysis. Positive findings remain with both existing directions explicitly PARTIAL. Mixed
+ fluorescence is not species-resolved abundance, and the small human comparison is observational. No new molecular
+ mechanism, pathogen-enhancement design or wet-lab instruction is added.
+ evidence:
+ - reference: PMID:39345197
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: the specific mechanism of its influence on oral diseases at the molecular level still need further
+ studies
+ explanation: The primary discussion leaves molecular mediation unresolved.
+ attaches_to:
+ - ecological_interactions#Veillonella-Associated gtf Expression and Mixed-Biofilm EPS
+ - ecological_interactions#Mixed-Biofilm and Stress-Response Phenotypes
+ - ecological_interactions#Rodent Coinfection Caries Outcome
+curation_history:
+- timestamp: '2026-10-07T18:45:53Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain measured expression and EPS, not direct enzyme activity or colonization.; Retain in-vitro composite
+ phenotypes at community scope with correct modality.; Retain the positive rodent outcome, not proven human adult
+ causation. Issue#1774; reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
+ llm_assisted: true
diff --git a/kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml b/kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml
index fa5c6724c..87efc5a38 100644
--- a/kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml
+++ b/kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml
@@ -115,9 +115,10 @@ taxonomy:
explanation: Identifies BS3 as the IrrE-enhanced B. subtilis member used in the final consortium.
ecological_interactions:
- name: BS3 ethanol detoxification of brewing wastewater
- description: Bacillus subtilis BS3 converts residual ethanol in brewing wastewater to acetate via heterologous alcohol dehydrogenase
- and aldehyde dehydrogenase, removing an inhibitor of S. oneidensis extracellular electron transfer.
- interaction_type: COMMENSALISM
+ description: Bacillus subtilis BS3 converts residual ethanol in brewing wastewater to acetate via heterologous
+ alcohol dehydrogenase and aldehyde dehydrogenase, removing an inhibitor of S. oneidensis extracellular electron
+ transfer. This supports facilitation of SO3 electron transfer, but does not establish that BS3 is unaffected
+ by SO3 as required for COMMENSALISM.
scope: PAIRWISE
source_taxon:
preferred_term: Bacillus subtilis 168 BS3
@@ -140,8 +141,10 @@ ecological_interactions:
label: acetate
downstream:
- target: MtrC/OmcA and riboflavin NCM reduction
- description: Removing ethanol relieves inhibition of the S. oneidensis EET machinery that reduces NCM for metal oxide
- leaching.
+ description: Ethanol removal relieves inhibition of Shewanella electron transfer and thereby supports NCM leaching
+ in the authors' consortium model. The detoxification comparisons were conducted in predecessor strains; the
+ final SO3-BS3 synthesis retains this function, without separately isolating its quantitative contribution
+ from the other modifications.
evidence:
- reference: PMID:42733304
supports: SUPPORT
@@ -150,9 +153,11 @@ ecological_interactions:
residual ethanol in the brewing wastewater into acetate via the Adh‐AldH dual enzyme cascade reaction.
explanation: Directly supports the BS3-to-SO3 detoxification interaction in the final SO3-BS3 consortium.
- name: MtrC/OmcA and riboflavin NCM reduction
- description: Shewanella oneidensis SO3 catabolizes lactate from brewing wastewater and transfers electrons to NCM black
- mass either directly through outer-membrane cytochromes MtrC/OmcA or indirectly through riboflavin, reducing NCM metal
- oxides and releasing Li, Ni, Co, and Mn into solution.
+ description: Shewanella oneidensis SO3 catabolizes lactate from brewing wastewater and transfers electrons to
+ NCM black mass either directly through outer-membrane cytochromes MtrC/OmcA or indirectly through riboflavin,
+ reducing NCM metal oxides and releasing Li, Ni, Co, and Mn into solution. Final-consortium cytochrome perturbations
+ and the reduced-riboflavin assay support the EET interpretation. The proposed direct and shuttle routes are
+ not a quantitative partition of in-consortium electron flux.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Shewanella oneidensis MR-1 SO3
@@ -188,17 +193,24 @@ ecological_interactions:
- reference: PMID:42733304
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The generated electrons were then used to reduce NCM via the EET mechanism. Specifically, the electrons generated
- from strain SO3 could be either directly transferred to NCM via outer membrane c‐Cyts MtrC and OmcA, or first transferred
- to riboflavin molecules via MtrC and OmcA.
- explanation: Supports MtrC/OmcA- and riboflavin-mediated electron transfer from SO3 to NCM in the final SO3-BS3 consortium.
+ snippet: The generated electrons were then used to reduce NCM via the EET mechanism. Specifically, the electrons
+ generated from strain SO3 could be either directly transferred to NCM via outer membrane c‐Cyts MtrC and OmcA,
+ or first transferred to riboflavin molecules via MtrC and OmcA.
+ explanation: Supports MtrC/OmcA- and riboflavin-mediated electron transfer from SO3 to NCM in the final SO3-BS3
+ consortium.
- reference: PMID:42733304
supports: SUPPORT
evidence_source: IN_VITRO
snippet: strain BS3 in the SO3‐BS3 consortium eliminated the ethanol inhibition on EET of S. oneidensis by converting
- residual ethanol in the brewing wastewater into acetate via the Adh‐AldH dual enzyme cascade reaction. Also, strain
- BS3 synthesized riboflavin, which was employed as an electron shuttle for promoting the EET of S. oneidensis.
+ residual ethanol in the brewing wastewater into acetate via the Adh‐AldH dual enzyme cascade reaction. Also,
+ strain BS3 synthesized riboflavin, which was employed as an electron shuttle for promoting the EET of S. oneidensis.
explanation: Supports the BS3 contribution to the riboflavin-enhanced NCM reduction phenotype.
+ - reference: PMID:42733304
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: confirming that the disruption of MtrC and OmcA significantly inhibited the EET process in strain SO3.
+ explanation: Direct final-consortium perturbation support for EET involvement; not a quantitative direct/shuttle
+ flux partition.
environmental_factors:
- name: Total leached Li, Ni, Co, and Mn
value: 102.4 mg/L total dissolved metal ions after 14 days
@@ -306,23 +318,43 @@ metal_notes: The NCM black mass leaching target contained Li, Ni, Co, and Mn; PM
for all four elements.
discussions:
- discussion_id: SO3_BS3_SCALE_UP_STABILITY
- prompt: The source established a 14-day laboratory proof of concept but explicitly left larger-scale, long-term stability
- unresolved, especially under natural variation in raw brewing-wastewater composition.
+ prompt: The source established a 14-day laboratory proof of concept but explicitly left larger-scale, long-term
+ stability unresolved, especially under natural variation in raw brewing-wastewater composition.
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- growth_media#Moutai brewing wastewater with spent NCM black mass
- rationale: Raw brewing wastewater varied by batch and the authors identified large-scale reproducibility as a future optimization
- target, so the current record should not assert demonstrated industrial stability.
+ rationale: Raw brewing wastewater varied by batch and the authors identified large-scale reproducibility as a
+ future optimization target, so the current record should not assert demonstrated industrial stability.
evidence:
- reference: PMID:42733304
supports: SUPPORT
evidence_source: full_text
- snippet: the long‐term stability and reproducibility of the microbial consortium at a larger scale needed to be thoroughly
- considered, in particular under the condition of natural fluctuations in raw brewing wastewater compositions
+ snippet: the long‐term stability and reproducibility of the microbial consortium at a larger scale needed to
+ be thoroughly considered, in particular under the condition of natural fluctuations in raw brewing wastewater
+ compositions
explanation: Records the authors' stated scale-up uncertainty without asserting it as a demonstrated limitation.
posed_by: claude
posed_date: '2026-09-18'
+- discussion_id: battery_graph_evidence_and_model_scope
+ prompt: What is the reciprocal fitness effect and relative contribution of the retained processes?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: Primary predecessor comparisons support ethanol removal, electron-transfer improvement and leaching.
+ Final-consortium perturbations and riboflavin evidence support the retained reduction node. Neither benefit
+ to SO3 nor greater leaching establishes neutral fitness of BS3 in the exact pair, so the optional COMMENSALISM
+ type is removed without denying the supported facilitation. Direct-versus-shuttle flux and the isolated contribution
+ of detoxification in the final consortium are not quantified by the cited comparisons. The existing scale-up
+ discussion remains unchanged.
+ evidence:
+ - reference: PMID:42733304
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: confirming that the ethanol inhibition of the EET of the SO1‐BS1 consortium was significantly alleviated
+ explanation: Identifies the predecessor consortium used for the detoxification comparison.
+ attaches_to:
+ - ecological_interactions#BS3 ethanol detoxification of brewing wastewater
+ - ecological_interactions#MtrC/OmcA and riboflavin NCM reduction
curation_history:
- timestamp: '2026-09-18T08:56:51Z'
curator: claude
@@ -332,5 +364,19 @@ curation_history:
- timestamp: '2026-09-18T09:05:04Z'
curator: claude
action: UPDATE_COMMUNITY
- changes: 'Addressed adversarial-review issues #941 and #942 by adding exact medium-condition and Ni/Co viability evidence.'
+ changes: 'Addressed adversarial-review issues #941 and #942 by adding exact medium-condition and Ni/Co viability
+ evidence.'
+ llm_assisted: true
+- timestamp: '2026-10-07T18:45:53Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain detoxification and its leaching direction without an unsupported neutral-partner fitness claim.;
+ Retain the primary EET interpretation while distinguishing perturbation support from quantitative flux partition.
+ Issue#1775; reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
+ llm_assisted: true
+- timestamp: '2026-10-07T18:50:16Z'
+ curator: codex
+ action: FIX_ADVERSARIAL_REVIEW_FINDINGS
+ changes: Attach direct primary-result evidence to the retained MtrC/OmcA and riboflavin NCM reduction interpretation
+ after adversarial diff review; no new node, direction, mechanism or protocol. Issue#1775.
llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 0a9238b29..047bc7ce9 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -1092,3 +1092,20 @@ evidence and cultivation confounding are recorded. Caches and non-graph raw
blocks are unchanged, not globally certified. No new topology or provider
spend. Repairs #1766-#1769 await protected-main merge; non-graph #1770 stays
open. Self-review is not independent approval or corpus completion.
+
+## Batch97: Evidence Modality And Host Outcomes
+
+[Decisions](decisions/20261007-four-records-batch97.yaml),
+[validation](validation-20261007-batch97.json),
+[cache provenance](cache-provenance-20261007-batch97.json) and
+[self-adversarial review](adversarial-review-20261007-batch97.yaml) cover
+three oral-biofilm records and the SO3-BS3 battery-bioleaching consortium.
+All 11 nodes and seven directions remain. In-vitro observations, composite
+community phenotypes and rodent disease outcomes are distinguished; supported
+facilitation remains, with unisolated mediation marked PARTIAL. The battery
+graph retains detoxification and EET without asserting neutral partner fitness.
+Direct-result citations were added after adversarial diff review, with separate
+append-only correction histories. Caches and non-graph blocks are unchanged.
+No new topology, experimental instructions or provider spend. Repairs
+#1772-#1775 await protected-main merge; non-graph #1776 remains open.
+Self-review is not independent approval or corpus completion.
diff --git a/reports/causal_graph_review/adversarial-review-20261007-batch97.yaml b/reports/causal_graph_review/adversarial-review-20261007-batch97.yaml
new file mode 100644
index 000000000..a6b98230d
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261007-batch97.yaml
@@ -0,0 +1,403 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: c33f6896716f6cfa4ccaac9b3ad97359de0674f9
+scope:
+- kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml
+- kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml
+- kb/communities/SMutans_VParvula_ASC_Biofilm.yaml
+- kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
+validation_report: reports/causal_graph_review/validation-20261007-batch97.json
+findings:
+- issue: 1772
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate Candida biofilm facilitation from rodent disease outcome
+ disposition: Close only after protected-main merge.
