The dropout experiment identified Trinickia sp. MC as the dominant single contributor: removing MC reduced sclerotia mortality, and MC mono-inoculation alone accelerated sclerotia mortality.
The dropout series and single-member comparison identify Trinickia MC as the strongest resolved contributor to accelerated sclerotium mortality. Its contribution is context- and time-dependent, not proof that MC is uniquely necessary for all eventual mortality or that every other member reinforces it. The primary discussion reports attenuation by the remaining nine-member group and eventual mortality from assemblies lacking MC. This node records the named member's contribution to the community intervention; Sclerotinia is the external challenge context, not a thirteenth consortium member.
-
Xenium spatial profiling of inoculated sclerotia showed that Massilia sp. TB221 and R20 were early interior colonizers by day 3, while Ralstonia sp. R4 and Trinickia sp. MC progressively increased in interior layers at days 5 to 7 and MC exceeded every other member across all five layers by day 14.
+
Spatial profiling detected early interior colonization by Massilia TB221 and R20, later interior enrichment of Ralstonia R4 and Trinickia MC, and MC dominance across the sampled layers at the final observation. These distribution and timing observations are not demonstrated competition-reducing niche partitioning or evidence that early colonization itself causes mortality. The MC contribution is supported independently by the dropout comparison, not inferred solely from its location.
+
Participating Taxa:
+
+ Massilia sp. TB221,
+
+ Massilia sp. R20,
+
+ Ralstonia sp. R4,
+
+ Trinickia sclerotiorum sp. nov. MC
+
+
+
@@ -1252,7 +1262,7 @@
Associated Datasets
- Knowledge gaps & discussions (2)
+ Knowledge gaps & discussions (3)
@@ -1324,6 +1334,41 @@
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which mechanisms explain the context-dependent antagonism and spatial associations?
+
+
Mortality contrasts support the community and MC treatment effects, while the spatial profile alone does not establish facilitation, resource competition or reduced competition among bacteria. Nonadditive effects and eventual mortality in assemblies lacking MC limit an essential-member interpretation. Molecular mechanisms remain unresolved; no new pathway, culturing procedure or genetic design is introduced. Existing taxonomic and partial-coverage discussions remain unchanged.
+
+
Attaches to: ecological_interactions#Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia, ecological_interactions#Trinickia MC Key Contribution to Sclerotia Mortality, ecological_interactions#Spatial Invasion of Sclerotia by SynCom Members
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
dropping TsMC significantly decreased mortality and its mono-inoculation alone could accelerate sclerotia mortality
+
Supports a dropout-resolved MC contribution in the tested comparisons, not universal necessity or an additive contribution model.
+
+
+
+
@@ -1754,15 +1799,11 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("defense response to fungus");
-
-
var evidenceCount = 1;
nodes.push({
@@ -1787,15 +1828,11 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("defense response to fungus");
-
-
var evidenceCount = 1;
nodes.push({
@@ -1820,7 +1857,7 @@
Evidence
(function() {
var intId = "interaction:2";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1840,6 +1877,23 @@
Evidence
+ var participantKeys = [
+
+ "Massilia sp. TB221",
+
+ "Massilia sp. R20",
+
+ "Ralstonia sp. R4",
+
+ "Trinickia sclerotiorum sp. nov. MC"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/history/records/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism/2026-10-07T203744Z-codex-e34e15.yaml b/history/records/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism/2026-10-07T203744Z-codex-e34e15.yaml
new file mode 100644
index 000000000..86b73cc5c
--- /dev/null
+++ b/history/records/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism/2026-10-07T203744Z-codex-e34e15.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml
+ slug: Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism
+session:
+ id: 2026-10-07T203744Z-codex-e34e15
+ timestamp: '2026-10-07T20:37:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1784
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain yeast-to-alga carbon supply without requiring fermentation as its sole route.;
+ Retain algal reduced-nitrogen supply and the conditional reciprocal resource loop; mediation
+ strength remains PARTIAL.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
diff --git a/history/records/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture/2026-10-07T203744Z-codex-d0f5ea.yaml b/history/records/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture/2026-10-07T203744Z-codex-d0f5ea.yaml
new file mode 100644
index 000000000..035f5c24b
--- /dev/null
+++ b/history/records/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture/2026-10-07T203744Z-codex-d0f5ea.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml
+ slug: Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture
+session:
+ id: 2026-10-07T203744Z-codex-d0f5ea
+ timestamp: '2026-10-07T20:37:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1785
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain condition-dependent coauxotrophic mutualism, distinct from product formation.;
+ Retain the intended divided-pathway handoff and PARTIAL production direction without direct
+ flux certainty.; Retain the measured titer comparison without assigning mutualism or conversion-efficiency
+ benefit to the aggregate endpoint.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
diff --git a/history/records/Salar_Atacama_Lithium_Brine_Community/2026-10-07T203744Z-codex-599245.yaml b/history/records/Salar_Atacama_Lithium_Brine_Community/2026-10-07T203744Z-codex-599245.yaml
new file mode 100644
index 000000000..9362d1603
--- /dev/null
+++ b/history/records/Salar_Atacama_Lithium_Brine_Community/2026-10-07T203744Z-codex-599245.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml
+ slug: Salar_Atacama_Lithium_Brine_Community
+session:
+ id: 2026-10-07T203744Z-codex-599245
+ timestamp: '2026-10-07T20:37:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1786
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain observed community differences at community scope; remove unmeasured pairwise
+ benefit and physiological causation.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
diff --git a/history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T203745Z-codex-dc367a.yaml b/history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T203745Z-codex-dc367a.yaml
new file mode 100644
index 000000000..5676dca91
--- /dev/null
+++ b/history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T203745Z-codex-dc367a.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml
+ slug: Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
+session:
+ id: 2026-10-07T203745Z-codex-dc367a
+ timestamp: '2026-10-07T20:37:45Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1787
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain full-community antagonism with all twelve inoculum identities, without competition/defense
+ ontology overclaims.; Retain the dropout-supported pairwise MC contribution and its direction,
+ without universal necessity or additivity.; Retain measured spatial timing and scoped
+ participants, without niche-partitioning or colonization-causality claims.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
diff --git a/history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T204135Z-codex-cb916b.yaml b/history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T204135Z-codex-cb916b.yaml
new file mode 100644
index 000000000..069c3f358
--- /dev/null
+++ b/history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T204135Z-codex-cb916b.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml
+ slug: Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
+session:
+ id: 2026-10-07T204135Z-codex-cb916b
+ timestamp: '2026-10-07T20:41:35Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1787
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ summary: Keep the MC dropout result at community-contribution scope with only MC as participant
+ and the fungal challenge as external context; do not assert a pairwise consortium-membership
+ relation.
+ details: Corrects the scope introduced in history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T203745Z-codex-dc367a.yaml;
+ failed preflight is retained privately at /private/tmp/communitymech-batch99/preflight-network.json
diff --git a/kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml b/kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml
index d1ef5e5f3..879f91389 100644
--- a/kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml
+++ b/kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml
@@ -60,8 +60,9 @@ taxonomy:
- CROSS_FEEDER
ecological_interactions:
- name: Yeast Carbon Dioxide Provisioning
- description: S. cerevisiae metabolizes glucose and releases carbon dioxide that is assimilated
- photosynthetically by C. reinhardtii under carbon-limited coculture conditions.
+ description: In the sealed illuminated coculture, yeast glucose metabolism supplies carbon dioxide assimilated
+ by the algal partner. This is the carbon arm of the authors' experimentally supported reciprocal carbon/nitrogen
+ mutualism. The source does not isolate fermentation as the only route of yeast carbon dioxide production.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -84,53 +85,26 @@ ecological_interactions:
id: CHEBI:16526
label: carbon dioxide
biological_processes:
- - preferred_term: fermentation
- term:
- id: GO:0006113
- label: fermentation
- preferred_term: photosynthesis
term:
id: GO:0015979
label: photosynthesis
downstream:
- target: Algal Reduced Nitrogen Provisioning
- description: Yeast-derived carbon dioxide is fixed photosynthetically by
- C. reinhardtii, sustaining the algal partner that reduces nitrite to
- ammonia for S. cerevisiae.
+ description: 'PARTIAL: yeast-derived carbon dioxide sustains the alga that supplies reduced nitrogen to yeast,
+ closing the resource-dependence loop. Coculture and resource-availability comparisons support this reciprocal
+ mechanism, but do not separately quantify how a change in carbon transfer changes ammonia release.'
evidence:
- reference: PMID:24994654
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: S. cerevisiae metabolizes glucose to carbon dioxide (CO2), a carbon source that C. reinhardtii fixes via photosynthesis
+ snippet: S. cerevisiae metabolizes glucose to carbon dioxide (CO2), a carbon source that C. reinhardtii fixes
+ via photosynthesis
explanation: Supports yeast glucose metabolism supplying the carbon dioxide fixed by the algal partner.
-- name: Algal Oxygen Provisioning
- description: C. reinhardtii releases photosynthetic oxygen that supports aerobic yeast metabolism in
- the sealed coculture.
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Chlamydomonas reinhardtii
- term:
- id: NCBITaxon:3055
- label: Chlamydomonas reinhardtii
- target_taxon:
- preferred_term: Saccharomyces cerevisiae
- term:
- id: NCBITaxon:4932
- label: Saccharomyces cerevisiae
- metabolites:
- - preferred_term: dioxygen
- term:
- id: CHEBI:15379
- label: dioxygen
- biological_processes:
- - preferred_term: photosynthesis
- term:
- id: GO:0015979
- label: photosynthesis
- name: Algal Reduced Nitrogen Provisioning
- description: C. reinhardtii metabolizes nitrite and releases ammonia, providing reduced nitrogen that
- supports S. cerevisiae growth.
+ description: Algal nitrite metabolism supplies ammonia usable by yeast in the carbon/nitrogen mutualism. The dependence
+ is conditional on the resource environment, not an unconditional property of these species; external reduced
+ nitrogen can remove yeast dependence on the alga.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -159,9 +133,9 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Yeast Carbon Dioxide Provisioning
- description: Algal reduction of nitrite to ammonia supplies the nitrogen
- source that lets S. cerevisiae proliferate and keep producing carbon
- dioxide from glucose.
+ description: 'PARTIAL: algal reduced nitrogen sustains yeast growth and therefore the yeast partner supplying
+ carbon dioxide. This reciprocal support is consistent with the reported dependence, not a measured feedback
+ gain or a separate temporal causal experiment.'
evidence:
- reference: PMID:24994654
supports: SUPPORT
@@ -261,13 +235,37 @@ curation_history:
- timestamp: '2026-09-13T00:56:50Z'
curator: codex
action: RECONCILE_PAYWALLED_EVIDENCE_REMOVAL
- changes: "Reapplied PR #766's 17 unsupported evidence removals onto current main, preserving its newer
- interaction curation; retained abstract-supported evidence. Re-evidencing debt remains tracked in
- #765."
+ changes: 'Reapplied PR #766''s 17 unsupported evidence removals onto current main, preserving its newer interaction
+ curation; retained abstract-supported evidence. Re-evidencing debt remains tracked in #765.'
llm_assisted: true
- timestamp: '2026-10-01T05:00:58Z'
curator: codex
action: EVIDENCE_CAUSAL_GRAPH_NODES
- changes: Added cached PMID:24994654 evidence to the yeast carbon-dioxide and algal reduced-nitrogen interaction nodes that
- participate in the reciprocal causal graph.
+ changes: Added cached PMID:24994654 evidence to the yeast carbon-dioxide and algal reduced-nitrogen interaction
+ nodes that participate in the reciprocal causal graph.
llm_assisted: true
+- timestamp: '2026-10-07T20:37:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain yeast-to-alga carbon supply without requiring fermentation as its sole route.; Retain algal reduced-nitrogen
+ supply and the conditional reciprocal resource loop; mediation strength remains PARTIAL. Issue#1784; reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
+ llm_assisted: true
+discussions:
+- discussion_id: alga_graph_evidence_scope
+ prompt: Is algal oxygen release a demonstrated additional benefit to yeast in this exact coculture?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: The primary manuscript depicts oxygen release, but the reviewed main text establishes reciprocal carbon/nitrogen
+ dependence rather than an isolated oxygen-mediated yeast benefit. The two-node resource loop is retained with
+ PARTIAL mediation limits. The oxygen-benefit assertion is removed pending exact-system evidence. This does not
+ assert that yeast cannot use oxygen. Broader re-evidencing remains in issue765, and cache-version/license provenance
+ is tracked separately.
+ evidence:
+ - reference: PMID:24994654
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: an environment requiring reciprocal carbon and nitrogen exchange
+ explanation: The abstract supports the established reciprocal resource basis, not an oxygen-specific benefit.
+ attaches_to:
+ - ecological_interactions#Yeast Carbon Dioxide Provisioning
+ - ecological_interactions#Algal Reduced Nitrogen Provisioning
diff --git a/kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml b/kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml
index c4fb10da2..54a14dcf5 100644
--- a/kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml
+++ b/kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml
@@ -175,10 +175,10 @@ related_ingredients:
explanation: Supports resveratrol as the target product of the FLO1 coculture.
ecological_interactions:
- name: Met-Trp4 Coauxotrophic Cross-Feeding
- description: >-
- The two engineered S. cerevisiae auxotrophs require one another for growth
- in SM medium; the Met-Trp4 pair couples a met14-deficient cell-1 lineage
- with a trp4-deficient cell-2 lineage in a defined cross-feeding coculture.
+ description: The Met-Trp4 coauxotrophic yeast pair forms a mutually dependent growth system in the tested medium
+ lacking the complementary required nutrients. This growth relationship is distinct from the resveratrol pathway
+ handoff and does not by itself establish enhanced product titer or unconditional dependence in supplemented
+ environments.
interaction_type: MUTUALISM
scope: COMMUNITY_LEVEL
participating_taxa:
@@ -194,17 +194,14 @@ ecological_interactions:
- reference: PMID:41491832
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- two auxotrophic cells, cell 1 and cell 2, must be present simultaneously
- to form cross-feeding for growth
- explanation: >-
- Supports the mutual dependence of the engineered two-member auxotrophic
- yeast cocultures.
+ snippet: two auxotrophic cells, cell 1 and cell 2, must be present simultaneously to form cross-feeding for
+ growth
+ explanation: Supports the mutual dependence of the engineered two-member auxotrophic yeast cocultures.
- name: Resveratrol Pathway Division of Labor
- description: >-
- The met14 cell-1 partner runs module A to convert L-tyrosine into the
- p-coumaric acid intermediate, which is then routed to the trp4 cell-2
- partner carrying module B for conversion into resveratrol.
+ description: The existing met14 module-A and trp4 module-B partners divide the resveratrol pathway around p-coumaric
+ acid. The reported module assignment and product/intermediate measurements support the intended metabolic handoff,
+ but do not directly quantify intercellular transfer flux or show that it alone explains the FLO1-associated
+ production increment.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -224,27 +221,23 @@ ecological_interactions:
label: trans-4-coumaric acid
downstream:
- target: FLO1 Adhesion-Enhanced Resveratrol Production
- description: >-
- The divided module A/module B pathway supplies the p-coumaric-acid
- handoff used by the FLO1 Met-Trp4 A-B bioproduction coculture.
+ description: 'PARTIAL: the divided pathway supplies the precursor-to-product route in the tested FLO1 coculture,
+ enabling resveratrol synthesis. It does not independently explain the increase over the no-FLO1 control; adhesion-dependent
+ transfer efficiency was not isolated as the mediator.'
evidence:
- reference: PMID:41491832
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- Module A contained FjTAL, catalyzing L-tyrosine to p-coumaric acid, while
- module B contained At4CL and VvVST1, converting p-coumaric acid to
- resveratrol
- explanation: >-
- Supports the module A to module B p-coumaric-acid handoff in the divided
- resveratrol pathway.
+ snippet: Module A contained FjTAL, catalyzing L-tyrosine to p-coumaric acid, while module B contained At4CL
+ and VvVST1, converting p-coumaric acid to resveratrol
+ explanation: Supports the assigned two-module pathway and intended precursor handoff, not a directly measured
+ intercellular flux or isolated cause of the FLO1 increment.
- name: FLO1 Adhesion-Enhanced Resveratrol Production
- description: >-
- Adding the FLO1 adhesion system to the Met-Trp4 A-B division-of-labor
- coculture increased resveratrol production compared with the no-FLO1
- Met-Trp4 A-B coculture, the corresponding FLO1 noncross-feeding control,
- and the full-pathway monoculture control.
- interaction_type: MUTUALISM
+ description: The tested Met-Trp4 A-B:FLO1 coculture produced more resveratrol than its no-FLO1 counterpart, the
+ corresponding FLO1 noncross-feeding control and the full-pathway monoculture. This is an aggregate production
+ endpoint, not by itself a mutualistic fitness measurement. The higher titer co-occurred with precursor accumulation
+ and lower biomass in this configuration; it does not establish more efficient precursor conversion or a universal
+ benefit of adhesion across yeast pairs.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Saccharomyces cerevisiae 007 met14 module A FLO1 cell 1
@@ -259,21 +252,13 @@ ecological_interactions:
- reference: PMID:41491832
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- Notably, the pair Met-Trp4, in the presence of FLO1, always increased
- production
- explanation: >-
- Supports FLO1 adhesion as beneficial for resveratrol production in the
- Met-Trp4 background.
+ snippet: Notably, the pair Met-Trp4, in the presence of FLO1, always increased production
+ explanation: Supports FLO1 adhesion as beneficial for resveratrol production in the Met-Trp4 background.
- reference: PMID:41491832
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- Met–Trp4A–B:FLO1 produced 0.67 μM of resveratrol, a 2.47-fold increase
- compared to Mctrl
- explanation: >-
- Quantifies the Met-Trp4 A-B:FLO1 endpoint against the full-pathway
- monoculture control.
+ snippet: Met–Trp4A–B:FLO1 produced 0.67 μM of resveratrol, a 2.47-fold increase compared to Mctrl
+ explanation: Quantifies the Met-Trp4 A-B:FLO1 endpoint against the full-pathway monoculture control.
growth_media:
- name: SM medium
temperature: '30'
@@ -363,18 +348,41 @@ curation_history:
- timestamp: '2026-09-27T03:08:31Z'
curator: codex
action: CREATE_YEAST_ADHESION_RESVERATROL_COCULTURE
- changes: >-
- Created CommunityMech:000445 from PMID:41491832 and DOI
- 10.1038/s41589-025-02081-1 with evidence-backed Met-Trp4 FLO1 S.
- cerevisiae membership, FjTAL/At4CL/VvVST1 resveratrol pathway division of
- labor, coauxotrophic cross-feeding, FLO1 adhesion enhancement, SM medium,
- and microplate bioproduction conditions.
+ changes: Created CommunityMech:000445 from PMID:41491832 and DOI 10.1038/s41589-025-02081-1 with evidence-backed
+ Met-Trp4 FLO1 S. cerevisiae membership, FjTAL/At4CL/VvVST1 resveratrol pathway division of labor, coauxotrophic
+ cross-feeding, FLO1 adhesion enhancement, SM medium, and microplate bioproduction conditions.
llm_assisted: true
- timestamp: '2026-10-02T06:15:13Z'
curator: codex
action: REVIEW_CAUSAL_GRAPH
- changes: Removed the Met-Trp4 coauxotrophic cross-feeding to
- FLO1-enhanced-resveratrol edge because it described an auxotrophic test
- background rather than the divided-pathway cause of the FLO1 production
- endpoint.
+ changes: Removed the Met-Trp4 coauxotrophic cross-feeding to FLO1-enhanced-resveratrol edge because it described
+ an auxotrophic test background rather than the divided-pathway cause of the FLO1 production endpoint.
llm_assisted: true
+- timestamp: '2026-10-07T20:37:42Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain condition-dependent coauxotrophic mutualism, distinct from product formation.; Retain the intended
+ divided-pathway handoff and PARTIAL production direction without direct flux certainty.; Retain the measured
+ titer comparison without assigning mutualism or conversion-efficiency benefit to the aggregate endpoint. Issue#1785;
+ reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
+ llm_assisted: true
+discussions:
+- discussion_id: resveratrol_graph_evidence_scope
+ prompt: How much of the FLO1-associated titer increment is mediated by intercellular precursor transfer?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: The production comparison and coauxotrophic mutualism are supported, but neither an endpoint titer
+ nor pathway assignment independently measures transfer efficiency or reciprocal fitness. The source explicitly
+ leaves aggregate morphology and metabolic exchange for further study. Preserve the one existing direction as
+ PARTIAL, without restoring the previously removed growth-background arrow.
+ evidence:
+ - reference: PMID:41491832
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Systematic investigation of aggregate morphology and its impact on metabolic exchange represents an
+ important direction for future research
+ explanation: The authors distinguish their demonstrated production endpoint from unresolved exchange mechanisms.
+ attaches_to:
+ - ecological_interactions#Met-Trp4 Coauxotrophic Cross-Feeding
+ - ecological_interactions#Resveratrol Pathway Division of Labor
+ - ecological_interactions#FLO1 Adhesion-Enhanced Resveratrol Production
diff --git a/kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml b/kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml
index ee9fde211..4cadf6320 100644
--- a/kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml
+++ b/kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml
@@ -244,227 +244,48 @@ taxonomy:
Xanthomonadaceae dominated the bacterial community in the concentrated brine
explanation: Documents Staphylococcaceae as abundant bacterial family
ecological_interactions:
-- name: Lithium Tolerance and Osmoadaptation
- description: 'The entire halophilic community exhibits exceptional tolerance to extremely high lithium
- concentrations (up to 58 g/L in concentrated brines) and total salinity (34.7-55.6%). Both halophilic
- archaea (Halovenus, Natronomonas, Haloarcula, Halobacterium) and the halophilic bacterium Salinibacter
- employ the "salt-in" osmoadaptation strategy, accumulating high intracellular concentrations of potassium
- ions and compatible solutes to maintain osmotic balance. Lithium acts as a selective pressure that
- modulates community composition, with archaeal diversity maximized in natural brine (lower Li) and
- bacterial diversity increased in concentrated brine (higher Li). This differential response suggests
- distinct lithium tolerance mechanisms between archaeal and bacterial lineages.
-
- '
- interaction_type: COMMENSALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Halovenus
- term:
- id: NCBITaxon:1377992
- label: Halovenus
- target_taxon:
- preferred_term: Salinibacter
- term:
- id: NCBITaxon:146918
- label: Salinibacter
- metabolites:
- - preferred_term: lithium
- term:
- id: CHEBI:49713
- label: lithium(1+)
- concentration: 1,500 mg/L (natural brine) to 58 g/L (concentrated brine)
- - preferred_term: potassium(1+)
- term:
- id: CHEBI:29103
- label: potassium(1+)
- notes: Accumulated intracellularly for osmotic balance
- - preferred_term: sodium chloride
- term:
- id: CHEBI:26710
- label: sodium chloride
- concentration: 34.7% to 55.6% total salinity
- biological_processes:
- - preferred_term: response to osmotic stress
- term:
- id: GO:0006970
- label: response to osmotic stress
- - preferred_term: cellular response to salt stress
- term:
- id: GO:1902074
- label: response to salt
- downstream:
- - target: Organic Matter Degradation in Hypersaline Brine
- description: Osmoadapted organisms drive heterotrophic activity in extreme salinity
+- name: Community Composition Across Natural and Concentrated Brines
+ description: 'The surveyed natural and industrially concentrated brines differed in taxonomic composition: bacterial
+ phylogenetic richness/diversity was higher in concentrated brine, whereas archaeal diversity was greater in
+ natural brine. These are community profiles across changing ionic composition and salinity, not a controlled
+ lithium-only effect or a mutual benefit between named taxa. The listed participants identify the existing curated
+ subset, not a complete community census or evidence that every member occurs in both samples. Salinibacter was
+ detected in natural brine but not the concentrated sample. Specific osmoadaptation, substrate exchange and nutrient-recycling
+ mechanisms remain unmeasured by this comparison.'