+- issue: 1773
+ severity: P2
+ status: addressed_in_this_change
+ finding: Correct Selenomonas graph evidence modality and outcome scope
+ disposition: Close only after protected-main merge.
+- issue: 1774
+ severity: P2
+ status: addressed_in_this_change
+ finding: Bound Veillonella expression and rodent outcome claims
+ disposition: Close only after protected-main merge.
+- issue: 1775
+ severity: P2
+ status: addressed_in_this_change
+ finding: Retain SO3-BS3 detoxification without an untested neutral partner effect
+ disposition: Close only after protected-main merge.
+- issue: 1776
+ severity: P2
+ status: open_non_graph_follow_up
+ finding: Review oral-biofilm non-graph evidence labels and model boundaries
+ disposition: Separate non-graph curation required.
+adversarial_checks:
+- Fresh both-root baseline preceded source reads. Four whole records and all11nodes/7directions accounted for; all
+ retained,5nodes renamed. No new topology or provider spend.
+- Candida mutualism and directional biofilm facilitation remain. EPS evidence is IN_VITRO; the rodent carriage/lesion
+ endpoint is COMMUNITY_LEVEL. The existing lesion arrow is PARTIAL mediation, not a proven human causal effect.
+- Selenomonas entrapment and structure evidence is IN_VITRO. Retain experimentally supported S. mutans-to-S. sputigena
+ facilitation and the structural direction. The primary matrix-disruption and ex-vivo evidence must not be erased
+ as mere association. Mixed acidogenesis and rodent lesions are not recipient colonization measurements.
+- Veillonella gtf expression and EPS fluorescence remain, without independently quantified enzyme activity or species-resolved
+ cell abundance. Correct the in-vitro source, use named community participants for composite outcomes, and distinguish
+ rodent intervention from adult human association. Both mediator directions are PARTIAL.
+- Battery detoxification, EET and leaching remain. Beneficial detoxification does not establish neutral fitness
+ of BS3 in the exact pair, so COMMENSALISM is removed. Predecessor comparisons and the final-consortium interpretation
+ are distinguished; perturbation and riboflavin evidence is not a quantitative partition of direct/shuttle flux.
+ Earlier scale-up discussion preserved.
+- Adversarial diff review found that two newly explicit interpretation statements lacked direct result quotations
+ at the node. Added source-matched Selenomonas structural and SO3 perturbation quotations, with two new correction
+ histories referencing and preserving the initial histories. Both fixes preceded final validation; no interrupted
+ attempt.
+- All16graph and4new-discussion quotations match fresh primary text and unchanged caches. Candida XML retrieval
+ failed; fresh abstract/PubMed captions and selected primary sections for the other sources were read. Truncated
+ flattened cache output is not a complete cache-body read. No figure pixels, supplements or raw-data certification.
+- Four records changed;456otherrecords,923caches, canonical taxonomy and all non-graph raw blocks preserved. Six
+ append-only histories. No culture procedures, genetic designs or pathogen-enhancement instructions added. Non-graph1776
+ remains separate.
+- 'Connectivity census: records with community scope399->402,mixed125->128,taxa1536->1542,solely credited1266 unchanged.
+ Exactly named two-member participant lists explain the change; narrow bounds updated with dedicated scope tests.
+ Initial regression found an incomplete participant allowlist (887passed/1failed). Added exactly the three intentional
+ users; equality guard retained. Failed output and initial snapshot preserved, complete regression rerun; unchanged
+ earlier gates digest-checked on resume.'
+- Eight focused tests and888combined regressions passed;44output records and digests retained. Whole-record gates
+ and six history gates ran.56network warnings unchanged,zero structural defects. Deterministic rendering and exact
+ HTML description parsing are not screenshots; postcommit docs-current remains a separate gate.
+- Fresh all-state issue title/body and ignored/hidden-inclusive local dedup with stated exclusions performed;941/942
+ read and distinct. PRs/comments not exhaustive. Repairs1772-1775 close only after protected-main merge;1776 remains
+ open. Linux DOI-cache1091 and loader1703 not certified.
+- Self-adversarial review is COMMENT, not independent approval. No protection bypass, CI fabrication or automatic
+ issue closure. Corpus304reviewed/108pending/48needs_research remains incomplete.
+adversarial_prepublication_fix:
+ findings:
+ - issue: 1773
+ details: Attach direct primary-result evidence to the retained Honeycomb Biofilm Acidogenesis interpretation
+ after adversarial diff review; no new node, direction, mechanism or protocol.
+ preserved_initial_histories:
+ history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T184554Z-codex-0f7a08.yaml: 6489f27ee2b5c35d4131815469e2761ff1cd7e3ed53a87bb08782f65d1739230
+ correction_history: history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T185016Z-codex-9c291b.yaml
+ - issue: 1775
+ details: Attach direct primary-result evidence to the retained MtrC/OmcA and riboflavin NCM reduction interpretation
+ after adversarial diff review; no new node, direction, mechanism or protocol.
+ preserved_initial_histories:
+ history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T184554Z-codex-3515ec.yaml: fa0a65de9df956d2143f1370a94d1aacec667c3ba2280b3fa7f2664060aa798b
+ correction_history: history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T185016Z-codex-8bc7a6.yaml
+ timing: Both corrections preceded final validation; no interrupted verification attempt.
+ participant_fixture_correction:
+ details: Initial regression:887passed/1failed because the explicit participant allowlist lacked the three newly
+ curated oral records. Added exactly those three entries after measured census; equality guard retained. Failed
+ output and initial validation snapshot preserved; full regression rerun, unchanged earlier gates digest-checked
+ on resume.
+ failed_output: /private/tmp/communitymech-batch97/verification-final/regressions-attempt1.log
+ failed_output_sha256: 8fa08d48a4811313045065e543271e7296247431252649fd350220a53197978f
+ initial_snapshot: /private/tmp/communitymech-batch97/validation-initial.json
+ initial_snapshot_sha256: 46a188ae9e6357498dbdd9175ba4e84c9e473ba37b3abd57fe08fbc9a128c4de
+verification:
+ combined_regressions: 888 passed in 507.98s (0:08:27)
+ new_regression_tests: 8
+ total_recorded_gate_outputs: 44
+ primary_graph_snippet_proof:
+ graph_quotations: 16
+ new_discussion_quotations: 4
+ fresh_primary_matches: 20
+ retained_nodes: 11
+ removed_nodes: 0
+ retained_arrows: 7
+ removed_arrows: 0
+ new_nodes_or_directions: 0
+ scope: Selected primary results/discussions for Selenomonas, Veillonella and battery; Candida abstract and PubMed
+ captions. All quotations matched, not automatic entailment or figure-pixel certification.
+ references: Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091
+ remains. Literal matches do not establish entailment; Candida full text unavailable and other sources read in
+ stated sections. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
+ snippet_counts_by_record:
+ kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml:
+ MATCH: 13
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml:
+ MATCH: 13
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/SMutans_VParvula_ASC_Biofilm.yaml:
+ MATCH: 13
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml:
+ MATCH: 17
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 8939
+ categories:
+ MATCH: 8804
+ RENDERING: 20
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 38
+ NOCONTENT: 76
+ caveat: Both-root informational audit exit0 is not clean-corpus certification; literal matches are not entailment.
+ network:
+ existing_findings_preserved: 56
+ added_findings: {}
+ removed_findings: {}
+ interpretation: All11nodes7directions retained with evidence-modality, outcome-scope and mediation corrections.
+ All56warnings unchanged,zero structural defects.
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml: f3e566e8551faa3722556919317158cc3f7e5cc14a8efb44c0517b02519e907b
+ tests/test_causal_review_batch97.py: 4eb722b7646f410036a63562b2bf464bd272ef3f9cfb9b81767306d5ed7eb9da
+ tests/test_participating_taxa.py: 609b5ce90381373a0201fca0d8a391052403d62ad11ca412653c012b5d560eb0
+ tests/test_community_level_connectivity_credit.py: 2bbf90543ae806230d546f26ad572aa97f9ace8895076a314006b8e4c5c51686
+ reports/causal_graph_review/README.md: 00275ecb17f43571008c91f4066c5b90a44e640ce0833a684d55a051518ab45f
+ reports/causal_graph_review/cache-provenance-20261007-batch97.json: 2b4ae0fb1591e187d73ef784979e2c69def0e1bcb111ef6eec0e64bec01ba43d
+ kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml: fb7d747151fb52f52127e035683a77dcb1596d6f1fc97ac1e8635298ce24fd34
+ kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml: 8c32ed74a997011d25ad1e3501b42f6da246ba28e23d58a85a92ee9fad169846
+ kb/communities/SMutans_VParvula_ASC_Biofilm.yaml: 1c331f8546d510e5a20819f77901353203ba43b317c92f5bdb4ad8ab2364e265
+ kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml: b70b100dcdc43b4caf560b3794f0165db3b7c99410a7ba8d5b811825ebdceef4
+ unchanged_records: 456
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 768
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Correct existing node categories, source modality and mediation strength; retain all existing
+ directions without new topology.
+ post_commit_docs_current: Separate publication gate, not preasserted.