+ scope: COMMUNITY_LEVEL
evidence:
- reference: doi:10.1029/2018JG004621
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: Further, our results showed that Bacteria were phylogenetically more diverse and rich in
- the concentrated brine, while archaeal diversity was maximized in the natural brine
- explanation: Documents lithium as selective modulator of community diversity
- - reference: doi:10.1029/2018JG004621
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: Bacteria were phylogenetically more diverse and rich in the concentrated brine, while archaeal
- diversity was maximized in the natural brine
- explanation: Shows differential response of bacteria vs archaea to lithium concentration
-- name: Organic Matter Degradation in Hypersaline Brine
- description: 'Both archaeal and bacterial community members engage in aerobic heterotrophic degradation
- of organic matter in the hypersaline brine ecosystem. Halophilic archaea (Halovenus, Natronomonas,
- Haloarcula, Halobacterium) and the halophilic bacterium Salinibacter utilize diverse carbon sources
- including polysaccharides, proteins, and simple organic compounds. The community demonstrates functional
- redundancy in organic matter processing, with multiple taxa capable of degrading similar substrates.
- This metabolic activity supports nutrient cycling in the lithium-rich brine environment and represents
- the primary energy flow pathway in this extreme ecosystem.
-
- '
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Halovenus
+ snippet: Further, our results showed that Bacteria were phylogenetically more diverse and rich in the concentrated
+ brine, while archaeal diversity was maximized in the natural brine
+ explanation: Supports the measured community diversity comparison, not lithium-only causation or a particular
+ physiological adaptation.
+ participating_taxa:
+ - preferred_term: Halovenus
term:
id: NCBITaxon:1377992
label: Halovenus
- metabolites:
- - preferred_term: organic molecular entity
- term:
- id: CHEBI:50860
- label: organic molecular entity
- notes: Diverse organic carbon sources including polysaccharides, proteins, amino acids
- biological_processes:
- - preferred_term: aerobic respiration
- term:
- id: GO:0009060
- label: aerobic respiration
- downstream:
- - target: Nutrient Remineralization in Lithium Brine
- description: Organic degradation releases inorganic nutrients
- evidence:
- - reference: doi:10.1029/2018JG004621
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: 'Brines only supported a single archaeal family (Halobacteriaceae): natural brines included
- the archaeal genera Halovenus, Natronomonas, Haloarcula, and Halobacterium'
- explanation: Documents archaeal heterotrophic activity in brines
-- name: Nutrient Remineralization in Lithium Brine
- description: 'Heterotrophic degradation by archaeal and bacterial community members results in remineralization
- of nutrients (nitrogen, phosphorus, trace metals) from organic matter. This nutrient cycling is critical
- for sustaining microbial productivity in the oligotrophic brine environment where external nutrient
- inputs are limited. Remineralized nutrients become available for uptake by the same or other community
- members, creating a closed nutrient cycle that supports long-term community stability despite extreme
- salinity and lithium stress.
-
- '
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Natronomonas
+ - preferred_term: Natronomonas
term:
id: NCBITaxon:63743
label: Natronomonas
- target_taxon:
- preferred_term: Haloarcula
+ - preferred_term: Haloarcula
term:
id: NCBITaxon:2237
label: Haloarcula
- metabolites:
- - preferred_term: inorganic nutrient
- term:
- id: CHEBI:33284
- label: nutrient
- notes: Including nitrogen, phosphorus, trace metals from organic degradation
- biological_processes:
- - preferred_term: nitrogen cycle metabolic process
- term:
- id: GO:0071941
- label: nitrogen cycle metabolic process
- evidence:
- - reference: doi:10.1029/2018JG004621
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: The concentrated lithium brines of the Salar de Atacama represent one of the most saline
- environments described to date (dominated by LiCl)
- explanation: Implies nutrient cycling supports community persistence in extreme conditions
-- name: Bacteriorhodopsin-Mediated Phototrophy
- description: 'Halobacterium species possess bacteriorhodopsin, a light-driven proton pump that generates
- ATP through photophosphorylation without requiring organic carbon. This phototrophic capability provides
- metabolic flexibility in the high solar radiation environment of Salar de Atacama (6.3 × 10⁶ cal/m²/day,
- 3,700 mm/year evaporation). Phototrophy supplements heterotrophic metabolism during periods of organic
- carbon limitation and contributes to the overall energy budget of the community. The bacteriorhodopsin
- pathway represents a unique adaptation to the extreme light exposure in this high-altitude (2,300
- m) desert environment.
-
- '
- interaction_type: COMMENSALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Halobacterium
+ - preferred_term: Halobacterium
term:
id: NCBITaxon:2239
label: Halobacterium
- metabolites:
- - preferred_term: photon
- term:
- id: CHEBI:30212
- label: photon
- concentration: 6.3 × 10⁶ cal/m²/day solar radiation
- - preferred_term: ATP
- term:
- id: CHEBI:15422
- label: ATP
- notes: Generated via bacteriorhodopsin proton pumping
- biological_processes:
- - preferred_term: photosynthesis, light reaction
- term:
- id: GO:0019684
- label: photosynthesis, light reaction
- evidence:
- - reference: doi:10.1029/2018JG004621
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: The concentrated lithium brines of the Salar de Atacama represent one of the most saline
- environments described to date (dominated by LiCl)
- explanation: Documents extreme light exposure that selects for phototrophic capability
-- name: Bacterial Heterotrophic Activity and Functional Redundancy
- description: 'Staphylococcaceae members contribute to heterotrophic organic matter processing in natural
- brine, working alongside Salinibacter to provide functional redundancy in bacterial metabolism. As
- one of the most abundant bacterial families in natural brine, Staphylococcaceae exhibits halotolerance
- and participates in degradation of organic compounds. This bacterial functional redundancy complements
- the archaeal heterotrophs and enhances community resilience to environmental fluctuations. The presence
- of multiple bacterial families capable of heterotrophic activity ensures continued nutrient cycling
- even if individual taxa decline due to lithium concentration changes during industrial processing.
-
- '
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Staphylococcaceae members
- term:
- id: NCBITaxon:90964
- label: Staphylococcaceae
- target_taxon:
- preferred_term: Salinibacter
+ - preferred_term: Salinibacter
term:
id: NCBITaxon:146918
label: Salinibacter
- metabolites:
- - preferred_term: organic molecular entity
+ - preferred_term: Staphylococcaceae members
term:
- id: CHEBI:50860
- label: organic molecular entity
- notes: Diverse organic carbon sources
- biological_processes:
- - preferred_term: aerobic respiration
- term:
- id: GO:0009060
- label: aerobic respiration
- evidence:
- - reference: doi:10.1029/2018JG004621
- supports: SUPPORT
- evidence_source: IN_VIVO
- snippet: The most abundant bacterial families in natural brine were Rhodothermaceae and Staphylococcaceae;
- Xanthomonadaceae dominated the bacterial community in the concentrated brine
- explanation: Documents Staphylococcaceae as abundant bacterial family in natural brine
+ id: NCBITaxon:90964
+ label: Staphylococcaceae
environmental_factors:
- name: Lithium Concentration
value: 1,500
@@ -674,3 +495,30 @@ growth_media:
However, for both strains, optimum growth was attained at 37°C, and growth
was lowest at 20°C.
explanation: Documents the 37°C growth optimum across the tested 20-45°C range for the brine isolates.
+discussions:
+- discussion_id: brine_graph_evidence_scope
+ prompt: Which physiological or intertaxon mechanisms account for the observed brine community differences?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: The primary study measures composition in two brines and discusses candidate adaptation mechanisms
+ using background literature. It does not isolate lithium from covarying ions/salinity or establish the former
+ graph's organic degradation, closed nutrient recycling, phototrophy and functional-redundancy claims. Those
+ four nodes and both unsupported directions are removed. This is an evidentiary limit, not proof that the processes
+ are absent from the ecosystem.
+ evidence:
+ - reference: doi:10.1029/2018JG004621
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Further, our results showed that Bacteria were phylogenetically more diverse and rich in the concentrated
+ brine, while archaeal diversity was maximized in the natural brine
+ explanation: Supports the measured community diversity comparison, not lithium-only causation or a particular
+ physiological adaptation.
+ attaches_to:
+ - ecological_interactions#Community Composition Across Natural and Concentrated Brines
+curation_history:
+- timestamp: '2026-10-07T20:37:43Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain observed community differences at community scope; remove unmeasured pairwise benefit and physiological
+ causation. Issue#1786; reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
+ llm_assisted: true
diff --git a/kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml b/kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml
index 99db31418..17de040dd 100644
--- a/kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml
+++ b/kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml
@@ -286,9 +286,9 @@ taxonomy:
- *id001
ecological_interactions:
- name: Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
- description: The full twelve-strain bacterial SynCom antagonizes mature Sclerotinia sclerotiorum sclerotia in static tube
- co-culture, increasing mortality after 1 day and reaching complete sclerotia mortality by 14 days.
- interaction_type: COMPETITION
+ description: The full twelve-member inoculum increased sclerotium mortality relative to the control in the reported
+ laboratory comparison. This establishes a community treatment effect, not equal antagonistic contributions by
+ every member, resource competition with the fungus or a demonstrated cellular defense-response pathway.
scope: COMMUNITY_LEVEL
target_taxon:
preferred_term: Sclerotinia sclerotiorum
@@ -296,60 +296,107 @@ ecological_interactions:
id: NCBITaxon:5180
label: Sclerotinia sclerotiorum
gtdb_grounding_status: NO_GTDB_EQUIVALENT
- biological_processes:
- - preferred_term: defense response to fungus
- term:
- id: GO:0050832
- label: defense response to fungus
evidence:
- reference: PMID:42523014
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: When sclerotia were inoculated with the SynCom, sclerotia mortality was significantly increased after 1-day co-culture
- with the SynCom, gradually reaching 100.0% mortality by 14-day co-culture
+ snippet: When sclerotia were inoculated with the SynCom, sclerotia mortality was significantly increased after
+ 1-day co-culture with the SynCom, gradually reaching 100.0% mortality by 14-day co-culture
explanation: Supports full-SynCom causality for the sclerotium mortality phenotype.
-- name: Trinickia MC Key Contribution to Sclerotia Mortality
- description: 'The dropout experiment identified Trinickia sp. MC as the dominant single contributor: removing MC reduced
- sclerotia mortality, and MC mono-inoculation alone accelerated sclerotia mortality.'
- interaction_type: COMPETITION
- scope: COMMUNITY_LEVEL
participating_taxa:
+ - preferred_term: Caballeronia zhejiangensis N8
+ term:
+ id: NCBITaxon:871203
+ label: Caballeronia zhejiangensis
+ - preferred_term: Cupriavidus sp. N4
+ term:
+ id: NCBITaxon:106589
+ label: Cupriavidus
+ - preferred_term: Massilia sp. R20
+ term:
+ id: NCBITaxon:149698
+ label: Massilia
+ - preferred_term: Massilia sp. TB221
+ term:
+ id: NCBITaxon:149698
+ label: Massilia
+ - preferred_term: Massilia sp. RB201
+ term:
+ id: NCBITaxon:149698
+ label: Massilia
+ - preferred_term: Massilia sp. RB202
+ term:
+ id: NCBITaxon:149698
+ label: Massilia
+ - preferred_term: Paraburkholderia sp. I59
+ term:
+ id: NCBITaxon:1822464
+ label: Paraburkholderia
+ - preferred_term: Paraburkholderia phenoliruptrix TB211
+ term:
+ id: NCBITaxon:252970
+ label: Paraburkholderia phenoliruptrix
+ - preferred_term: Paraburkholderia phymatum R7
+ term:
+ id: NCBITaxon:148447
+ label: Paraburkholderia phymatum
+ - preferred_term: Paraburkholderia sp. T17
+ term:
+ id: NCBITaxon:1822464
+ label: Paraburkholderia
+ - preferred_term: Ralstonia sp. R4
+ term:
+ id: NCBITaxon:48736
+ label: Ralstonia
- preferred_term: Trinickia sclerotiorum sp. nov. MC
term:
id: NCBITaxon:2571160
label: Trinickia
+- name: Trinickia MC Key Contribution to Sclerotia Mortality
+ description: The dropout series and single-member comparison identify Trinickia MC as the strongest resolved contributor
+ to accelerated sclerotium mortality. Its contribution is context- and time-dependent, not proof that MC is uniquely
+ necessary for all eventual mortality or that every other member reinforces it. The primary discussion reports
+ attenuation by the remaining nine-member group and eventual mortality from assemblies lacking MC. This node
+ records the named member's contribution to the community intervention; Sclerotinia is the external challenge
+ context, not a thirteenth consortium member.