+ failed_attempts:
+ - check: regressions
+ command:
+ - /Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3
+ - -m
+ - pytest
+ - -q
+ - tests/test_causal_review_batch10.py
+ - tests/test_causal_review_batch11.py
+ - tests/test_causal_review_batch12.py
+ - tests/test_causal_review_batch13.py
+ - tests/test_causal_review_batch14.py
+ - tests/test_causal_review_batch15.py
+ - tests/test_causal_review_batch16.py
+ - tests/test_causal_review_batch17.py
+ - tests/test_causal_review_batch18.py
+ - tests/test_causal_review_batch19.py
+ - tests/test_causal_review_batch20.py
+ - tests/test_causal_review_batch21.py
+ - tests/test_causal_review_batch22.py
+ - tests/test_causal_review_batch23.py
+ - tests/test_causal_review_batch24.py
+ - tests/test_causal_review_batch25.py
+ - tests/test_causal_review_batch27.py
+ - tests/test_causal_review_batch28.py
+ - tests/test_causal_review_batch29.py
+ - tests/test_causal_review_batch30.py
+ - tests/test_causal_review_batch31.py
+ - tests/test_causal_review_batch32.py
+ - tests/test_causal_review_batch33.py
+ - tests/test_causal_review_batch34.py
+ - tests/test_causal_review_batch35.py
+ - tests/test_causal_review_batch36.py
+ - tests/test_causal_review_batch37.py
+ - tests/test_causal_review_batch38.py
+ - tests/test_causal_review_batch39.py
+ - tests/test_causal_review_batch40.py
+ - tests/test_causal_review_batch41.py
+ - tests/test_causal_review_batch42.py
+ - tests/test_causal_review_batch43.py
+ - tests/test_causal_review_batch44.py
+ - tests/test_causal_review_batch45.py
+ - tests/test_causal_review_batch46.py
+ - tests/test_causal_review_batch47.py
+ - tests/test_causal_review_batch48.py
+ - tests/test_causal_review_batch49.py
+ - tests/test_causal_review_batch5.py
+ - tests/test_causal_review_batch50.py
+ - tests/test_causal_review_batch51.py
+ - tests/test_causal_review_batch52.py
+ - tests/test_causal_review_batch53.py
+ - tests/test_causal_review_batch54.py
+ - tests/test_causal_review_batch55.py
+ - tests/test_causal_review_batch56.py
+ - tests/test_causal_review_batch57.py
+ - tests/test_causal_review_batch58.py
+ - tests/test_causal_review_batch59.py
+ - tests/test_causal_review_batch6.py
+ - tests/test_causal_review_batch60.py
+ - tests/test_causal_review_batch61.py
+ - tests/test_causal_review_batch62.py
+ - tests/test_causal_review_batch63.py
+ - tests/test_causal_review_batch64.py
+ - tests/test_causal_review_batch65.py
+ - tests/test_causal_review_batch66.py
+ - tests/test_causal_review_batch67.py
+ - tests/test_causal_review_batch68.py
+ - tests/test_causal_review_batch69.py
+ - tests/test_causal_review_batch7.py
+ - tests/test_causal_review_batch70.py
+ - tests/test_causal_review_batch71.py
+ - tests/test_causal_review_batch72.py
+ - tests/test_causal_review_batch73.py
+ - tests/test_causal_review_batch74.py
+ - tests/test_causal_review_batch75.py
+ - tests/test_causal_review_batch76.py
+ - tests/test_causal_review_batch77.py
+ - tests/test_causal_review_batch78.py
+ - tests/test_causal_review_batch79.py
+ - tests/test_causal_review_batch8.py
+ - tests/test_causal_review_batch80.py
+ - tests/test_causal_review_batch81.py
+ - tests/test_causal_review_batch82.py
+ - tests/test_causal_review_batch83.py
+ - tests/test_causal_review_batch84.py
+ - tests/test_causal_review_batch85.py
+ - tests/test_causal_review_batch86.py
+ - tests/test_causal_review_batch87.py
+ - tests/test_causal_review_batch88.py
+ - tests/test_causal_review_batch89.py
+ - tests/test_causal_review_batch9.py
+ - tests/test_causal_review_batch90.py
+ - tests/test_causal_review_batch91.py
+ - tests/test_causal_review_batch92.py
+ - tests/test_causal_review_batch93.py
+ - tests/test_causal_review_batch94.py
+ - tests/test_causal_review_batch95.py
+ - tests/test_causal_review_batch96.py
+ - tests/test_causal_review_batch97.py
+ - tests/test_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: 1
+ expected_exit_codes:
+ - 0
+ log: /private/tmp/communitymech-batch97/verification-final/regressions-attempt1.log
+ log_sha256: 8fa08d48a4811313045065e543271e7296247431252649fd350220a53197978f
+ output_tail: "........................................................................ [ 8%]\n........................................................................\
+ \ [ 16%]\n........................................................................ [ 24%]\n........................................................................\
+ \ [ 32%]\n........................................................................ [ 40%]\n........................................................................\
+ \ [ 48%]\n........................................................................ [ 56%]\n........................................................................\
+ \ [ 64%]\n........................................................................ [ 72%]\n........................................................................\
+ \ [ 81%]\n........................................................................ [ 89%]\n...............F........................................................\
+ \ [ 97%]\n........................ [100%]\n===================================\
+ \ FAILURES ===================================\n_________________ test_the_corpus_is_unchanged_by_this_feature\
+ \ _________________\n\n def test_the_corpus_is_unchanged_by_this_feature():\n \"\"\"Only the records\
+ \ that mean to use the slot do.\n \n Asserted on the corpus rather than trusted from the schema:\
+ \ an\n `ifabsent` or a default that quietly populated the slot would change 312\n records' connectivity\
+ \ without anyone editing a record. That is still the\n failure this catches \u2014 a silent default\
+ \ would put every record in `users`,\n not just the three named below.\n \"\"\"\n users\
+ \ = {\n path.name\n for path in record_files()\n for interaction in (yaml.safe_load(path.read_text())\
+ \ or {}).get(\"ecological_interactions\")\n or []\n if isinstance(interaction, dict)\
+ \ and interaction.get(\"participating_taxa\")\n }\n> assert users == USERS, (\n f\"\
+ {len(users)} records use participating_taxa, expected {len(USERS)}. \"\n f\"Adding a user is fine\
+ \ \u2014 but the connectivity numbers in \"\n f\"tests/test_community_level_connectivity_credit.py\
+ \ were measured \"\n f\"before the slot was used, so re-check them and then update USERS. \"\n\
+ \ f\"Added: {sorted(users - USERS)}. Removed: {sorted(USERS - users)}\"\n )\nE AssertionError:\
+ \ 262 records use participating_taxa, expected 259. Adding a user is fine \u2014 but the connectivity numbers\
+ \ in tests/test_community_level_connectivity_credit.py were measured before the slot was used, so re-check\
+ \ them and then update USERS. Added: ['SMutans_CAlbicans_ECC_Biofilm.yaml', 'SMutans_SSputigena_ECC_Pathobiont.yaml',\
+ \ 'SMutans_VParvula_ASC_Biofilm.yaml']. Removed: []\nE assert {'AMD_Acidoph...re.yaml', ...} == {'AMD_Acidoph...re.yaml',\
+ \ ...}\nE \nE Extra items in the left set:\nE 'SMutans_CAlbicans_ECC_Biofilm.yaml'\n\
+ E 'SMutans_SSputigena_ECC_Pathobiont.yaml'\nE 'SMutans_VParvula_ASC_Biofilm.yaml'\nE \
+ \ Use -v to get more diff\n\ntests/test_participating_taxa.py:444: AssertionError\n===========================\
+ \ short test summary info ============================\nFAILED tests/test_participating_taxa.py::test_the_corpus_is_unchanged_by_this_feature\n\
+ 1 failed, 887 passed in 356.49s (0:05:56)\n"
+ disposition: Exact participant allowlist adds the three explicitly curated oral records after measured census;
+ equality guard remains. Full regression suite rerun.
+ initial_validation_snapshot:
+ path: /private/tmp/communitymech-batch97/validation-initial.json
+ sha256: 46a188ae9e6357498dbdd9175ba4e84c9e473ba37b3abd57fe08fbc9a128c4de
+ final_verification: false
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 399
+ mixed: 125
+ community_level_only: 274
+ taxa: 1536
+ credited_solely_by_the_rule: 1266
+ current:
+ records: 460
+ with_community_level: 402
+ mixed: 128
+ community_level_only: 274
+ taxa: 1542
+ credited_solely_by_the_rule: 1266
+ delta:
+ records: 0
+ with_community_level: 3
+ mixed: 3
+ community_level_only: 0
+ taxa: 6
+ credited_solely_by_the_rule: 0
+ interpretation: Three oral records now include community outcomes with exactly two named participants. Measured
+ records with community scope399->402,mixed125->128,taxa1536->1542;solely credited1266 unchanged. Bounds reflect
+ reviewed scope changes, not validator weakening.
+corpus:
+ records: 460
+ nodes: 1410
+ edges: 572
+ review_status_counts:
+ needs_research: 48
+ pending: 108
+ reviewed: 304
+limitations:
+- Four whole records, all11originalnodes and7arrows reviewed and retained, with5node renames. Four records changed.
+ No new topology, Edison dryrun, submission or credits.
+- Candida fresh primary abstract and PubMed figure captions read. Full-text XML retrieval returned HTTP500; complete
+ main text, figure pixels, supplements and raw data not reviewed. Mutualism and positive biofilm facilitation remain;
+ the rodent outcome is community-scoped and mediation PARTIAL.
+- Selenomonas fresh abstract1-30 and primary results/discussion210-575 read, including matrix-disruption and ex-vivo
+ evidence. Do not demote the supported structural direction to mere correlation. Human observations are cross-sectional;
+ the rodent mediation bridge is PARTIAL. No figure pixels, supplements or raw data reviewed.
+- Veillonella fresh abstract1-28 and results/discussion110-355 read, with initially truncated284-355 reread. Measured
+ expression and mixed fluorescence are not direct catalytic activity, species-resolved abundance or isolated mediation.
+ Rodent outcome is not proven human causation.
+- Battery fresh abstract1-24, results94-140,169-293,352-503, discussion504-606 and conclusions607-622 read. Predecessor
+ detoxification experiments and final-consortium EET evidence distinguished. Reciprocal neutral fitness and relative
+ direct/shuttle flux are not established. Existing scale-up discussion preserved.
+- Relevant cache abstracts and graph quotations checked, with long flattened cache output truncated; fresh structured
+ main-text sections used for the detailed review. Complete cache-body review is not claimed. All923caches unchanged;
+ no new primary body published.
+- All456otherrecords and non-graph raw blocks preserved. Six append-only histories, including two evidence-attachment
+ corrections. Taxonomy, culture conditions and engineering designs unchanged, not recertified. Two-member community
+ participant lists copy only canonical identity fields.
+- Fresh all-state issue title/body dedup and ignored/hidden-inclusive local search with .git/docs/site/references_cache
+ excluded; relevant caches separately inspected. Prior941/942 read and distinct. PRs/comments not exhaustively
+ searched. Repair1772-1775 close only after protected-main merge; non-graph1776 remains open.
+- Source-based self-adversarial review is not independent approval or corpus completion. Loader1703 and DOI-cache
+ casing1091 remain outside scope. Denied/pending Edison scopes unchanged. No pathogen-enhancement instructions,
+ wet-lab protocol or new mechanism added. Validation and publication not preasserted.
+- Initial regression:887passed/1failed because the explicit participant allowlist lacked the three newly curated
+ oral records. Added exactly those three entries after measured census; equality guard retained. Failed output
+ and initial validation snapshot preserved; full regression rerun, unchanged earlier gates digest-checked on resume.
diff --git a/reports/causal_graph_review/cache-provenance-20261007-batch97.json b/reports/causal_graph_review/cache-provenance-20261007-batch97.json
new file mode 100644
index 000000000..1936df74b
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261007-batch97.json
@@ -0,0 +1,60 @@
+{
+ "changes": [],
+ "baseline_files_preserved": 923,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch97/baseline.json": "ede5a161ca66c4bdc6450d19e779fbc3d2aee08d7afcf0a9c9e57a8a8dd8567e",
+ "/private/tmp/communitymech-batch97/battery-metadata.json": "41c656be7622aa22ea8f1b1af1052729928654dec4af9fd9441ece3506cb88a9",
+ "/private/tmp/communitymech-batch97/battery-primary.txt": "c01a8e04eb7f10ce2c359f988ac0c42275e8208195bb2c1577981e929c9ea8dc",
+ "/private/tmp/communitymech-batch97/battery-primary.xml": "91e9a5ca80f57d058e20707f7c5e8c0e07ca1a1b1d267831eee06fc697d4621e",
+ "/private/tmp/communitymech-batch97/candida-metadata.json": "5a2349f942517b545c9adabee4dc27b3857f583e1c77864a1ea9f8da56c85c18",
+ "/private/tmp/communitymech-batch97/candida-primary.txt": "9bab45b340bd4b71ef7bd10f3107c3728150b535362ee17d5b26d97e77642407",
+ "/private/tmp/communitymech-batch97/dedup-local-current.txt": "970144be8ba390676ebb5ef401aa4e015f015eb44d4076538383808dc3912e11",
+ "/private/tmp/communitymech-batch97/issue-dedup-current.json": "54ba4e90fb91134e9dd418e979b22e73dca8848c084ae4723f92130ec67fdbf4",
+ "/private/tmp/communitymech-batch97/primary-manifest.json": "84767fd3690ee33c6b12e409ab182280b670caf32644c48a8451b0bd35d8ede9",
+ "/private/tmp/communitymech-batch97/selenomonas-metadata.json": "8e54de31eea5cdae31582b47f20b3eea046ad50d3a74ec5b64cbf004256c05b9",
+ "/private/tmp/communitymech-batch97/selenomonas-primary.txt": "3ef65121edd043a85bc01bec5f70ff7e4388e7cb3b61c6a980ad3ef2c4fce7aa",
+ "/private/tmp/communitymech-batch97/selenomonas-primary.xml": "aa6cc5944d1f9b128ea7003bc381371413eac96a593f95172cbcf037f9fde0f4",
+ "/private/tmp/communitymech-batch97/veillonella-metadata.json": "92548fa0d732f063abaf3da33909e5c8044e581b3922020a22e3fa8702c7d4f3",
+ "/private/tmp/communitymech-batch97/veillonella-primary.txt": "11f5ef4450510023a026dfed4f22fe159f37a9c8ff77dc1a51f99cc4bfd11266",
+ "/private/tmp/communitymech-batch97/veillonella-primary.xml": "a984fc8e39a1253c545f4a6ec88549a5a473d79d70888d950a1ede7fe06334a1",
+ "references_cache/PMID_24566629.txt": "9a07e4ed752845aa4cca4470f6cd618d0e20751ba2ee54f7b8d41b82dac33f8f",
+ "references_cache/PMID_37217495.txt": "a8a73065c6c19e26d3c06834c1ac8f73490d89fd8ba8c58e88d574488a229964",
+ "references_cache/PMID_39345197.txt": "6eb5c9e68d24684185a4d1d34637456094f19ff7411843713f809e935ac9ed7f",
+ "references_cache/PMID_42733304.txt": "a764e9f7ae1279fae1376f52eb6f7422a012d9f7da9bcaf224de7dbdb27b7fce"
+ },
+ "source_access": [
+ {
+ "reference": "PMID:24566629",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A24566629+AND+SRC%3AMED&format=json&resultType=core",
+ "accessed_scope": "Candida fresh primary abstract and PubMed figure captions read. Full-text XML retrieval returned HTTP500; complete main text, figure pixels, supplements and raw data not reviewed. Mutualism and positive biofilm facilitation remain; the rodent outcome is community-scoped and mediation PARTIAL.",
+ "fulltext_error": "XML returned HTTP500; no full text retrieved."
+ },
+ {
+ "reference": "PMID:37217495",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10202936/fullTextXML",
+ "accessed_scope": "Selenomonas fresh abstract1-30 and primary results/discussion210-575 read, including matrix-disruption and ex-vivo evidence. Do not demote the supported structural direction to mere correlation. Human observations are cross-sectional; the rodent mediation bridge is PARTIAL. No figure pixels, supplements or raw data reviewed.",
+ "fulltext_error": null
+ },
+ {
+ "reference": "PMID:39345197",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11537095/fullTextXML",
+ "accessed_scope": "Veillonella fresh abstract1-28 and results/discussion110-355 read, with initially truncated284-355 reread. Measured expression and mixed fluorescence are not direct catalytic activity, species-resolved abundance or isolated mediation. Rodent outcome is not proven human causation.",
+ "fulltext_error": null
+ },
+ {
+ "reference": "PMID:42733304",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13572860/fullTextXML",
+ "accessed_scope": "Battery fresh abstract1-24, results94-140,169-293,352-503, discussion504-606 and conclusions607-622 read. Predecessor detoxification experiments and final-consortium EET evidence distinguished. Reciprocal neutral fitness and relative direct/shuttle flux are not established. Existing scale-up discussion preserved.",
+ "fulltext_error": null
+ }
+ ],
+ "limitations": [
+ "Four whole records, all11originalnodes and7arrows reviewed and retained, with5node renames. Four records changed. No new topology, Edison dryrun, submission or credits.",
+ "Candida fresh primary abstract and PubMed figure captions read. Full-text XML retrieval returned HTTP500; complete main text, figure pixels, supplements and raw data not reviewed. Mutualism and positive biofilm facilitation remain; the rodent outcome is community-scoped and mediation PARTIAL.",
+ "Selenomonas fresh abstract1-30 and primary results/discussion210-575 read, including matrix-disruption and ex-vivo evidence. Do not demote the supported structural direction to mere correlation. Human observations are cross-sectional; the rodent mediation bridge is PARTIAL. No figure pixels, supplements or raw data reviewed.",
+ "Veillonella fresh abstract1-28 and results/discussion110-355 read, with initially truncated284-355 reread. Measured expression and mixed fluorescence are not direct catalytic activity, species-resolved abundance or isolated mediation. Rodent outcome is not proven human causation.",
+ "Battery fresh abstract1-24, results94-140,169-293,352-503, discussion504-606 and conclusions607-622 read. Predecessor detoxification experiments and final-consortium EET evidence distinguished. Reciprocal neutral fitness and relative direct/shuttle flux are not established. Existing scale-up discussion preserved.",
+ "Relevant cache abstracts and graph quotations checked, with long flattened cache output truncated; fresh structured main-text sections used for the detailed review. Complete cache-body review is not claimed. All923caches unchanged; no new primary body published.",
+ "All456otherrecords and non-graph raw blocks preserved. Six append-only histories, including two evidence-attachment corrections. Taxonomy, culture conditions and engineering designs unchanged, not recertified. Two-member community participant lists copy only canonical identity fields."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml b/reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
new file mode 100644
index 000000000..5233ea30e
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
@@ -0,0 +1,584 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: c33f6896716f6cfa4ccaac9b3ad97359de0674f9
+baseline_commit: c33f6896716f6cfa4ccaac9b3ad97359de0674f9
+base_tree: fc57e4db87610250b8e83800970d3fa200a1d3c3
+pre_source_baseline_sha256: ede5a161ca66c4bdc6450d19e779fbc3d2aee08d7afcf0a9c9e57a8a8dd8567e
+issues:
+- 1772
+- 1773
+- 1774
+- 1775
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1776
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 1033
+ matching_issues:
+ - 941
+ - 942
+ ignored_hidden_local_search: true
+source_access:
+- reference: PMID:24566629
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A24566629+AND+SRC%3AMED&format=json&resultType=core
+ accessed_scope: Candida fresh primary abstract and PubMed figure captions read. Full-text XML retrieval returned
+ HTTP500; complete main text, figure pixels, supplements and raw data not reviewed. Mutualism and positive biofilm
+ facilitation remain; the rodent outcome is community-scoped and mediation PARTIAL.
+ fulltext_error: XML returned HTTP500; no full text retrieved.
+- reference: PMID:37217495
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10202936/fullTextXML
+ accessed_scope: Selenomonas fresh abstract1-30 and primary results/discussion210-575 read, including matrix-disruption
+ and ex-vivo evidence. Do not demote the supported structural direction to mere correlation. Human observations
+ are cross-sectional; the rodent mediation bridge is PARTIAL. No figure pixels, supplements or raw data reviewed.
+ fulltext_error: null
+- reference: PMID:39345197
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11537095/fullTextXML
+ accessed_scope: Veillonella fresh abstract1-28 and results/discussion110-355 read, with initially truncated284-355
+ reread. Measured expression and mixed fluorescence are not direct catalytic activity, species-resolved abundance
+ or isolated mediation. Rodent outcome is not proven human causation.
+ fulltext_error: null
+- reference: PMID:42733304
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13572860/fullTextXML
+ accessed_scope: Battery fresh abstract1-24, results94-140,169-293,352-503, discussion504-606 and conclusions607-622
+ read. Predecessor detoxification experiments and final-consortium EET evidence distinguished. Reciprocal neutral
+ fitness and relative direct/shuttle flux are not established. Existing scale-up discussion preserved.
+ fulltext_error: null
+primary_artifacts:
+ /private/tmp/communitymech-batch97/baseline.json: ede5a161ca66c4bdc6450d19e779fbc3d2aee08d7afcf0a9c9e57a8a8dd8567e
+ /private/tmp/communitymech-batch97/battery-metadata.json: 41c656be7622aa22ea8f1b1af1052729928654dec4af9fd9441ece3506cb88a9
+ /private/tmp/communitymech-batch97/battery-primary.txt: c01a8e04eb7f10ce2c359f988ac0c42275e8208195bb2c1577981e929c9ea8dc
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+ /private/tmp/communitymech-batch97/candida-metadata.json: 5a2349f942517b545c9adabee4dc27b3857f583e1c77864a1ea9f8da56c85c18
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+ /private/tmp/communitymech-batch97/primary-manifest.json: 84767fd3690ee33c6b12e409ab182280b670caf32644c48a8451b0bd35d8ede9
+ /private/tmp/communitymech-batch97/selenomonas-metadata.json: 8e54de31eea5cdae31582b47f20b3eea046ad50d3a74ec5b64cbf004256c05b9
+ /private/tmp/communitymech-batch97/selenomonas-primary.txt: 3ef65121edd043a85bc01bec5f70ff7e4388e7cb3b61c6a980ad3ef2c4fce7aa
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+ /private/tmp/communitymech-batch97/veillonella-primary.xml: a984fc8e39a1253c545f4a6ec88549a5a473d79d70888d950a1ede7fe06334a1
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+ references_cache/PMID_37217495.txt: a8a73065c6c19e26d3c06834c1ac8f73490d89fd8ba8c58e88d574488a229964
+ references_cache/PMID_39345197.txt: 6eb5c9e68d24684185a4d1d34637456094f19ff7411843713f809e935ac9ed7f
+ references_cache/PMID_42733304.txt: a764e9f7ae1279fae1376f52eb6f7422a012d9f7da9bcaf224de7dbdb27b7fce
+ /private/tmp/communitymech-batch97/validation-initial.json: 46a188ae9e6357498dbdd9175ba4e84c9e473ba37b3abd57fe08fbc9a128c4de
+ /private/tmp/communitymech-batch97/verification-final/regressions-attempt1.log: 8fa08d48a4811313045065e543271e7296247431252649fd350220a53197978f
+primary_graph_snippet_count: 16
+snippet_checks:
+- record: SMutans_CAlbicans_ECC_Biofilm
+ node: Cross-Kingdom Biofilm Enhancement
+ evidence_index: 0
+ reference: PMID:24566629
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/candida-primary.txt
+ cache_artifact: references_cache/PMID_24566629.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_CAlbicans_ECC_Biofilm
+ node: Candida-Driven EPS Amplification of Streptococcus mutans
+ evidence_index: 0
+ reference: PMID:24566629
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/candida-primary.txt
+ cache_artifact: references_cache/PMID_24566629.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_CAlbicans_ECC_Biofilm
+ node: Rodent Coinfection Carriage and Caries Outcome
+ evidence_index: 0
+ reference: PMID:24566629
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/candida-primary.txt
+ cache_artifact: references_cache/PMID_24566629.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_CAlbicans_ECC_Biofilm
+ node: Rodent Coinfection Carriage and Caries Outcome
+ evidence_index: 1
+ reference: PMID:24566629
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/candida-primary.txt
+ cache_artifact: references_cache/PMID_24566629.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_SSputigena_ECC_Pathobiont
+ node: Streptococcal Exoglucan Entrapment of Selenomonas sputigena
+ evidence_index: 0
+ reference: PMID:37217495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/selenomonas-primary.txt
+ cache_artifact: references_cache/PMID_37217495.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_SSputigena_ECC_Pathobiont
+ node: Honeycomb Biofilm Acidogenesis
+ evidence_index: 0
+ reference: PMID:37217495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/selenomonas-primary.txt
+ cache_artifact: references_cache/PMID_37217495.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_SSputigena_ECC_Pathobiont
+ node: Rodent Coinfection Caries Outcome
+ evidence_index: 0
+ reference: PMID:37217495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/selenomonas-primary.txt
+ cache_artifact: references_cache/PMID_37217495.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_VParvula_ASC_Biofilm
+ node: Veillonella-Associated gtf Expression and Mixed-Biofilm EPS
+ evidence_index: 0
+ reference: PMID:39345197
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/veillonella-primary.txt
+ cache_artifact: references_cache/PMID_39345197.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_VParvula_ASC_Biofilm
+ node: Veillonella-Associated gtf Expression and Mixed-Biofilm EPS
+ evidence_index: 1
+ reference: PMID:39345197
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/veillonella-primary.txt
+ cache_artifact: references_cache/PMID_39345197.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_VParvula_ASC_Biofilm
+ node: Mixed-Biofilm and Stress-Response Phenotypes
+ evidence_index: 0
+ reference: PMID:39345197
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/veillonella-primary.txt
+ cache_artifact: references_cache/PMID_39345197.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_VParvula_ASC_Biofilm
+ node: Rodent Coinfection Caries Outcome
+ evidence_index: 0
+ reference: PMID:39345197
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/veillonella-primary.txt
+ cache_artifact: references_cache/PMID_39345197.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SO3_BS3_Lithium_Battery_Bioleaching_Consortium
+ node: BS3 ethanol detoxification of brewing wastewater
+ evidence_index: 0
+ reference: PMID:42733304
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/battery-primary.txt
+ cache_artifact: references_cache/PMID_42733304.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SO3_BS3_Lithium_Battery_Bioleaching_Consortium
+ node: MtrC/OmcA and riboflavin NCM reduction
+ evidence_index: 0
+ reference: PMID:42733304
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/battery-primary.txt
+ cache_artifact: references_cache/PMID_42733304.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SO3_BS3_Lithium_Battery_Bioleaching_Consortium
+ node: MtrC/OmcA and riboflavin NCM reduction
+ evidence_index: 1
+ reference: PMID:42733304
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/battery-primary.txt
+ cache_artifact: references_cache/PMID_42733304.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_SSputigena_ECC_Pathobiont
+ node: Honeycomb Biofilm Acidogenesis
+ evidence_index: 1
+ reference: PMID:37217495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/selenomonas-primary.txt
+ cache_artifact: references_cache/PMID_37217495.txt
+ scope: Direct result quotation added after source-based adversarial diff review; normalized match to fresh primary
+ text and maintained cache.