+ scope: COMMUNITY_LEVEL
target_taxon:
preferred_term: Sclerotinia sclerotiorum
term:
id: NCBITaxon:5180
label: Sclerotinia sclerotiorum
gtdb_grounding_status: NO_GTDB_EQUIVALENT
- biological_processes:
- - preferred_term: defense response to fungus
- term:
- id: GO:0050832
- label: defense response to fungus
downstream:
- target: Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
- description: Trinickia sp. MC is the strongest member-level contributor resolved by the dropout series.
+ description: The decrease in mortality following MC removal supports a causal contribution to the full-community
+ outcome over the measured time course. This is not an additive decomposition of member effects or proof of
+ universal necessity; other-member effects can attenuate MC and later reach the same endpoint.
evidence:
- reference: PMID:42523014
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: dropping TsMC significantly decreased mortality and its mono-inoculation alone could accelerate sclerotia mortality
- explanation: Supports Trinickia sp. MC as the dominant dropout-validated contributor to sclerotia mortality.
+ snippet: dropping TsMC significantly decreased mortality and its mono-inoculation alone could accelerate sclerotia
+ mortality
+ explanation: Supports a dropout-resolved MC contribution in the tested comparisons, not universal necessity
+ or an additive contribution model.
+ participating_taxa:
+ - preferred_term: Trinickia sclerotiorum sp. nov. MC
+ term:
+ id: NCBITaxon:2571160
+ label: Trinickia
- name: Spatial Invasion of Sclerotia by SynCom Members
- description: Xenium spatial profiling of inoculated sclerotia showed that Massilia sp. TB221 and R20 were early interior
- colonizers by day 3, while Ralstonia sp. R4 and Trinickia sp. MC progressively increased in interior layers at days 5
- to 7 and MC exceeded every other member across all five layers by day 14.
- interaction_type: NICHE_PARTITIONING
+ description: Spatial profiling detected early interior colonization by Massilia TB221 and R20, later interior
+ enrichment of Ralstonia R4 and Trinickia MC, and MC dominance across the sampled layers at the final observation.
+ These distribution and timing observations are not demonstrated competition-reducing niche partitioning or evidence
+ that early colonization itself causes mortality. The MC contribution is supported independently by the dropout
+ comparison, not inferred solely from its location.
scope: COMMUNITY_LEVEL
evidence:
- reference: PMID:42523014
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: By 3-day co-culture, Massilia sp. TB221 and Massilia sp. R20 had reached the interior sclerotia
- (layer 1 to 4)
+ snippet: By 3-day co-culture, Massilia sp. TB221 and Massilia sp. R20 had reached the interior sclerotia (layer
+ 1 to 4)
explanation: Supports Massilia sp. TB221 and Massilia sp. R20 as early interior sclerotium colonizers.
- reference: PMID:42523014
supports: SUPPORT
@@ -360,9 +407,26 @@ ecological_interactions:
- reference: PMID:42523014
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: By 14-day co-culture, when sclerotia viability was completely suppressed, the relative abundance of Trinickia
- sp. MC exceeded all other SynCom members simultaneously across layer 1 to 5
+ snippet: By 14-day co-culture, when sclerotia viability was completely suppressed, the relative abundance of
+ Trinickia sp. MC exceeded all other SynCom members simultaneously across layer 1 to 5
explanation: Supports Trinickia sp. MC dominance across all five sclerotium layers at day 14.
+ participating_taxa:
+ - preferred_term: Massilia sp. TB221
+ term:
+ id: NCBITaxon:149698
+ label: Massilia
+ - preferred_term: Massilia sp. R20
+ term:
+ id: NCBITaxon:149698
+ label: Massilia
+ - preferred_term: Ralstonia sp. R4
+ term:
+ id: NCBITaxon:48736
+ label: Ralstonia
+ - preferred_term: Trinickia sclerotiorum sp. nov. MC
+ term:
+ id: NCBITaxon:2571160
+ label: Trinickia
environmental_factors:
- name: flooded non-autoclaved soil source condition
value: 5-day burial under flooding
@@ -497,42 +561,64 @@ external_resources:
explanation: Gives the DOI of the primary publication.
discussions:
- discussion_id: trinickia_mc_species_ncbitaxon_gap
- prompt: Has Trinickia sclerotiorum sp. nov. MC been assigned an NCBITaxon species identifier or stable strain genome assembly
- accession that should replace the current genus-level grounding?
+ prompt: Has Trinickia sclerotiorum sp. nov. MC been assigned an NCBITaxon species identifier or stable strain
+ genome assembly accession that should replace the current genus-level grounding?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- taxonomy#Trinickia sclerotiorum sp. nov. MC
- rationale: The 2026 paper describes MC as a novel Trinickia species using core-gene phylogeny, ANI and dDDH, but the local
- NCBITaxon snapshot resolves Trinickia and not the proposed species name.
+ rationale: The 2026 paper describes MC as a novel Trinickia species using core-gene phylogeny, ANI and dDDH, but
+ the local NCBITaxon snapshot resolves Trinickia and not the proposed species name.
evidence:
- reference: PMID:42523014
supports: SUPPORT
evidence_source: full_text
- snippet: These results indicate TsMC does not belong to any known Trinickia species and thus we describe this strain as
- a new species, Trinickia sclerotiorum sp. nov. type strain MC
- explanation: Supports the novel-species status that is not yet available as a species-level local NCBITaxon term.
+ snippet: These results indicate TsMC does not belong to any known Trinickia species and thus we describe this
+ strain as a new species, Trinickia sclerotiorum sp. nov. type strain MC
+ explanation: Supports the novel-species status that is not yet available as a species-level local NCBITaxon
+ term.
posed_by: codex
posed_date: '2026-09-13'
- discussion_id: sclerotia_syncom_partial_abundance_coverage
- prompt: Which additional bacteria in the 5-day flooded-soil sclerotium microbiome account for the abundance not captured
- by the twelve-strain SynCom?
+ prompt: Which additional bacteria in the 5-day flooded-soil sclerotium microbiome account for the abundance not
+ captured by the twelve-strain SynCom?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- engineering_design
- ecological_interactions#Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
- rationale: The SynCom covered most of the 5-day SF microbiome at genus level but only 56.3% at species level, so the full
- flooded-soil sclerotium microbiome may include interaction complexity absent from the defined assembly.
+ rationale: The SynCom covered most of the 5-day SF microbiome at genus level but only 56.3% at species level,
+ so the full flooded-soil sclerotium microbiome may include interaction complexity absent from the defined assembly.
evidence:
- reference: PMID:42523014
supports: SUPPORT
evidence_source: full_text
- snippet: As our SynCom represents only 56.3% bacterial abundance of 5-day SF microbiome, higher level of the complexity
- in the bacteria-bacteria interaction may not be captured in this study
+ snippet: As our SynCom represents only 56.3% bacterial abundance of 5-day SF microbiome, higher level of the
+ complexity in the bacteria-bacteria interaction may not be captured in this study
explanation: Records the authors' caveat about the partial species-level coverage of the defined SynCom.
posed_by: codex
posed_date: '2026-09-13'
+- discussion_id: sclerotia_graph_evidence_scope
+ prompt: Which mechanisms explain the context-dependent antagonism and spatial associations?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: Mortality contrasts support the community and MC treatment effects, while the spatial profile alone
+ does not establish facilitation, resource competition or reduced competition among bacteria. Nonadditive effects
+ and eventual mortality in assemblies lacking MC limit an essential-member interpretation. Molecular mechanisms
+ remain unresolved; no new pathway, culturing procedure or genetic design is introduced. Existing taxonomic and
+ partial-coverage discussions remain unchanged.
+ evidence:
+ - reference: PMID:42523014
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: dropping TsMC significantly decreased mortality and its mono-inoculation alone could accelerate sclerotia
+ mortality
+ explanation: Supports a dropout-resolved MC contribution in the tested comparisons, not universal necessity
+ or an additive contribution model.
+ attaches_to:
+ - ecological_interactions#Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
+ - ecological_interactions#Trinickia MC Key Contribution to Sclerotia Mortality
+ - ecological_interactions#Spatial Invasion of Sclerotia by SynCom Members
metals_present: []
rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
@@ -541,16 +627,29 @@ curation_history:
- timestamp: '2026-09-13T17:00:42Z'
curator: codex
action: CREATE_COMMUNITY
- changes: Created CommunityMech:000364 for the twelve-strain Sclerotinia sclerotiorum sclerotia biocontrol SynCom from PMID:42523014
- / doi:10.1093/ismejo/wrag201, preserving all strain designations, exact PubMed and open-access manuscript snippets, genus-level
- Massilia and Paraburkholderia GTDB groundings, and explicit unresolved statuses for the remaining bacterial taxa.
+ changes: Created CommunityMech:000364 for the twelve-strain Sclerotinia sclerotiorum sclerotia biocontrol SynCom
+ from PMID:42523014 / doi:10.1093/ismejo/wrag201, preserving all strain designations, exact PubMed and open-access
+ manuscript snippets, genus-level Massilia and Paraburkholderia GTDB groundings, and explicit unresolved statuses
+ for the remaining bacterial taxa.
llm_assisted: true
- timestamp: '2026-09-13T17:07:17Z'
curator: codex
action: RESOLVE_REVIEW_ISSUE
- changes: >-
- Replaced the broad Xenium spatial summary evidence with exact day-3, day-5-to-7
- and day-14 layer-level snippets from PMID:42523014, and added exact method
- snippets for SynCom OD600 normalization, the 28-probe Xenium panel and
- Xenium signal-density extraction to resolve adversarial-review issue #852.
+ changes: 'Replaced the broad Xenium spatial summary evidence with exact day-3, day-5-to-7 and day-14 layer-level
+ snippets from PMID:42523014, and added exact method snippets for SynCom OD600 normalization, the 28-probe Xenium
+ panel and Xenium signal-density extraction to resolve adversarial-review issue #852.'
+ llm_assisted: true
+- timestamp: '2026-10-07T20:37:43Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain full-community antagonism with all twelve inoculum identities, without competition/defense ontology
+ overclaims.; Retain the dropout-supported pairwise MC contribution and its direction, without universal necessity
+ or additivity.; Retain measured spatial timing and scoped participants, without niche-partitioning or colonization-causality
+ claims. Issue#1787; reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
+ llm_assisted: true
+- timestamp: '2026-10-07T20:41:33Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH_SCOPE_CORRECTION
+ changes: Keep the MC dropout result at community-contribution scope with only MC as participant and the fungal
+ challenge as external context; do not assert a pairwise consortium-membership relation. Issue#1787; reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 088d61132..e948af966 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -1125,3 +1125,21 @@ replicate. Caches and non-graph blocks remain unchanged, not recertified.
No new topology or provider spend. Repairs #1778-#1781 await protected-main
merge; non-graph #1782 and ontology #463 remain open. Self-review is not
independent approval or corpus completion.
+
+## Batch99: Resource Loops And Claim Scope
+
+[Decisions](decisions/20261007-four-records-batch99.yaml),
+[validation](validation-20261007-batch99.json),
+[cache provenance](cache-provenance-20261007-batch99.json) and
+[self-adversarial review](adversarial-review-20261007-batch99.yaml) cover the
+yeast-alga mutualism, resveratrol yeast coculture, Atacama brine and sclerotia
+biocontrol community. Nine of fourteen nodes and four of six directions remain.
+Reciprocal resource dependence and measured treatment outcomes remain, with
+unisolated mediation distinguished from direct causal evidence. Unsupported
+oxygen-benefit and brine metabolic claims are removed. Spatial timing does not
+establish niche partitioning; dropout contribution is not universal necessity.
+Two accepted-manuscript quotations have explicit final-version wording checks.