+- record: SO3_BS3_Lithium_Battery_Bioleaching_Consortium
+ node: MtrC/OmcA and riboflavin NCM reduction
+ evidence_index: 2
+ reference: PMID:42733304
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/battery-primary.txt
+ cache_artifact: references_cache/PMID_42733304.txt
+ scope: Direct result quotation added after source-based adversarial diff review; normalized match to fresh primary
+ text and maintained cache.
+discussion_snippet_checks:
+- record: SMutans_CAlbicans_ECC_Biofilm
+ node: candida_graph_evidence_and_model_scope
+ evidence_index: 0
+ reference: PMID:24566629
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/candida-primary.txt
+ cache_artifact: references_cache/PMID_24566629.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_SSputigena_ECC_Pathobiont
+ node: selenomonas_graph_evidence_and_model_scope
+ evidence_index: 0
+ reference: PMID:37217495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/selenomonas-primary.txt
+ cache_artifact: references_cache/PMID_37217495.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SMutans_VParvula_ASC_Biofilm
+ node: veillonella_graph_evidence_and_model_scope
+ evidence_index: 0
+ reference: PMID:39345197
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/veillonella-primary.txt
+ cache_artifact: references_cache/PMID_39345197.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+- record: SO3_BS3_Lithium_Battery_Bioleaching_Consortium
+ node: battery_graph_evidence_and_model_scope
+ evidence_index: 0
+ reference: PMID:42733304
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch97/battery-primary.txt
+ cache_artifact: references_cache/PMID_42733304.txt
+ scope: Literal-normalized quotation matched to fresh primary text and maintained cache; entailment separately
+ reviewed.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Correct existing node categories, source modality and mediation strength; retain all existing directions
+ without new topology.
+limitations:
+- Four whole records, all11originalnodes and7arrows reviewed and retained, with5node renames. Four records changed.
+ No new topology, Edison dryrun, submission or credits.
+- Candida fresh primary abstract and PubMed figure captions read. Full-text XML retrieval returned HTTP500; complete
+ main text, figure pixels, supplements and raw data not reviewed. Mutualism and positive biofilm facilitation remain;
+ the rodent outcome is community-scoped and mediation PARTIAL.
+- Selenomonas fresh abstract1-30 and primary results/discussion210-575 read, including matrix-disruption and ex-vivo
+ evidence. Do not demote the supported structural direction to mere correlation. Human observations are cross-sectional;
+ the rodent mediation bridge is PARTIAL. No figure pixels, supplements or raw data reviewed.
+- Veillonella fresh abstract1-28 and results/discussion110-355 read, with initially truncated284-355 reread. Measured
+ expression and mixed fluorescence are not direct catalytic activity, species-resolved abundance or isolated mediation.
+ Rodent outcome is not proven human causation.
+- Battery fresh abstract1-24, results94-140,169-293,352-503, discussion504-606 and conclusions607-622 read. Predecessor
+ detoxification experiments and final-consortium EET evidence distinguished. Reciprocal neutral fitness and relative
+ direct/shuttle flux are not established. Existing scale-up discussion preserved.
+- Relevant cache abstracts and graph quotations checked, with long flattened cache output truncated; fresh structured
+ main-text sections used for the detailed review. Complete cache-body review is not claimed. All923caches unchanged;
+ no new primary body published.
+- All456otherrecords and non-graph raw blocks preserved. Six append-only histories, including two evidence-attachment
+ corrections. Taxonomy, culture conditions and engineering designs unchanged, not recertified. Two-member community
+ participant lists copy only canonical identity fields.
+- Fresh all-state issue title/body dedup and ignored/hidden-inclusive local search with .git/docs/site/references_cache
+ excluded; relevant caches separately inspected. Prior941/942 read and distinct. PRs/comments not exhaustively
+ searched. Repair1772-1775 close only after protected-main merge; non-graph1776 remains open.
+- Source-based self-adversarial review is not independent approval or corpus completion. Loader1703 and DOI-cache
+ casing1091 remain outside scope. Denied/pending Edison scopes unchanged. No pathogen-enhancement instructions,
+ wet-lab protocol or new mechanism added. Validation and publication not preasserted.
+- Initial regression:887passed/1failed because the explicit participant allowlist lacked the three newly curated
+ oral records. Added exactly those three entries after measured census; equality guard retained. Failed output
+ and initial validation snapshot preserved; full regression rerun, unchanged earlier gates digest-checked on resume.
+records:
+- path: kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml
+ id: CommunityMech:000083
+ original_sha256: fd497717e1b5fc11f099628ab6f666617da3b94f9b7237c533b766586a1134bc
+ record_sha256: fb7d747151fb52f52127e035683a77dcb1596d6f1fc97ac1e8635298ce24fd34
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
+ scope: Whole record and every existing node/direction reviewed, with source-access limits; not new-mechanism discovery
+ or non-graph certification.
+ summary: Retain supported mutualism and a PARTIAL rodent-outcome direction.; Retain positive Candida-to-S. mutans
+ biofilm facilitation with the correct in-vitro source.; Retain the positive rodent carriage/lesion outcome at
+ community scope, not pairwise colonization.
+ node_decisions:
+ - node: Cross-Kingdom Biofilm Enhancement
+ rationale: Retain supported mutualism and a PARTIAL rodent-outcome direction.
+ - node: Candida-Driven EPS Amplification of Streptococcus mutans
+ rationale: Retain positive Candida-to-S. mutans biofilm facilitation with the correct in-vitro source.
+ - node: Rodent Coinfection Carriage and Caries Outcome
+ rationale: Retain the positive rodent carriage/lesion outcome at community scope, not pairwise colonization.
+ removed_node_decisions: []
+ renamed_nodes:
+ Synergistic Caries Virulence: Rodent Coinfection Carriage and Caries Outcome
+ edges_before:
+ - &id001
+ source: Cross-Kingdom Biofilm Enhancement
+ target: Synergistic Caries Virulence
+ description: The enhanced dual-species plaque biofilm is the infection state that drives higher microbial carriage
+ and more aggressive carious lesions in vivo.
+ - &id003
+ source: Candida-Driven EPS Amplification of Streptococcus mutans
+ target: Cross-Kingdom Biofilm Enhancement
+ description: Candida-driven exopolysaccharide accumulation increases the biomass and viable S. mutans burden
+ of the cross-kingdom plaque biofilm.
+ edges_after:
+ - &id002
+ source: Cross-Kingdom Biofilm Enhancement
+ target: Rodent Coinfection Carriage and Caries Outcome
+ description: 'PARTIAL: the mixed biofilm provides the proposed context for the greater disease severity in the
+ rodent model. Coinfection establishes an effect on carriage and lesions, but does not isolate biofilm quantity
+ as the necessary mediator of the lesion outcome or establish human disease causation.'
+ - &id004
+ source: Candida-Driven EPS Amplification of Streptococcus mutans
+ target: Cross-Kingdom Biofilm Enhancement
+ description: Candida-driven exopolysaccharide accumulation increases the biomass and viable S. mutans burden
+ of the cross-kingdom plaque biofilm.
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: Existing direction retained with source-specific community or PARTIAL mediation limits.
+ - before: *id003
+ after: *id004
+ rationale: Existing direction retained with source-specific community or PARTIAL mediation limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:24566629
+ issues:
+ - 1772
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/SMutans_CAlbicans_ECC_Biofilm/2026-10-07T184553Z-codex-1564ae.yaml
+- path: kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml
+ id: CommunityMech:000084
+ original_sha256: 8f05ef662f7d86883b11f0d480776d2baa9208bc7170926e9d871aa93745bbfa
+ record_sha256: 8c32ed74a997011d25ad1e3501b42f6da246ba28e23d58a85a92ee9fad169846
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
+ scope: Whole record and every existing node/direction reviewed, with source-access limits; not new-mechanism discovery
+ or non-graph certification.
+ summary: Retain supported directional colonization facilitation and the existing structural link, correcting modality.;
+ Retain community structure and acidogenesis, with positive perturbation evidence and PARTIAL in-vivo mediation.;
+ Retain the rodent disease comparison at two-member community scope.
+ node_decisions:
+ - node: Streptococcal Exoglucan Entrapment of Selenomonas sputigena
+ rationale: Retain supported directional colonization facilitation and the existing structural link, correcting
+ modality.
+ - node: Honeycomb Biofilm Acidogenesis
+ rationale: Retain community structure and acidogenesis, with positive perturbation evidence and PARTIAL in-vivo
+ mediation.
+ - node: Rodent Coinfection Caries Outcome
+ rationale: Retain the rodent disease comparison at two-member community scope.
+ removed_node_decisions: []
+ renamed_nodes:
+ Pathobiont-Enhanced Cariogenicity: Rodent Coinfection Caries Outcome
+ edges_before:
+ - &id005
+ source: Streptococcal Exoglucan Entrapment of Selenomonas sputigena
+ target: Honeycomb Biofilm Acidogenesis
+ description: Exoglucan entrapment immobilizes and supports S. sputigena in the mixed biofilm, leading to a honeycomb-like
+ superstructure around S. mutans that enhances acidogenesis.
+ - &id007
+ source: Honeycomb Biofilm Acidogenesis
+ target: Pathobiont-Enhanced Cariogenicity
+ description: The structured S. mutans-S. sputigena biofilm intensifies acidogenesis, providing the local virulence
+ context for the extensive enamel lesions observed during coinfection.
+ edges_after:
+ - &id006
+ source: Streptococcal Exoglucan Entrapment of Selenomonas sputigena
+ target: Honeycomb Biofilm Acidogenesis
+ description: Exoglucan entrapment immobilizes and supports S. sputigena in the mixed biofilm, leading to a honeycomb-like
+ superstructure around S. mutans that enhances acidogenesis.
+ - &id008
+ source: Honeycomb Biofilm Acidogenesis
+ target: Rodent Coinfection Caries Outcome
+ description: 'PARTIAL: the structured acidic biofilm is the proposed mediator of the rodent lesion outcome.
+ The primary in-vitro disruption and ex-vivo enamel results support the structure-to-damage interpretation,
+ while the rodent coinfection comparison does not independently isolate that mediator in vivo.'
+ retained_edge_decisions:
+ - before: *id005
+ after: *id006
+ rationale: Existing direction retained with source-specific community or PARTIAL mediation limits.
+ - before: *id007
+ after: *id008
+ rationale: Existing direction retained with source-specific community or PARTIAL mediation limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:37217495
+ issues:
+ - 1773
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 2
+ history_files:
+ - history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T184554Z-codex-0f7a08.yaml
+ - history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T185016Z-codex-9c291b.yaml
+- path: kb/communities/SMutans_VParvula_ASC_Biofilm.yaml
+ id: CommunityMech:000085
+ original_sha256: e338cc985345cc89832ac86fb78cf530ea0383cf81506b18f7a8b4159408e54f
+ record_sha256: 1c331f8546d510e5a20819f77901353203ba43b317c92f5bdb4ad8ab2364e265
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
+ scope: Whole record and every existing node/direction reviewed, with source-access limits; not new-mechanism discovery
+ or non-graph certification.
+ summary: Retain measured expression and EPS, not direct enzyme activity or colonization.; Retain in-vitro composite
+ phenotypes at community scope with correct modality.; Retain the positive rodent outcome, not proven human adult
+ causation.
+ node_decisions:
+ - node: Veillonella-Associated gtf Expression and Mixed-Biofilm EPS
+ rationale: Retain measured expression and EPS, not direct enzyme activity or colonization.
+ - node: Mixed-Biofilm and Stress-Response Phenotypes
+ rationale: Retain in-vitro composite phenotypes at community scope with correct modality.
+ - node: Rodent Coinfection Caries Outcome
+ rationale: Retain the positive rodent outcome, not proven human adult causation.
+ removed_node_decisions: []
+ renamed_nodes:
+ Veillonella parvula Boost of Streptococcus mutans Glucosyltransferase-EPS Output: Veillonella-Associated gtf
+ Expression and Mixed-Biofilm EPS
+ Veillonella parvula Promotion of Streptococcus mutans Biofilm Virulence: Mixed-Biofilm and Stress-Response Phenotypes
+ Pathobiont-Driven Adult Severe Caries Exacerbation: Rodent Coinfection Caries Outcome
+ edges_before:
+ - &id009
+ source: Veillonella parvula Boost of Streptococcus mutans Glucosyltransferase-EPS Output
+ target: Veillonella parvula Promotion of Streptococcus mutans Biofilm Virulence
+ description: Increased S. mutans glucosyltransferase expression and EPS production strengthen the sucrose-grown
+ mixed biofilm matrix that V. parvula makes denser and more viable.
+ - &id011
+ source: Veillonella parvula Promotion of Streptococcus mutans Biofilm Virulence
+ target: Pathobiont-Driven Adult Severe Caries Exacerbation
+ description: Veillonella-driven mature biofilm formation and stress tolerance set up the dual-species biofilm
+ virulence measured as worsened rodent caries.
+ edges_after:
+ - &id010
+ source: Veillonella-Associated gtf Expression and Mixed-Biofilm EPS
+ target: Mixed-Biofilm and Stress-Response Phenotypes
+ description: 'PARTIAL: increased EPS is proposed to contribute to the observed mixed-biofilm phenotype. The
+ expression and imaging comparisons do not independently isolate the expression-to-phenotype mediator or establish
+ its contribution to the separate stress-response assays.'
+ - &id012
+ source: Mixed-Biofilm and Stress-Response Phenotypes
+ target: Rodent Coinfection Caries Outcome
+ description: 'PARTIAL: the in-vitro phenotypes are proposed contributors to the greater rodent disease outcome.
+ The coinfection experiment supports the overall disease effect, but does not independently identify which
+ phenotype mediates it or prove a causal effect in adults.'
+ retained_edge_decisions:
+ - before: *id009
+ after: *id010
+ rationale: Existing direction retained with source-specific community or PARTIAL mediation limits.
+ - before: *id011
+ after: *id012
+ rationale: Existing direction retained with source-specific community or PARTIAL mediation limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:39345197
+ issues:
+ - 1774
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/SMutans_VParvula_ASC_Biofilm/2026-10-07T184554Z-codex-a80c30.yaml
+- path: kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml
+ id: CommunityMech:000385
+ original_sha256: bd1ee43066c9eb8bfb9b64e9eaa643070de41a0662cc4aeed2881294c2c5793a
+ record_sha256: b70b100dcdc43b4caf560b3794f0165db3b7c99410a7ba8d5b811825ebdceef4
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml
+ scope: Whole record and every existing node/direction reviewed, with source-access limits; not new-mechanism discovery
+ or non-graph certification.
+ summary: Retain detoxification and its leaching direction without an unsupported neutral-partner fitness claim.;
+ Retain the primary EET interpretation while distinguishing perturbation support from quantitative flux partition.
+ node_decisions:
+ - node: BS3 ethanol detoxification of brewing wastewater
+ rationale: Retain detoxification and its leaching direction without an unsupported neutral-partner fitness claim.
+ - node: MtrC/OmcA and riboflavin NCM reduction
+ rationale: Retain the primary EET interpretation while distinguishing perturbation support from quantitative
+ flux partition.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id013
+ source: BS3 ethanol detoxification of brewing wastewater
+ target: MtrC/OmcA and riboflavin NCM reduction
+ description: Removing ethanol relieves inhibition of the S. oneidensis EET machinery that reduces NCM for metal
+ oxide leaching.
+ edges_after:
+ - &id014
+ source: BS3 ethanol detoxification of brewing wastewater
+ target: MtrC/OmcA and riboflavin NCM reduction
+ description: Ethanol removal relieves inhibition of Shewanella electron transfer and thereby supports NCM leaching
+ in the authors' consortium model. The detoxification comparisons were conducted in predecessor strains; the
+ final SO3-BS3 synthesis retains this function, without separately isolating its quantitative contribution
+ from the other modifications.
+ retained_edge_decisions:
+ - before: *id013
+ after: *id014
+ rationale: Existing direction retained with source-specific community or PARTIAL mediation limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:42733304
+ issues:
+ - 1775
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 2
+ history_files:
+ - history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T184554Z-codex-3515ec.yaml
+ - history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T185016Z-codex-8bc7a6.yaml
+adversarial_prepublication_fix:
+ findings:
+ - issue: 1773
+ details: Attach direct primary-result evidence to the retained Honeycomb Biofilm Acidogenesis interpretation
+ after adversarial diff review; no new node, direction, mechanism or protocol.
+ preserved_initial_histories:
+ history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T184554Z-codex-0f7a08.yaml: 6489f27ee2b5c35d4131815469e2761ff1cd7e3ed53a87bb08782f65d1739230
+ correction_history: history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T185016Z-codex-9c291b.yaml
+ - issue: 1775
+ details: Attach direct primary-result evidence to the retained MtrC/OmcA and riboflavin NCM reduction interpretation
+ after adversarial diff review; no new node, direction, mechanism or protocol.
+ preserved_initial_histories:
+ history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T184554Z-codex-3515ec.yaml: fa0a65de9df956d2143f1370a94d1aacec667c3ba2280b3fa7f2664060aa798b
+ correction_history: history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T185016Z-codex-8bc7a6.yaml
+ timing: Both corrections preceded final validation; no interrupted verification attempt.
+ participant_fixture_correction:
+ details: Initial regression:887passed/1failed because the explicit participant allowlist lacked the three newly
+ curated oral records. Added exactly those three entries after measured census; equality guard retained. Failed
+ output and initial validation snapshot preserved; full regression rerun, unchanged earlier gates digest-checked
+ on resume.