+Caches and non-graph blocks are unchanged, not recertified. No new topology,
+experimental instructions or provider spend. Repairs #1784-#1787 await protected
+main merge; non-graph #1788, cache provenance #1789 and re-evidencing #765 stay
+open. Self-review is not independent approval or corpus completion.
diff --git a/reports/causal_graph_review/adversarial-review-20261007-batch99.yaml b/reports/causal_graph_review/adversarial-review-20261007-batch99.yaml
new file mode 100644
index 000000000..f7cd6e9a1
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261007-batch99.yaml
@@ -0,0 +1,254 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: af0cc46dc2b6438010297cea796110a22ed78771
+scope:
+- kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml
+- kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml
+- kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml
+- kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
+validation_report: reports/causal_graph_review/validation-20261007-batch99.json
+findings:
+- issue: 1784
+ severity: P2
+ status: addressed_in_this_change
+ finding: Bound yeast-alga causal loop and remove unmeasured oxygen benefit
+ disposition: Close only after protected-main merge.
+- issue: 1785
+ severity: P2
+ status: addressed_in_this_change
+ finding: Distinguish resveratrol production enhancement from mutualistic fitness
+ disposition: Close only after protected-main merge.
+- issue: 1786
+ severity: P2
+ status: addressed_in_this_change
+ finding: Remove unsupported Atacama brine exchange and nutrient-cycle graph claims
+ disposition: Close only after protected-main merge.
+- issue: 1787
+ severity: P2
+ status: addressed_in_this_change
+ finding: Correct sclerotia biocontrol interaction labels and contributor scope
+ disposition: Close only after protected-main merge.
+- issue: 1788
+ severity: P2
+ status: open_non_graph_follow_up
+ finding: Review non-graph brine scope and sclerotia manuscript-version discrepancies
+ disposition: Separate non-graph curation required.
+- issue: 1789
+ severity: P2
+ status: open_non_graph_follow_up
+ finding: Reconcile yeast-alga cache body with its abstract-only and license notice
+ disposition: Separate non-graph curation required.
+adversarial_checks:
+- Fresh both-root baseline preceded source reads. Four whole records/all14nodes/6directions reviewed. Nine nodes/four
+ existing directions remain; five unsupported nodes/two arrows removed, one rename. No new topology/provider spend.
+- 'Yeast-alga: retain reciprocal carbon/nitrogen dependence and both directions with PARTIAL mediation bounds. Oxygen
+ release alone does not establish a yeast benefit. Do not infer fermentation as the sole carbon-dioxide source.'
+- 'Resveratrol: coauxotrophy remains MUTUALISM, pathway handoff remains CROSS_FEEDING, but aggregate titer is not
+ mutualistic fitness. Retain controls, precursor accumulation and biomass tradeoff; the existing pathway-to-production
+ direction is PARTIAL, not an isolated explanation of the FLO1 increment.'
+- 'Atacama: retain the community composition comparison without lithium-only causation. Taxon presence is not demonstrated
+ exchange, nutrient recycling, phototrophy or functional redundancy. Four functional nodes and both arrows removed;
+ no claim that these processes are biologically impossible.'
+- 'Sclerotia: retain laboratory treatment effects and the MC dropout contribution, but not resource competition,
+ defense-process ontology, niche-partitioning or colonization-only causation. Preserve nonadditivity and time dependence.
+ The fungal challenge remains external to the twelve-member consortium.'
+- Adversarial preflight identified an UNKNOWN_TARGET error after initially assigning MC pairwise scope. Corrected
+ to a one-participant community-contribution node; appended a fifth history, preserving the original four. Failed
+ preflight exit3/output digest is recorded. Audit rules were not weakened.
+- All12graph and4new-discussion quotations match maintained caches. Fourteen match fresh primary text after normalization.
+ Two spatial excerpts have explicit accepted-manuscript/final-article wording equivalences, with final text separately
+ checked; they are not mislabeled literal matches. No full-cache, figure-pixel, supplement or raw-data certification.
+- Four records changed;456otherrecords,923caches and all non-graph raw blocks preserved. Exactly one participant-list
+ user added. Community-level census402->403 reflects Atacama, with exactly six existing members; mixed128unchanged,
+ community-only274->275, taxa1542->1548 and solely community-credited1268->1274. Only the community-level bound
+ increases by one; no runtime connectivity rule changes.
+- Eight focused tests and904combined regressions passed.43finalgate records/digests include five history validations.
+ Network retains56pre-existing warnings and zero structural defects. HTML-description parsing/deterministic rendering
+ is not screenshots; postcommit docs-current is separate.
+- Six matching all-state issue bodies read after ignored/hidden-inclusive dedup with recorded exclusions. Graph1784-1787
+ await protected-main merge; non-graph1788/provenance1789 and broader765 stay open. Access limits include XML500
+ and direct403; normal public pages were used without bypass. Loader1703/Linux DOI-cache1091 not certified.
+- Self-adversarial COMMENT is not independent approval. No protection bypass, fabricated CI or premature closure.
+ Corpus312reviewed/100pending/48needs_research is not complete.
+adversarial_prepublication_fix:
+ findings:
+ - issue: 1787
+ finding: Pairwise scope incorrectly applied consortium-member validation to an external fungal challenge.
+ disposition: Keep the MC dropout result at community-contribution scope with only MC as participant and the
+ fungal challenge as external context; do not assert a pairwise consortium-membership relation.
+ preserved_initial_histories:
+ history/records/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism/2026-10-07T203744Z-codex-e34e15.yaml: e66b28def57972ffacf422722d2ad0ed50bb01b0b59326b8fc9d25ae53ccf755
+ history/records/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture/2026-10-07T203744Z-codex-d0f5ea.yaml: ee532658b263d5c3d448f8c0fa3f45d313fd9994c609131a7724067c756cf514
+ history/records/Salar_Atacama_Lithium_Brine_Community/2026-10-07T203744Z-codex-599245.yaml: 0bbbb168df42120949b0ff42f876ec87516d8f854947d7449463930a5d294a03
+ history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T203745Z-codex-dc367a.yaml: 5b2a6839c615e4dd3bdf58871236580ef7dee4eeff93cc61a95d52c49bb0cac4
+ correction_history: history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T204135Z-codex-cb916b.yaml
+ preflight:
+ command:
+ - /Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3
+ - -m
+ - communitymech.cli
+ - audit-network
+ - --json
+ exit_code: 3
+ log: /private/tmp/communitymech-batch99/preflight-network.json
+ log_sha256: ae22e472a4cdd0a7ab551479ebaa0be0b5cbd0228e91e51872d638ea217856a3
+ status: Corrected before final full verification; no audit severity rule changed.
+verification:
+ combined_regressions: 904 passed in 453.95s (0:07:33)
+ new_regression_tests: 8
+ total_recorded_gate_outputs: 43
+ primary_graph_snippet_proof:
+ graph_quotations: 12
+ new_discussion_quotations: 4
+ fresh_primary_literal_matches: 14
+ documented_manuscript_version_equivalents: 2
+ all_cached_literal_matches: 16
+ retained_nodes: 9
+ removed_nodes: 5
+ retained_arrows: 4
+ removed_arrows: 2
+ new_nodes_or_directions: 0
+ scope: Two sclerotia spatial excerpts differ between accepted manuscript and final article, with exact final
+ wording separately matched. All other reviewed quotations match fresh primary text literally after normalization;
+ entailment is a separate review.
+ 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; primary access and section limits are recorded in the
+ ledger. CLI Total checks counts issues,not executed checks. Loader1703 not certified.
+ snippet_counts_by_record:
+ kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml:
+ MATCH: 6
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml:
+ MATCH: 17
+ RENDERING: 1
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:
+ MATCH: 23
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml:
+ MATCH: 34
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 8947
+ categories:
+ MATCH: 8812
+ 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: Five unsupported nodes/two arrows removed; all56pre-existing warnings unchanged,zero structural
+ defects. Initial external-target scope error corrected without changing audit rules.
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml: d074d1dd6b8e027bb5c8174d73c1d3c9493e80fe254a5326386369fb6ebd4167
+ tests/test_causal_review_batch99.py: bbf33fc0ee37a4dcf83afbb4bbceada82f22d68db28ffb0e7df2c5c9dc388470
+ tests/test_participating_taxa.py: 66913594c22331ac6cb551eef0a2ca8cf6c468875ae38e1dc98c1a1af21af9f3
+ tests/test_community_level_connectivity_credit.py: b758fe7bfd3428e33fbc9c6ac1cf363747bcad39cac1a28dc659bfbbd6532512
+ reports/causal_graph_review/README.md: 87d16c9a996950f759d8b0a2fe8560f3f00daa895f01fbd5b0fbfa6e97223685
+ reports/causal_graph_review/cache-provenance-20261007-batch99.json: a1739bef0423fe4536237e3bbd3828e3b60acbd3e18fae08f8e33819a7348cac
+ kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml: fec7e6a58cc17fca35752ff7a4d5c8bbd012cde000682fabef435f0f0e55f80d
+ kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml: d7f617d83df5d01dc2dafc8d7944fe482f4c9046d78337fd6c19040c95ec6baa
+ kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml: 4e9934084bc572a4f98d5f209c5b21d853e5e3405d5ba5059be0f05cd18f00dd
+ kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml: b76f915e08d08faf1516698a67c53bb6e25f912bd8d4803dfe55412f1a100a3e
+ unchanged_records: 456
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 782
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Remove unsupported existing claims and bound retained directions; no new mechanisms or topology.
+ post_commit_docs_current: Separate publication gate, not preasserted.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 402
+ mixed: 128
+ community_level_only: 274
+ taxa: 1542
+ credited_solely_by_the_rule: 1268
+ current:
+ records: 460
+ with_community_level: 403
+ mixed: 128
+ community_level_only: 275
+ taxa: 1548
+ credited_solely_by_the_rule: 1274
+ delta:
+ records: 0
+ with_community_level: 1
+ mixed: 0
+ community_level_only: 1
+ taxa: 6
+ credited_solely_by_the_rule: 6
+ interpretation: Atacama becomes a community-profile node with six named existing taxa. MC remains a one-participant
+ community contribution, with external fungal challenge not made a consortium member. Community-level count402->403
+ and solely community-credited taxa1268->1274 reflect this scope correction, not a runtime-rule change. Exact
+ participant allowlist adds one stem; only the community-level census ceiling increases by one.
+corpus:
+ records: 460
+ nodes: 1405
+ edges: 570
+ review_status_counts:
+ needs_research: 48
+ pending: 100
+ reviewed: 312
+limitations:
+- Four whole records and all14originalnodes/6arrows reviewed. Retain9nodes/4arrows, remove5unsupportednodes/2arrows,
+ rename1node. Four changed records; no new topology or Edison submission/spend.
+- 'Yeast-alga: fresh abstract and public PMC author-manuscript main text1-155, including Figure1 caption, read.
+ Reciprocal carbon/nitrogen support retained; oxygen release is not an isolated yeast benefit. EuropePMC XML returnedHTTP500;
+ normal public PMC HTML succeeded. Existing body quotations remain, no new body text cached; issue1789 tracks inconsistent
+ cache provenance and765 broader re-evidencing.'
+- 'Resveratrol: fresh primary results227-277/309-389 and discussion391-455 read. Condition-dependent coauxotrophy
+ and titer comparisons retained; no direct transfer-flux claim or inference that increased product titer establishes
+ mutualistic fitness. Precursor accumulation and biomass tradeoff retained.'
+- 'Brine: publisher web-rendered abstract163-168, main text190-310 including methods and results read. EuropePMC
+ DOI search returned no record; direct publisher fetch403 stopped, normal public web text was available. Two-brine
+ composition comparison is not a lithium-only perturbation or demonstrated functional exchange. Four unsupported
+ functional nodes removed, not asserted biologically impossible.'
+- 'Sclerotia: fresh final primary results385-466 and discussion480-540 read. Three nodes and dropout-supported direction
+ retained; spatial order is not causation or competition relief. Only graph claims changed; no new wet-lab/genetic
+ instructions. Cached accepted-manuscript quotations match directly; two spatial excerpts differ slightly from
+ final article (range rendering and added that of), with both versions recorded and exact normalized final-text
+ checks. Non-graph version differences remain in1788.'