+ failed_output: /private/tmp/communitymech-batch97/verification-final/regressions-attempt1.log
+ failed_output_sha256: 8fa08d48a4811313045065e543271e7296247431252649fd350220a53197978f
+ initial_snapshot: /private/tmp/communitymech-batch97/validation-initial.json
+ initial_snapshot_sha256: 46a188ae9e6357498dbdd9175ba4e84c9e473ba37b3abd57fe08fbc9a128c4de
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 5798a14a6..367edfeb8 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -348,10 +348,10 @@ kb/communities/Rifle_Uranium_Reducing_Community.yaml CommunityMech:000060 5232c8
kb/communities/Rumen_Substrate_Adapted_Lignocellulose_Enrichment_Consortia.yaml CommunityMech:000389 410363912e73521cefc995b7bbc58bd97e0390cf4c3197215346dde0aa2bcf80 3 1 80.0 reports/causal_graph_review/decisions/20261007-four-records-batch96.yaml reviewed
kb/communities/SF356_Cellulose_Degrader.yaml CommunityMech:000061 0d056f8e6b611f25f39e521ad50507e2c5ef40a4a68a4a6da983d36dd45b5733 4 3 95.0 reports/causal_graph_review/decisions/20261007-four-records-batch96.yaml reviewed
kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml CommunityMech:000080 c2acfe799a9cf91799a1238d5ca2c5b23b7020e6182055aa0cefea75799bfef0 3 0 68.3 reports/causal_graph_review/decisions/20261007-four-records-batch96.yaml reviewed
-kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml CommunityMech:000083 fd497717e1b5fc11f099628ab6f666617da3b94f9b7237c533b766586a1134bc 3 2 100.0 pending
-kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml CommunityMech:000084 8f05ef662f7d86883b11f0d480776d2baa9208bc7170926e9d871aa93745bbfa 3 2 100.0 pending
-kb/communities/SMutans_VParvula_ASC_Biofilm.yaml CommunityMech:000085 e338cc985345cc89832ac86fb78cf530ea0383cf81506b18f7a8b4159408e54f 3 2 100.0 pending
-kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml CommunityMech:000385 bd1ee43066c9eb8bfb9b64e9eaa643070de41a0662cc4aeed2881294c2c5793a 2 1 80.0 pending
+kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml CommunityMech:000083 fb7d747151fb52f52127e035683a77dcb1596d6f1fc97ac1e8635298ce24fd34 3 2 96.7 reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml reviewed
+kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml CommunityMech:000084 8c32ed74a997011d25ad1e3501b42f6da246ba28e23d58a85a92ee9fad169846 3 2 93.3 reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml reviewed
+kb/communities/SMutans_VParvula_ASC_Biofilm.yaml CommunityMech:000085 1c331f8546d510e5a20819f77901353203ba43b317c92f5bdb4ad8ab2364e265 3 2 90.0 reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml reviewed
+kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml CommunityMech:000385 b70b100dcdc43b4caf560b3794f0165db3b7c99410a7ba8d5b811825ebdceef4 2 1 75.0 reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml reviewed
kb/communities/SPRUCE_Peatland_Methane_Cycling_Community.yaml CommunityMech:000135 59b8348c81bd5f061d065274bcdf97ca9fd489bff10670286ee9c4c95b60cd47 3 2 100.0 pending
kb/communities/SPRUCE_Peatland_Warming_Community.yaml CommunityMech:000319 b46447214a813d8672657826db35ba07d47c7a42148a15776953519917d9472d 4 2 100.0 pending
kb/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.yaml CommunityMech:000140 63e9edaea88ef427528fae9620a415ea833bdb123ebd83cfb6c7573d30ff0be0 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 6f5332be1..b71a63b64 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -8,8 +8,8 @@
"records_without_edges": 175,
"review_status_counts": {
"needs_research": 48,
- "pending": 112,
- "reviewed": 300
+ "pending": 108,
+ "reviewed": 304
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261007-batch97.json b/reports/causal_graph_review/validation-20261007-batch97.json
new file mode 100644
index 000000000..6e4b41c85
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261007-batch97.json
@@ -0,0 +1,1274 @@
+{
+ "base_commit": "c33f6896716f6cfa4ccaac9b3ad97359de0674f9",
+ "scope": [
+ "kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml",
+ "kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml",
+ "kb/communities/SMutans_VParvula_ASC_Biofilm.yaml",
+ "kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch97.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/focused.log",
+ "log_sha256": "f128aac74c75918703ee44bd128d57a24ccbed8630e53876bc958d4359987797",
+ "output_tail": "........ [100%]\n8 passed in 1.85s\n"
+ },
+ {
+ "check": "SMutans_CAlbicans_ECC_Biofilm-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_CAlbicans_ECC_Biofilm-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "SMutans_CAlbicans_ECC_Biofilm-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch97/SMutans_CAlbicans_ECC_Biofilm-strict.tsv",
+ "kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_CAlbicans_ECC_Biofilm-strict.log",
+ "log_sha256": "2d5fc63383c9e6de51123889470c6c8d551f198d3d19bf965417afa5521ee9ed",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch97/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-batch97/SMutans_CAlbicans_ECC_Biofilm-strict.tsv\n"
+ },
+ {
+ "check": "SMutans_CAlbicans_ECC_Biofilm-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_CAlbicans_ECC_Biofilm-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "SMutans_CAlbicans_ECC_Biofilm-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_CAlbicans_ECC_Biofilm-references.log",
+ "log_sha256": "83361b88347682c3441c88897344bb7ba8a4f9b5ff2de45d8fab5c07dde7213f",
+ "output_tail": "Validating kb/communities/SMutans_CAlbicans_ECC_Biofilm.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/SMutans_CAlbicans_ECC_Biofilm.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": "SMutans_CAlbicans_ECC_Biofilm-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_CAlbicans_ECC_Biofilm-snippets.log",
+ "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
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+ "command": [
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+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_CAlbicans_ECC_Biofilm-rank.log",
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+ "command": [
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+ "expected_exit_codes": [
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+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_SSputigena_ECC_Pathobiont-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
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+ "kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml"
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+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_SSputigena_ECC_Pathobiont-strict.log",
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+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_SSputigena_ECC_Pathobiont-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "SMutans_SSputigena_ECC_Pathobiont-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
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+ "--config",
+ "conf/reference_validator.yaml"
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+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_SSputigena_ECC_Pathobiont-references.log",
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+ "explained_output_tail": "Validating kb/communities/SMutans_SSputigena_ECC_Pathobiont.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": "SMutans_SSputigena_ECC_Pathobiont-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_SSputigena_ECC_Pathobiont-snippets.log",
+ "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_SSputigena_ECC_Pathobiont-rank.log",
+ "log_sha256": "b9b6d4ba8824d5fd7109a0cccddde2d092e6df9d0694bf47395eb7d57075b689",
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+ "command": [
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+ "HistoryRecord",
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+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_SSputigena_ECC_Pathobiont-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ "check": "SMutans_SSputigena_ECC_Pathobiont-history-1",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "HistoryRecord",
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+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_SSputigena_ECC_Pathobiont-history-1.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "expected_exit_codes": [
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+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
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+ "--out",
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+ "log_sha256": "0a52843d14b5b0449c54b8a0a4135fe4558f13c9cf3fbf69846e20e54ff97cd3",
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+ },
+ {
+ "check": "SMutans_VParvula_ASC_Biofilm-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/SMutans_VParvula_ASC_Biofilm.yaml",
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+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_VParvula_ASC_Biofilm-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "SMutans_VParvula_ASC_Biofilm-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/SMutans_VParvula_ASC_Biofilm.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_VParvula_ASC_Biofilm-references.log",
+ "log_sha256": "de161a1dfa893150b635a73c08e9c27fd499480779715447ef32f45c3d34dd68",
+ "output_tail": "Validating kb/communities/SMutans_VParvula_ASC_Biofilm.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/SMutans_VParvula_ASC_Biofilm.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": "SMutans_VParvula_ASC_Biofilm-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
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+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_VParvula_ASC_Biofilm-snippets.log",
+ "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
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+ "--format",
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+ ],
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+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_VParvula_ASC_Biofilm-rank.log",
+ "log_sha256": "4bb4257ac31bd7ba8ef8dbb207cef0777f710497f36b9fcd2776e28ea27fa27f",
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/SMutans_VParvula_ASC_Biofilm/2026-10-07T184554Z-codex-a80c30.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SMutans_VParvula_ASC_Biofilm-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
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+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
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+ "expected_exit_codes": [
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+ "log_sha256": "6b8c55bafe9ad61f655e55e9f72d2f7976a50b6c0ac15725c0a06b82e19ce6c1",
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+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
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+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
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+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SO3_BS3_Lithium_Battery_Bioleaching_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "SO3_BS3_Lithium_Battery_Bioleaching_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SO3_BS3_Lithium_Battery_Bioleaching_Consortium-references.log",
+ "log_sha256": "1975ad27d11564dda2533471e38a6ca73e0457b85f30b2aa2a607052293d5b53",
+ "output_tail": "Validating kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "SO3_BS3_Lithium_Battery_Bioleaching_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SO3_BS3_Lithium_Battery_Bioleaching_Consortium-snippets.log",
+ "log_sha256": "5f0e8a5be45b94195ee5599498c60e06ff8db089c85d0bf23969aa37351ca96e",
+ "output_tail": "# 17 evidence snippets scanned across 1 files\n MATCH 17\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": "SO3_BS3_Lithium_Battery_Bioleaching_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SO3_BS3_Lithium_Battery_Bioleaching_Consortium-rank.log",
+ "log_sha256": "3348e4af7f260acc8dac56f6be2a2298138888a87106eb007136f10873c4c0cb",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000385\",\n \"name\": \"SO3-BS3 Lithium-ion Battery Bioleaching Consortium\",\n \"score\": 75.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"additional_downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "SO3_BS3_Lithium_Battery_Bioleaching_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T184554Z-codex-3515ec.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SO3_BS3_Lithium_Battery_Bioleaching_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "SO3_BS3_Lithium_Battery_Bioleaching_Consortium-history-1",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T185016Z-codex-8bc7a6.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/SO3_BS3_Lithium_Battery_Bioleaching_Consortium-history-1.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-batch97/verification-final/inventory.log",
+ "log_sha256": "e4d13d6032a07ad1c09e7beb78e7273959a68e5274ccc9f0f277ac61aa1a5589",
+ "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\": 1410,\n \"edges\": 572,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 175,\n \"review_status_counts\": {\n \"needs_research\": 48,\n \"pending\": 108,\n \"reviewed\": 304\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-batch97/verification-final/network.log",
+ "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+ "output_tail": " \"total_genomes\": 17191,\n \"is_reclassified\": false,\n \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n },\n \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"mexZ\"\n },\n \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n \"evidence\": [\n {\n \"reference\": \"PMID:42153623\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/just-network-json.log",
+ "log_sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/rank-all.log",
+ "log_sha256": "fad584bdfa2094a5d8bfadf23211608db45d1f4ad897ac7ac4a6ed380d6b1e2b",