+- Relevant cache content and graph snippets checked. Flattened resveratrol cache search output was truncated, so
+ complete cache-body review is not claimed. No figure-pixel/supplement/raw-data review. All923caches unchanged;
+ fresh complete papers remain private local artifacts, not published.
+- All456otherrecords, canonical taxonomy and non-graph raw blocks preserved; four initial histories plus one append-only
+ scope-correction history. Identity-only participant lists use exact existing members. Brine participant list denotes
+ a curated subset across samples; full biocontrol inoculum does not imply equal contribution. No runtime connectivity
+ semantics changed.
+- Six matching all-state issue bodies read; fresh ignored/hidden-inclusive local dedup excluded .git/docs/site/references_cache,
+ with relevant caches separately inspected. Comments/PRs not exhaustive. Graph1784-1787 await protected-main merge.
+ Non-graph1788, provenance1789 and broader765 remain open.
+- Self-adversarial review is not independent approval or corpus completion. Loader1703 and DOI-cache1091 not certified.
+ Denied/unanswered Edison scopes unchanged. Validation and publication not preasserted.
diff --git a/reports/causal_graph_review/cache-provenance-20261007-batch99.json b/reports/causal_graph_review/cache-provenance-20261007-batch99.json
new file mode 100644
index 000000000..3f59145e5
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261007-batch99.json
@@ -0,0 +1,64 @@
+{
+ "changes": [],
+ "baseline_files_preserved": 923,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch99/alga-metadata.json": "41994c41d3bd406f73cbdcc1899ecae4d2ce2d9b79d692dd7edfabce21b8b6fd",
+ "/private/tmp/communitymech-batch99/alga-primary.txt": "0be25d355cea62fa7f1e432c574d856800de7a7e65bbcae625c464f5aca4be80",
+ "/private/tmp/communitymech-batch99/alga-publisher.html": "a191336a4c3a3d971730a4677b8fcfba7ed2ed7851b73789d7a76274d0529a70",
+ "/private/tmp/communitymech-batch99/alga-publisher.txt": "a08a42133516b75bc2689f07e5eddabb454553dc031298cec957cb2ae06a9bb9",
+ "/private/tmp/communitymech-batch99/baseline.json": "4eddccbe3aa2e4e320075b23c20d8a9445e8ee97cb71cae93c5e0e91de8854e5",
+ "/private/tmp/communitymech-batch99/brine-metadata.json": "19321c8455a193df9af12f73b5515a4d819bce83427f6ab62650e3fbef9aa299",
+ "/private/tmp/communitymech-batch99/brine-web-abstract.txt": "4dfba6f1c5b8f8e86dd738360c9577f69f0b0e74a03f0e4b1495d21ba05787d2",
+ "/private/tmp/communitymech-batch99/brine-web-results.txt": "62b63b393d1b49670d6df0dc62381ffad3dc99815f8d6fc01050c99c8190afff",
+ "/private/tmp/communitymech-batch99/dedup-local-current.txt": "e0cb4682ed93c311d852861d4d0e16a8967c8ad40d520a3cb7f7c279acb35771",
+ "/private/tmp/communitymech-batch99/issue-dedup-current.json": "190eac11304d9cbb1a197a5dcc231433e4b8380e6476c04509e2a3d41d5c561c",
+ "/private/tmp/communitymech-batch99/primary-manifest.json": "f2f6341b0ea3cfee4fac868de770fcd6ce1daffc85fc038736e994155f601f09",
+ "/private/tmp/communitymech-batch99/publisher-manifest.json": "5c03d4a06bbff29c5b0b48e83ffd79f644a0c50781c6456670b28cc508604dca",
+ "/private/tmp/communitymech-batch99/resveratrol-metadata.json": "d0caa58e82f39474ff1d0d69364b54daa85b394f0c3309ef752fc6aa5a9a0f5b",
+ "/private/tmp/communitymech-batch99/resveratrol-primary.txt": "86a4878aae9d9ea2c1f5bb66f05bcf8e2a6fe02fbbd8ed2ac0e06f6afd090f09",
+ "/private/tmp/communitymech-batch99/resveratrol-primary.xml": "b603906b52fd2447de1c1b976b993f1207ec08097555fec421da5d83fec1f0ee",
+ "/private/tmp/communitymech-batch99/sclerotia-metadata.json": "7c479d9940c422a9b5492eb4e1de43bfb75deca4457de9802afbd9d4ad1265a5",
+ "/private/tmp/communitymech-batch99/sclerotia-primary.txt": "480b73f04ffb591f059c609a34040c1681cfbacd8ca171e4a859b0f3d4768b48",
+ "/private/tmp/communitymech-batch99/sclerotia-primary.xml": "36927d702d7a5d7d1ce17db154250d5bebc57c3c1ed63d51230648a7e530a7ae",
+ "references_cache/PMID_24994654.md": "f6df25b9f7b415ad865d97134556f6bcd18ca1e36ab91f290cc2d525e35e08f9",
+ "references_cache/PMID_41491832.txt": "6860bca7ce19e9f4f9f187f2fd09c3dc064e4152e42152510e52fef19a8a8135",
+ "references_cache/PMID_42523014.txt": "78e19019cf62c0b4314eb190b977aa9202c75bf07da7e559eef3f14bf692acbd",
+ "references_cache/doi_10.1029_2018JG004621.md": "43e8953e1ca352c98c64d0ed00d504b97e6a7b3a0eb6db090989665f50b2b0e3"
+ },
+ "source_access": [
+ {
+ "reference": "PMID:24994654",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A24994654+AND+SRC%3AMED&format=json&resultType=core",
+ "accessed_scope": "Yeast-alga: fresh abstract and public PMC author-manuscript main text1-155, including Figure1 caption, read. Reciprocal carbon/nitrogen support retained; oxygen release is not an isolated yeast benefit. EuropePMC XML returnedHTTP500; normal public PMC HTML succeeded. Existing body quotations remain, no new body text cached; issue1789 tracks inconsistent cache provenance and765 broader re-evidencing.",
+ "fulltext_error": "XML returned HTTP500; no full text retrieved."
+ },
+ {
+ "reference": "PMID:41491832",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13303087/fullTextXML",
+ "accessed_scope": "Resveratrol: fresh primary results227-277/309-389 and discussion391-455 read. Condition-dependent coauxotrophy and titer comparisons retained; no direct transfer-flux claim or inference that increased product titer establishes mutualistic fitness. Precursor accumulation and biomass tradeoff retained.",
+ "fulltext_error": null
+ },
+ {
+ "reference": "PMID:42523014",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13615538/fullTextXML",
+ "accessed_scope": "Sclerotia: fresh final primary results385-466 and discussion480-540 read. Three nodes and dropout-supported direction retained; spatial order is not causation or competition relief. Only graph claims changed; no new wet-lab/genetic instructions. Cached accepted-manuscript quotations match directly; two spatial excerpts differ slightly from final article (range rendering and added that of), with both versions recorded and exact normalized final-text checks. Non-graph version differences remain in1788.",
+ "fulltext_error": null
+ },
+ {
+ "reference": "doi:10.1029/2018JG004621",
+ "url": "https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2018JG004621",
+ "accessed_scope": "Brine: publisher web-rendered abstract163-168, main text190-310 including methods and results read. EuropePMC DOI search returned no record; direct publisher fetch403 stopped, normal public web text was available. Two-brine composition comparison is not a lithium-only perturbation or demonstrated functional exchange. Four unsupported functional nodes removed, not asserted biologically impossible.",
+ "fulltext_error": "DOI absent from EuropePMC; direct403; public web main text read."
+ }
+ ],
+ "limitations": [
+ "Four whole records and all14originalnodes/6arrows reviewed. Retain9nodes/4arrows, remove5unsupportednodes/2arrows, rename1node. Four changed records; no new topology or Edison submission/spend.",
+ "Yeast-alga: fresh abstract and public PMC author-manuscript main text1-155, including Figure1 caption, read. Reciprocal carbon/nitrogen support retained; oxygen release is not an isolated yeast benefit. EuropePMC XML returnedHTTP500; normal public PMC HTML succeeded. Existing body quotations remain, no new body text cached; issue1789 tracks inconsistent cache provenance and765 broader re-evidencing.",
+ "Resveratrol: fresh primary results227-277/309-389 and discussion391-455 read. Condition-dependent coauxotrophy and titer comparisons retained; no direct transfer-flux claim or inference that increased product titer establishes mutualistic fitness. Precursor accumulation and biomass tradeoff retained.",
+ "Brine: publisher web-rendered abstract163-168, main text190-310 including methods and results read. EuropePMC DOI search returned no record; direct publisher fetch403 stopped, normal public web text was available. Two-brine composition comparison is not a lithium-only perturbation or demonstrated functional exchange. Four unsupported functional nodes removed, not asserted biologically impossible.",
+ "Sclerotia: fresh final primary results385-466 and discussion480-540 read. Three nodes and dropout-supported direction retained; spatial order is not causation or competition relief. Only graph claims changed; no new wet-lab/genetic instructions. Cached accepted-manuscript quotations match directly; two spatial excerpts differ slightly from final article (range rendering and added that of), with both versions recorded and exact normalized final-text checks. Non-graph version differences remain in1788.",
+ "Relevant cache content and graph snippets checked. Flattened resveratrol cache search output was truncated, so complete cache-body review is not claimed. No figure-pixel/supplement/raw-data review. All923caches unchanged; fresh complete papers remain private local artifacts, not published.",
+ "All456otherrecords, canonical taxonomy and non-graph raw blocks preserved; four initial histories plus one append-only scope-correction history. Identity-only participant lists use exact existing members. Brine participant list denotes a curated subset across samples; full biocontrol inoculum does not imply equal contribution. No runtime connectivity semantics changed.",
+ "Six matching all-state issue bodies read; fresh ignored/hidden-inclusive local dedup excluded .git/docs/site/references_cache, with relevant caches separately inspected. Comments/PRs not exhaustive. Graph1784-1787 await protected-main merge. Non-graph1788, provenance1789 and broader765 remain open."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml b/reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
new file mode 100644
index 000000000..383c241b8
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
@@ -0,0 +1,585 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: af0cc46dc2b6438010297cea796110a22ed78771
+baseline_commit: af0cc46dc2b6438010297cea796110a22ed78771
+base_tree: afcdcd4ca8a24c7deb82e3e48eea85e9564fc48f
+pre_source_baseline_sha256: 4eddccbe3aa2e4e320075b23c20d8a9445e8ee97cb71cae93c5e0e91de8854e5
+issues:
+- 1784
+- 1785
+- 1786
+- 1787
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1788
+- 1789
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 1043
+ matching_issues:
+ - 1133
+ - 1132
+ - 852
+ - 765
+ - 754
+ - 697
+ ignored_hidden_local_search: true
+source_access:
+- reference: PMID:24994654
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A24994654+AND+SRC%3AMED&format=json&resultType=core
+ accessed_scope: 'Yeast-alga: fresh abstract and public PMC author-manuscript main text1-155, including Figure1
+ caption, read. Reciprocal carbon/nitrogen support retained; oxygen release is not an isolated yeast benefit.
+ EuropePMC XML returnedHTTP500; normal public PMC HTML succeeded. Existing body quotations remain, no new body
+ text cached; issue1789 tracks inconsistent cache provenance and765 broader re-evidencing.'
+ fulltext_error: XML returned HTTP500; no full text retrieved.
+- reference: PMID:41491832
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13303087/fullTextXML
+ accessed_scope: 'Resveratrol: fresh primary results227-277/309-389 and discussion391-455 read. Condition-dependent
+ coauxotrophy and titer comparisons retained; no direct transfer-flux claim or inference that increased product
+ titer establishes mutualistic fitness. Precursor accumulation and biomass tradeoff retained.'
+ fulltext_error: null
+- reference: PMID:42523014
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13615538/fullTextXML
+ accessed_scope: 'Sclerotia: fresh final primary results385-466 and discussion480-540 read. Three nodes and dropout-supported
+ direction retained; spatial order is not causation or competition relief. Only graph claims changed; no new
+ wet-lab/genetic instructions. Cached accepted-manuscript quotations match directly; two spatial excerpts differ
+ slightly from final article (range rendering and added that of), with both versions recorded and exact normalized
+ final-text checks. Non-graph version differences remain in1788.'
+ fulltext_error: null
+- reference: doi:10.1029/2018JG004621
+ url: https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2018JG004621
+ accessed_scope: 'Brine: publisher web-rendered abstract163-168, main text190-310 including methods and results
+ read. EuropePMC DOI search returned no record; direct publisher fetch403 stopped, normal public web text was
+ available. Two-brine composition comparison is not a lithium-only perturbation or demonstrated functional exchange.
+ Four unsupported functional nodes removed, not asserted biologically impossible.'
+ fulltext_error: DOI absent from EuropePMC; direct403; public web main text read.
+primary_artifacts:
+ /private/tmp/communitymech-batch99/alga-metadata.json: 41994c41d3bd406f73cbdcc1899ecae4d2ce2d9b79d692dd7edfabce21b8b6fd
+ /private/tmp/communitymech-batch99/alga-primary.txt: 0be25d355cea62fa7f1e432c574d856800de7a7e65bbcae625c464f5aca4be80
+ /private/tmp/communitymech-batch99/alga-publisher.html: a191336a4c3a3d971730a4677b8fcfba7ed2ed7851b73789d7a76274d0529a70
+ /private/tmp/communitymech-batch99/alga-publisher.txt: a08a42133516b75bc2689f07e5eddabb454553dc031298cec957cb2ae06a9bb9
+ /private/tmp/communitymech-batch99/baseline.json: 4eddccbe3aa2e4e320075b23c20d8a9445e8ee97cb71cae93c5e0e91de8854e5
+ /private/tmp/communitymech-batch99/brine-metadata.json: 19321c8455a193df9af12f73b5515a4d819bce83427f6ab62650e3fbef9aa299
+ /private/tmp/communitymech-batch99/brine-web-abstract.txt: 4dfba6f1c5b8f8e86dd738360c9577f69f0b0e74a03f0e4b1495d21ba05787d2
+ /private/tmp/communitymech-batch99/brine-web-results.txt: 62b63b393d1b49670d6df0dc62381ffad3dc99815f8d6fc01050c99c8190afff
+ /private/tmp/communitymech-batch99/dedup-local-current.txt: e0cb4682ed93c311d852861d4d0e16a8967c8ad40d520a3cb7f7c279acb35771
+ /private/tmp/communitymech-batch99/issue-dedup-current.json: 190eac11304d9cbb1a197a5dcc231433e4b8380e6476c04509e2a3d41d5c561c
+ /private/tmp/communitymech-batch99/primary-manifest.json: f2f6341b0ea3cfee4fac868de770fcd6ce1daffc85fc038736e994155f601f09
+ /private/tmp/communitymech-batch99/publisher-manifest.json: 5c03d4a06bbff29c5b0b48e83ffd79f644a0c50781c6456670b28cc508604dca
+ /private/tmp/communitymech-batch99/resveratrol-metadata.json: d0caa58e82f39474ff1d0d69364b54daa85b394f0c3309ef752fc6aa5a9a0f5b
+ /private/tmp/communitymech-batch99/resveratrol-primary.txt: 86a4878aae9d9ea2c1f5bb66f05bcf8e2a6fe02fbbd8ed2ac0e06f6afd090f09
+ /private/tmp/communitymech-batch99/resveratrol-primary.xml: b603906b52fd2447de1c1b976b993f1207ec08097555fec421da5d83fec1f0ee
+ /private/tmp/communitymech-batch99/sclerotia-metadata.json: 7c479d9940c422a9b5492eb4e1de43bfb75deca4457de9802afbd9d4ad1265a5
+ /private/tmp/communitymech-batch99/sclerotia-primary.txt: 480b73f04ffb591f059c609a34040c1681cfbacd8ca171e4a859b0f3d4768b48
+ /private/tmp/communitymech-batch99/sclerotia-primary.xml: 36927d702d7a5d7d1ce17db154250d5bebc57c3c1ed63d51230648a7e530a7ae
+ references_cache/PMID_24994654.md: f6df25b9f7b415ad865d97134556f6bcd18ca1e36ab91f290cc2d525e35e08f9
+ references_cache/PMID_41491832.txt: 6860bca7ce19e9f4f9f187f2fd09c3dc064e4152e42152510e52fef19a8a8135
+ references_cache/PMID_42523014.txt: 78e19019cf62c0b4314eb190b977aa9202c75bf07da7e559eef3f14bf692acbd
+ references_cache/doi_10.1029_2018JG004621.md: 43e8953e1ca352c98c64d0ed00d504b97e6a7b3a0eb6db090989665f50b2b0e3
+primary_graph_snippet_count: 12
+snippet_checks:
+- record: Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism
+ node: Yeast Carbon Dioxide Provisioning
+ evidence_index: 0
+ reference: PMID:24994654
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: S. cerevisiae metabolizes glucose to carbon dioxide (CO2), a carbon source that C. reinhardtii
+ fixes via photosynthesis
+ matched_artifact: /private/tmp/communitymech-batch99/alga-publisher.txt
+ cache_artifact: references_cache/PMID_24994654.md
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism
+ node: Algal Reduced Nitrogen Provisioning
+ evidence_index: 0
+ reference: PMID:24994654
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: "C. reinhardtii reduces nitrite (NO2\u2212) into ammonia (NH3) (14), which yeast can use\
+ \ as a nitrogen source"
+ matched_artifact: /private/tmp/communitymech-batch99/alga-publisher.txt
+ cache_artifact: references_cache/PMID_24994654.md
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture
+ node: Met-Trp4 Coauxotrophic Cross-Feeding
+ evidence_index: 0
+ reference: PMID:41491832
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: two auxotrophic cells, cell 1 and cell 2, must be present simultaneously to form cross-feeding
+ for growth
+ matched_artifact: /private/tmp/communitymech-batch99/resveratrol-primary.txt
+ cache_artifact: references_cache/PMID_41491832.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture
+ node: Resveratrol Pathway Division of Labor
+ evidence_index: 0
+ reference: PMID:41491832
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: Module A contained FjTAL, catalyzing L-tyrosine to p-coumaric acid, while module B contained
+ At4CL and VvVST1, converting p-coumaric acid to resveratrol
+ matched_artifact: /private/tmp/communitymech-batch99/resveratrol-primary.txt
+ cache_artifact: references_cache/PMID_41491832.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture
+ node: FLO1 Adhesion-Enhanced Resveratrol Production
+ evidence_index: 0
+ reference: PMID:41491832
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: Notably, the pair Met-Trp4, in the presence of FLO1, always increased production
+ matched_artifact: /private/tmp/communitymech-batch99/resveratrol-primary.txt
+ cache_artifact: references_cache/PMID_41491832.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture
+ node: FLO1 Adhesion-Enhanced Resveratrol Production
+ evidence_index: 1
+ reference: PMID:41491832
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: "Met\u2013Trp4A\u2013B:FLO1 produced 0.67 \u03BCM of resveratrol, a 2.47-fold increase\
+ \ compared to Mctrl"
+ matched_artifact: /private/tmp/communitymech-batch99/resveratrol-primary.txt
+ cache_artifact: references_cache/PMID_41491832.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Salar_Atacama_Lithium_Brine_Community
+ node: Community Composition Across Natural and Concentrated Brines
+ evidence_index: 0
+ reference: doi:10.1029/2018JG004621
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: Further, our results showed that Bacteria were phylogenetically more diverse and rich in
+ the concentrated brine, while archaeal diversity was maximized in the natural brine
+ matched_artifact: /private/tmp/communitymech-batch99/brine-web-abstract.txt
+ cache_artifact: references_cache/doi_10.1029_2018JG004621.md
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
+ node: Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
+ evidence_index: 0
+ reference: PMID:42523014
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: When sclerotia were inoculated with the SynCom, sclerotia mortality was significantly increased
+ after 1-day co-culture with the SynCom, gradually reaching 100.0% mortality by 14-day co-culture
+ matched_artifact: /private/tmp/communitymech-batch99/sclerotia-primary.txt
+ cache_artifact: references_cache/PMID_42523014.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
+ node: Trinickia MC Key Contribution to Sclerotia Mortality
+ evidence_index: 0
+ reference: PMID:42523014
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: dropping TsMC significantly decreased mortality and its mono-inoculation alone could accelerate
+ sclerotia mortality
+ matched_artifact: /private/tmp/communitymech-batch99/sclerotia-primary.txt
+ cache_artifact: references_cache/PMID_42523014.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
+ node: Spatial Invasion of Sclerotia by SynCom Members
+ evidence_index: 0
+ reference: PMID:42523014
+ cache_matched: true
+ independent_primary_match: false
+ final_version_equivalent: true
+ final_version_snippet: By 3-day co-culture, Massilia sp. TB221 and Massilia sp. R20 had reached the interior sclerotia
+ (layer 1-4)
+ matched_artifact: /private/tmp/communitymech-batch99/sclerotia-primary.txt
+ cache_artifact: references_cache/PMID_42523014.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
+ node: Spatial Invasion of Sclerotia by SynCom Members
+ evidence_index: 1
+ reference: PMID:42523014
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: At 5- to 7-day co-culture, the relative abundance of Ralstonia sp. R4 and Trinickia sp.
+ MC increased progressively in the interior layers
+ matched_artifact: /private/tmp/communitymech-batch99/sclerotia-primary.txt
+ cache_artifact: references_cache/PMID_42523014.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
+ node: Spatial Invasion of Sclerotia by SynCom Members
+ evidence_index: 2
+ reference: PMID:42523014
+ cache_matched: true
+ independent_primary_match: false
+ final_version_equivalent: true
+ final_version_snippet: By 14-day co-culture, when sclerotia viability was completely suppressed, the relative
+ abundance of Trinickia sp. MC exceeded that of all other SynCom members simultaneously across layer 1-5
+ matched_artifact: /private/tmp/communitymech-batch99/sclerotia-primary.txt
+ cache_artifact: references_cache/PMID_42523014.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+discussion_snippet_checks:
+- record: Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism
+ node: alga_graph_evidence_scope
+ evidence_index: 0
+ reference: PMID:24994654
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: an environment requiring reciprocal carbon and nitrogen exchange
+ matched_artifact: /private/tmp/communitymech-batch99/alga-publisher.txt
+ cache_artifact: references_cache/PMID_24994654.md
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture
+ node: resveratrol_graph_evidence_scope
+ evidence_index: 0
+ reference: PMID:41491832
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: Systematic investigation of aggregate morphology and its impact on metabolic exchange represents
+ an important direction for future research
+ matched_artifact: /private/tmp/communitymech-batch99/resveratrol-primary.txt
+ cache_artifact: references_cache/PMID_41491832.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Salar_Atacama_Lithium_Brine_Community
+ node: brine_graph_evidence_scope
+ evidence_index: 0
+ reference: doi:10.1029/2018JG004621
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: Further, our results showed that Bacteria were phylogenetically more diverse and rich in
+ the concentrated brine, while archaeal diversity was maximized in the natural brine
+ matched_artifact: /private/tmp/communitymech-batch99/brine-web-abstract.txt
+ cache_artifact: references_cache/doi_10.1029_2018JG004621.md
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. Entailment separately reviewed.
+- record: Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom
+ node: sclerotia_graph_evidence_scope
+ evidence_index: 0
+ reference: PMID:42523014
+ cache_matched: true
+ independent_primary_match: true
+ final_version_equivalent: false
+ final_version_snippet: dropping TsMC significantly decreased mortality and its mono-inoculation alone could accelerate
+ sclerotia mortality
+ matched_artifact: /private/tmp/communitymech-batch99/sclerotia-primary.txt
+ cache_artifact: references_cache/PMID_42523014.txt
+ scope: Exact normalized cached manuscript quotation; two spatial quotations have explicitly recorded minor wording
+ differences in the fresh final article. 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: Remove unsupported existing claims and bound retained directions; no new mechanisms or topology.
+limitations:
+- Four whole records and all14originalnodes/6arrows reviewed. Retain9nodes/4arrows, remove5unsupportednodes/2arrows,
+ rename1node. Four changed records; no new topology or Edison submission/spend.
+- 'Yeast-alga: fresh abstract and public PMC author-manuscript main text1-155, including Figure1 caption, read.
+ Reciprocal carbon/nitrogen support retained; oxygen release is not an isolated yeast benefit. EuropePMC XML returnedHTTP500;
+ normal public PMC HTML succeeded. Existing body quotations remain, no new body text cached; issue1789 tracks inconsistent
+ cache provenance and765 broader re-evidencing.'
+- 'Resveratrol: fresh primary results227-277/309-389 and discussion391-455 read. Condition-dependent coauxotrophy
+ and titer comparisons retained; no direct transfer-flux claim or inference that increased product titer establishes
+ mutualistic fitness. Precursor accumulation and biomass tradeoff retained.'
+- 'Brine: publisher web-rendered abstract163-168, main text190-310 including methods and results read. EuropePMC
+ DOI search returned no record; direct publisher fetch403 stopped, normal public web text was available. Two-brine
+ composition comparison is not a lithium-only perturbation or demonstrated functional exchange. Four unsupported
+ functional nodes removed, not asserted biologically impossible.'
+- 'Sclerotia: fresh final primary results385-466 and discussion480-540 read. Three nodes and dropout-supported direction
+ retained; spatial order is not causation or competition relief. Only graph claims changed; no new wet-lab/genetic
+ instructions. Cached accepted-manuscript quotations match directly; two spatial excerpts differ slightly from
+ final article (range rendering and added that of), with both versions recorded and exact normalized final-text
+ checks. Non-graph version differences remain in1788.'
+- Relevant cache content and graph snippets checked. Flattened resveratrol cache search output was truncated, so
+ complete cache-body review is not claimed. No figure-pixel/supplement/raw-data review. All923caches unchanged;
+ fresh complete papers remain private local artifacts, not published.
+- All456otherrecords, canonical taxonomy and non-graph raw blocks preserved; four initial histories plus one append-only
+ scope-correction history. Identity-only participant lists use exact existing members. Brine participant list denotes
+ a curated subset across samples; full biocontrol inoculum does not imply equal contribution. No runtime connectivity
+ semantics changed.
+- Six matching all-state issue bodies read; fresh ignored/hidden-inclusive local dedup excluded .git/docs/site/references_cache,
+ with relevant caches separately inspected. Comments/PRs not exhaustive. Graph1784-1787 await protected-main merge.
+ Non-graph1788, provenance1789 and broader765 remain open.
+- Self-adversarial review is not independent approval or corpus completion. Loader1703 and DOI-cache1091 not certified.
+ Denied/unanswered Edison scopes unchanged. Validation and publication not preasserted.
+records:
+- path: kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml
+ id: CommunityMech:000165
+ original_sha256: 0b5b1da00631c5b9362a6c2b4cb62039c03243a81fe9ef5caf03f5f83f7ef12d
+ record_sha256: fec7e6a58cc17fca35752ff7a4d5c8bbd012cde000682fabef435f0f0e55f80d
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
+ scope: Whole record and every existing node/direction reviewed, with source-access limits; not new-mechanism discovery
+ or non-graph certification.
+ summary: Retain yeast-to-alga carbon supply without requiring fermentation as its sole route.; Retain algal reduced-nitrogen
+ supply and the conditional reciprocal resource loop; mediation strength remains PARTIAL.
+ node_decisions:
+ - node: Yeast Carbon Dioxide Provisioning
+ rationale: Retain yeast-to-alga carbon supply without requiring fermentation as its sole route.
+ - node: Algal Reduced Nitrogen Provisioning
+ rationale: Retain algal reduced-nitrogen supply and the conditional reciprocal resource loop; mediation strength
+ remains PARTIAL.
+ removed_node_decisions:
+ - node: Algal Oxygen Provisioning
+ rationale: Figure1 depicts algal oxygen release, but the reviewed main text does not isolate an oxygen-mediated
+ yeast benefit. Remove that asserted pairwise transfer, not the established carbon/nitrogen mutualism.
+ renamed_nodes: {}
+ edges_before:
+ - &id001
+ source: Yeast Carbon Dioxide Provisioning
+ target: Algal Reduced Nitrogen Provisioning
+ description: Yeast-derived carbon dioxide is fixed photosynthetically by C. reinhardtii, sustaining the algal
+ partner that reduces nitrite to ammonia for S. cerevisiae.
+ - &id003
+ source: Algal Reduced Nitrogen Provisioning
+ target: Yeast Carbon Dioxide Provisioning
+ description: Algal reduction of nitrite to ammonia supplies the nitrogen source that lets S. cerevisiae proliferate
+ and keep producing carbon dioxide from glucose.
+ edges_after:
+ - &id002
+ source: Yeast Carbon Dioxide Provisioning
+ target: Algal Reduced Nitrogen Provisioning
+ description: 'PARTIAL: yeast-derived carbon dioxide sustains the alga that supplies reduced nitrogen to yeast,
+ closing the resource-dependence loop. Coculture and resource-availability comparisons support this reciprocal
+ mechanism, but do not separately quantify how a change in carbon transfer changes ammonia release.'
+ - &id004
+ source: Algal Reduced Nitrogen Provisioning
+ target: Yeast Carbon Dioxide Provisioning
+ description: 'PARTIAL: algal reduced nitrogen sustains yeast growth and therefore the yeast partner supplying
+ carbon dioxide. This reciprocal support is consistent with the reported dependence, not a measured feedback
+ gain or a separate temporal causal experiment.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: Existing direction retained with conditional resource, PARTIAL mediation or dropout/nonadditivity
+ limits.
+ - before: *id003
+ after: *id004
+ rationale: Existing direction retained with conditional resource, PARTIAL mediation or dropout/nonadditivity
+ limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:24994654
+ issues:
+ - 1784
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism/2026-10-07T203744Z-codex-e34e15.yaml
+- path: kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml
+ id: CommunityMech:000445
+ original_sha256: 3a73be2842af7b380749e576dcdd2c679c415d9622e6c03dfce714674b94c6f1
+ record_sha256: d7f617d83df5d01dc2dafc8d7944fe482f4c9046d78337fd6c19040c95ec6baa
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
+ scope: Whole record and every existing node/direction reviewed, with source-access limits; not new-mechanism discovery
+ or non-graph certification.
+ summary: Retain condition-dependent coauxotrophic mutualism, distinct from product formation.; Retain the intended
+ divided-pathway handoff and PARTIAL production direction without direct flux certainty.; Retain the measured
+ titer comparison without assigning mutualism or conversion-efficiency benefit to the aggregate endpoint.
+ node_decisions:
+ - node: Met-Trp4 Coauxotrophic Cross-Feeding
+ rationale: Retain condition-dependent coauxotrophic mutualism, distinct from product formation.
+ - node: Resveratrol Pathway Division of Labor
+ rationale: Retain the intended divided-pathway handoff and PARTIAL production direction without direct flux
+ certainty.
+ - node: FLO1 Adhesion-Enhanced Resveratrol Production
+ rationale: Retain the measured titer comparison without assigning mutualism or conversion-efficiency benefit
+ to the aggregate endpoint.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id005
+ source: Resveratrol Pathway Division of Labor
+ target: FLO1 Adhesion-Enhanced Resveratrol Production
+ description: The divided module A/module B pathway supplies the p-coumaric-acid handoff used by the FLO1 Met-Trp4
+ A-B bioproduction coculture.
+ edges_after:
+ - &id006
+ source: Resveratrol Pathway Division of Labor
+ target: FLO1 Adhesion-Enhanced Resveratrol Production
+ description: 'PARTIAL: the divided pathway supplies the precursor-to-product route in the tested FLO1 coculture,
+ enabling resveratrol synthesis. It does not independently explain the increase over the no-FLO1 control; adhesion-dependent
+ transfer efficiency was not isolated as the mediator.'
+ retained_edge_decisions:
+ - before: *id005
+ after: *id006
+ rationale: Existing direction retained with conditional resource, PARTIAL mediation or dropout/nonadditivity
+ limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:41491832
+ issues:
+ - 1785
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture/2026-10-07T203744Z-codex-d0f5ea.yaml
+- path: kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml
+ id: CommunityMech:000062
+ original_sha256: 42d4efc5aebcc1f985d41206a50a60d09525c1c60997dd99ce987ba5e88f056b
+ record_sha256: 4e9934084bc572a4f98d5f209c5b21d853e5e3405d5ba5059be0f05cd18f00dd
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
+ scope: Whole record and every existing node/direction reviewed, with source-access limits; not new-mechanism discovery
+ or non-graph certification.
+ summary: Retain observed community differences at community scope; remove unmeasured pairwise benefit and physiological
+ causation.
+ node_decisions:
+ - node: Community Composition Across Natural and Concentrated Brines
+ rationale: Retain observed community differences at community scope; remove unmeasured pairwise benefit and
+ physiological causation.
+ removed_node_decisions:
+ - node: Organic Matter Degradation in Hypersaline Brine
+ rationale: Taxonomic presence does not establish organic substrate degradation, cross-feeding or the proposed
+ remineralization direction.
+ - node: Nutrient Remineralization in Lithium Brine
+ rationale: High-salinity occurrence does not demonstrate pairwise mutualism or a closed nutrient recycling mechanism.
+ - node: Bacteriorhodopsin-Mediated Phototrophy
+ rationale: The cited salinity statement does not demonstrate bacteriorhodopsin activity, ATP generation or commensalism
+ in this sample.
+ - node: Bacterial Heterotrophic Activity and Functional Redundancy
+ rationale: Co-occurrence does not establish substrate overlap, a redundancy benefit or pairwise carbon exchange.
+ renamed_nodes:
+ Lithium Tolerance and Osmoadaptation: Community Composition Across Natural and Concentrated Brines
+ edges_before:
+ - source: Lithium Tolerance and Osmoadaptation
+ target: Organic Matter Degradation in Hypersaline Brine
+ description: Osmoadapted organisms drive heterotrophic activity in extreme salinity
+ - source: Organic Matter Degradation in Hypersaline Brine
+ target: Nutrient Remineralization in Lithium Brine
+ description: Organic degradation releases inorganic nutrients
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Lithium Tolerance and Osmoadaptation
+ target: Organic Matter Degradation in Hypersaline Brine
+ description: Osmoadapted organisms drive heterotrophic activity in extreme salinity
+ rationale: The source community-profile comparison does not establish the proposed physiological or nutrient-cycle
+ mechanism.
+ - source: Organic Matter Degradation in Hypersaline Brine
+ target: Nutrient Remineralization in Lithium Brine
+ description: Organic degradation releases inorganic nutrients
+ rationale: The source community-profile comparison does not establish the proposed physiological or nutrient-cycle
+ mechanism.
+ references:
+ - doi:10.1029/2018JG004621
+ issues:
+ - 1786
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Salar_Atacama_Lithium_Brine_Community/2026-10-07T203744Z-codex-599245.yaml
+- path: kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml
+ id: CommunityMech:000364
+ original_sha256: d2978fd118d536e0ee1f0a687081fb2e9bba71aa795a1ad8feeb1e5457ddec72
+ record_sha256: b76f915e08d08faf1516698a67c53bb6e25f912bd8d4803dfe55412f1a100a3e
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml
+ scope: Whole record and every existing node/direction reviewed, with source-access limits; not new-mechanism discovery
+ or non-graph certification.
+ summary: Retain full-community antagonism with all twelve inoculum identities, without competition/defense ontology
+ overclaims.; Retain the dropout-supported pairwise MC contribution and its direction, without universal necessity
+ or additivity.; Retain measured spatial timing and scoped participants, without niche-partitioning or colonization-causality
+ claims.; Keep the MC dropout result at community-contribution scope with only MC as participant and the fungal
+ challenge as external context; do not assert a pairwise consortium-membership relation.
+ node_decisions:
+ - node: Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
+ rationale: Retain full-community antagonism with all twelve inoculum identities, without competition/defense
+ ontology overclaims.
+ - node: Trinickia MC Key Contribution to Sclerotia Mortality
+ rationale: Retain the scoped MC community contribution and existing dropout-supported direction with external
+ fungal context, without universal necessity/additivity or false consortium membership.
+ - node: Spatial