+ "output_tail": "ities/Soybean_N_Fixation_sfSynCom.yaml\tCommunityMech:000064\tSoybean N-Fixation Simplified SynCom\t4\t4\t0\t3\t2\t3\t\t0\t0\n402\t100.0\tkb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml\tCommunityMech:000267\tSphingobium-Rhodococcus Lignin-Dimer Valorization Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n403\t100.0\tkb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml\tCommunityMech:000326\tStaphylococcus-Candida Context-Dependent Biofilm Coculture\t2\t2\t0\t6\t2\t13\t\t0\t0\n404\t100.0\tkb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml\tCommunityMech:000254\tStordalen Mire Methylotrophic Methanogenesis Community\t3\t3\t0\t4\t4\t9\t\t0\t0\n405\t100.0\tkb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml\tCommunityMech:000335\tStreptomyces A2-A5-A11-M7 Pesticide-Bioremediation Consortium\t4\t4\t0\t4\t2\t5\t\t0\t0\n406\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t5\t2\t5\t\t0\t0\n407\t100.0\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t4\t\t0\t0\n408\t100.0\tkb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml\tCommunityMech:000222\tSulfide Spring Autotrophic CPR-Hosting Biofilm\t3\t3\t0\t3\t2\t4\t\t0\t0\n409\t100.0\tkb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml\tCommunityMech:000127\tSynComBac10 Chicken Intestinal SynCom\t3\t3\t0\t3\t2\t3\t\t0\t0\n410\t100.0\tkb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\tCommunityMech:000314\tSynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community\t5\t5\t0\t3\t2\t3\t\t0\t0\n411\t100.0\tkb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\tCommunityMech:000278\tSynCom BsBv Cigar Tobacco Leaf Fermentation\t2\t2\t0\t3\t2\t3\t\t0\t0\n412\t100.0\tkb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\tCommunityMech:000285\tSynCom + Chlorella sorokiniana Biogas-slurry Coupling System\t2\t2\t0\t5\t3\t5\t\t0\t0\n413\t100.0\tkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\tCommunityMech:000302\tSynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\t2\t2\t0\t3\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n417\t100.0\tkb/communities/Synechococcus_Bacillus_SPC.yaml\tCommunityMech:000065\tSynechococcus-Bacillus Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n418\t100.0\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n419\t100.0\tkb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\tCommunityMech:000198\tSynechococcus-Halomonas Light-Driven PHB Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\tCommunityMech:000167\tSynechococcus-Pseudomonas Phototrophic PHA and DNT Coculture\t2\t2\t0\t4\t2\t8\t\t0\t0\n421\t100.0\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n422\t100.0\tkb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\tCommunityMech:000211\tSynechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n424\t100.0\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t8\t\t0\t0\n425\t100.0\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic 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Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/render.log",
+ "log_sha256": "f235c49632c351c71b5d3419fa745e9f7db5f966abf7086ae026f1c006c240ff",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch97/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch97/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch97/docs/index.html\n"
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/render-repeat.log",
+ "log_sha256": "f235c49632c351c71b5d3419fa745e9f7db5f966abf7086ae026f1c006c240ff",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch97/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch97/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch97/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch97/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch96')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/connectivity-survey.log",
+ "log_sha256": "0e885b7acb2ae273e429a51ef58065c5f1966ee8e95a5e6720e4152baa695008",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 399, \"mixed\": 125, \"community_level_only\": 274, \"taxa\": 1536, \"credited_solely_by_the_rule\": 1266}, \"current\": {\"records\": 460, \"with_community_level\": 402, \"mixed\": 128, \"community_level_only\": 274, \"taxa\": 1542, \"credited_solely_by_the_rule\": 1266}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_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-batch97/verification-final/regressions.log",
+ "log_sha256": "852a7413648c9a5848ddb4599f464fb61f72d0821ba8c019b76e8cba1f84df52",
+ "output_tail": "........................................................................ [ 8%]\n........................................................................ [ 16%]\n........................................................................ [ 24%]\n........................................................................ [ 32%]\n........................................................................ [ 40%]\n........................................................................ [ 48%]\n........................................................................ [ 56%]\n........................................................................ [ 64%]\n........................................................................ [ 72%]\n........................................................................ [ 81%]\n........................................................................ [ 89%]\n........................................................................ [ 97%]\n........................ [100%]\n888 passed in 507.98s (0:08:27)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch97.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/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_batch97.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_community_level_connectivity_credit.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/audit-snippets-all.log",
+ "log_sha256": "d4c41224466abbd54b05f711d157e4204dc93d712943b56e91f6dcaa1bcae60b",
+ "output_tail": "# 8939 evidence snippets scanned across 460 files\n MATCH 8804\n RENDERING 20\n ASSEMBLED 1\n WEAK 0\n MISMATCH 38\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/verification-final/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ },
+ {
+ "check": "focused-final",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch97.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch97/focused-final.log",
+ "log_sha256": "3f1fec1302dc999c48f39a6d5569a6ba4e2c9d5a4784777a9e09f0b2dd106781",
+ "output_tail": "........ [100%]\n8 passed in 2.78s\n"
+ }
+ ],
+ "limitations": [
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+ "details": "Attach direct primary-result evidence to the retained Honeycomb Biofilm Acidogenesis interpretation after adversarial diff review; no new node, direction, mechanism or protocol.",
+ "preserved_initial_histories": {
+ "history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T184554Z-codex-0f7a08.yaml": "6489f27ee2b5c35d4131815469e2761ff1cd7e3ed53a87bb08782f65d1739230"
+ },
+ "correction_history": "history/records/SMutans_SSputigena_ECC_Pathobiont/2026-10-07T185016Z-codex-9c291b.yaml"
+ },
+ {
+ "issue": 1775,
+ "details": "Attach direct primary-result evidence to the retained MtrC/OmcA and riboflavin NCM reduction interpretation after adversarial diff review; no new node, direction, mechanism or protocol.",
+ "preserved_initial_histories": {
+ "history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T184554Z-codex-3515ec.yaml": "fa0a65de9df956d2143f1370a94d1aacec667c3ba2280b3fa7f2664060aa798b"
+ },
+ "correction_history": "history/records/SO3_BS3_Lithium_Battery_Bioleaching_Consortium/2026-10-07T185016Z-codex-8bc7a6.yaml"
+ }
+ ],
+ "timing": "Both corrections preceded final validation; no interrupted verification attempt.",
+ "participant_fixture_correction": {
+ "details": "Initial regression:887passed/1failed because the explicit participant allowlist lacked the three newly curated oral records. Added exactly those three entries after measured census; equality guard retained. Failed output and initial validation snapshot preserved; full regression rerun, unchanged earlier gates digest-checked on resume.",
+ "failed_output": "/private/tmp/communitymech-batch97/verification-final/regressions-attempt1.log",
+ "failed_output_sha256": "8fa08d48a4811313045065e543271e7296247431252649fd350220a53197978f",
+ "initial_snapshot": "/private/tmp/communitymech-batch97/validation-initial.json",
+ "initial_snapshot_sha256": "46a188ae9e6357498dbdd9175ba4e84c9e473ba37b3abd57fe08fbc9a128c4de"
+ }
+ },
+ "total_recorded_gate_outputs": 44
+}
diff --git a/tests/test_causal_review_batch97.py b/tests/test_causal_review_batch97.py
new file mode 100644
index 000000000..4d9179fe5
--- /dev/null
+++ b/tests/test_causal_review_batch97.py
@@ -0,0 +1,134 @@
+"""Keep evidence modality, microbial facilitation and host outcomes distinct."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261007-four-records-batch97.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_candida_positive_interactions_and_modality_survive():
+ _, _, docs = records()
+ biofilm, eps, outcome = docs[0]["ecological_interactions"]
+ assert biofilm["interaction_type"] == "MUTUALISM"
+ assert eps["interaction_type"] == "COLONIZATION_FACILITATION"
+ assert eps["evidence"][0]["evidence_source"] == "IN_VITRO"
+ assert eps["downstream"][0]["target"] == biofilm["name"]
+ assert biofilm["downstream"][0]["target"] == outcome["name"]
+ assert biofilm["downstream"][0]["description"].startswith("PARTIAL:")
+
+
+def test_selenomonas_retains_experimental_structure_support():
+ _, _, docs = records()
+ entrapment, biofilm, _ = docs[1]["ecological_interactions"]
+ assert entrapment["interaction_type"] == "COLONIZATION_FACILITATION"
+ assert entrapment["source_taxon"]["term"]["id"] == "NCBITaxon:1309"
+ assert entrapment["target_taxon"]["term"]["id"] == "NCBITaxon:69823"
+ assert all(n["evidence"][0]["evidence_source"] == "IN_VITRO" for n in [entrapment, biofilm])
+ assert not entrapment["downstream"][0]["description"].startswith("PARTIAL:")
+ assert "matrix-disruption" in biofilm["description"]
+ assert biofilm["downstream"][0]["description"].startswith("PARTIAL:")
+
+
+def test_veillonella_expression_is_not_catalytic_activity():
+ _, _, docs = records()
+ expression, biofilm, outcome = docs[2]["ecological_interactions"]
+ assert "interaction_type" not in expression
+ assert "do not independently measure catalytic enzyme activity" in expression["description"]
+ assert len(expression["evidence"]) == 2
+ assert biofilm["evidence"][0]["evidence_source"] == "IN_VITRO"
+ assert all(
+ n["downstream"][0]["description"].startswith("PARTIAL:") for n in [expression, biofilm]
+ )
+ assert outcome["name"] == "Rodent Coinfection Caries Outcome"
+ assert "human adult severe caries" in outcome["description"]
+
+
+def test_composite_and_host_outcomes_name_exact_members():
+ _, _, docs = records()
+ for doc in docs[:3]:
+ expected = [
+ {k: t["taxon_term"][k] for k in ["preferred_term", "term"]} for t in doc["taxonomy"]
+ ]
+ for node in doc["ecological_interactions"]:
+ if node["scope"] != "COMMUNITY_LEVEL":
+ continue
+ assert not any(k in node for k in ["interaction_type", "source_taxon", "target_taxon"])
+ assert node["participating_taxa"] == expected
+ assert len(expected) == 2
+ assert doc["ecological_interactions"][-1]["scope"] == "COMMUNITY_LEVEL"
+ assert all(
+ e["evidence_source"] == "IN_VIVO"
+ for e in doc["ecological_interactions"][-1]["evidence"]
+ )
+
+
+def test_battery_facilitation_is_not_neutral_fitness():
+ _, _, docs = records()
+ detox, reduction = docs[3]["ecological_interactions"]
+ assert detox["scope"] == "PAIRWISE" and "interaction_type" not in detox
+ assert "unaffected" in detox["description"]
+ assert detox["downstream"][0]["target"] == reduction["name"]
+ assert "predecessor" in detox["downstream"][0]["description"]
+ assert "not a quantitative partition" in reduction["description"]
+ assert docs[3]["discussions"][0]["discussion_id"] == "SO3_BS3_SCALE_UP_STABILITY"
+
+
+def test_all_nodes_and_directions_have_dispositions():
+ _, rows, docs = records()
+ assert sum(len(r["node_decisions"]) for r in rows) == 11
+ assert sum(len(r["renamed_nodes"]) for r in rows) == 5
+ assert sum(len(r["edges_before"]) for r in rows) == 7
+ assert sum(len(r["retained_edge_decisions"]) for r in rows) == 7
+ for row, doc in zip(rows, docs, strict=True):
+ assert row["removed_node_decisions"] == row["removed_edge_decisions"] == []
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert {r["node"] for r in row["node_decisions"]} == {
+ n["name"] for n in doc["ecological_interactions"]
+ }
+ for edge in row["retained_edge_decisions"]:
+ assert all(
+ row["renamed_nodes"].get(edge["before"][k], edge["before"][k]) == edge["after"][k]
+ for k in ["source", "target"]
+ )
+
+
+def test_source_proofs_and_append_only_history():
+ ledger, rows, docs = records()
+ assert len(ledger["snippet_checks"]) == ledger["primary_graph_snippet_count"] == 16
+ assert len(ledger["discussion_snippet_checks"]) == 4
+ assert all(
+ c["cache_matched"] and c["independent_primary_match"]
+ for c in ledger["snippet_checks"] + ledger["discussion_snippet_checks"]
+ )
+ for row, doc in zip(rows, docs, strict=True):
+ assert row["allowed_changed_fields"] == [
+ "curation_history",
+ "discussions",
+ "ecological_interactions",
+ ]
+ assert row["curation_events_added"] == len(row["history_files"])
+ assert row["curation_events_added"] == (
+ 2 if doc["id"] in ["CommunityMech:000084", "CommunityMech:000385"] else 1
+ )
+ assert doc["curation_history"][-1]["llm_assisted"]
+ assert (ROOT / row["history_files"][0]).is_file()
+
+
+def test_unresolved_scope_is_not_certified():
+ ledger, _, _ = records()
+ assert ledger["issues"] == [1772, 1773, 1774, 1775]
+ assert ledger["unresolved_non_graph_issues"] == [1776]
+ assert ledger["cache_changes"] == []
+ assert not ledger["independent_approval"]
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert any("HTTP500" in s for s in ledger["limitations"])
+ assert any("cross-sectional" in s for s in ledger["limitations"])
diff --git a/tests/test_community_level_connectivity_credit.py b/tests/test_community_level_connectivity_credit.py
index 230812c78..c74daee6f 100644
--- a/tests/test_community_level_connectivity_credit.py
+++ b/tests/test_community_level_connectivity_credit.py
@@ -102,7 +102,9 @@ def test_the_survey_sees_the_corpus(survey):
def test_most_records_carry_a_community_level_interaction(survey):
"""The rule's reach. #312 measured 156; ongoing curation reached 381."""
- assert 130 <= survey["with_community_level"] <= 400, survey
+ # #1772-#1774 separate host/community outcomes in three previously pairwise records.
+ # Census: 399 -> 402; exactly named participants, no extra solely-credited taxa.
+ assert 130 <= survey["with_community_level"] <= 402, survey
def test_the_mixed_records_are_where_the_coarseness_bites(survey):
@@ -117,7 +119,8 @@ def test_the_mixed_records_are_where_the_coarseness_bites(survey):
community-level-only records the credit is not
coarse — there is no pairwise edge it could be masking.
"""
- assert 35 <= survey["mixed"] <= 127, survey
+ # #1772-#1774 change the mixed-record census from 125 to 128.
+ assert 35 <= survey["mixed"] <= 128, survey
assert survey["mixed"] + survey["community_level_only"] == survey["with_community_level"]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 323e3ab7f..d219f18f0 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -389,6 +389,9 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Richmond_Mine_AMD_Biofilm.yaml",
"Rifle_Aquifer_Bioanode_EET_Community.yaml",
"SF356_Cellulose_Degrader.yaml",
+ "SMutans_CAlbicans_ECC_Biofilm.yaml",
+ "SMutans_SSputigena_ECC_Pathobiont.yaml",
+ "SMutans_VParvula_ASC_Biofilm.yaml",
"SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml",
"Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml",
"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml",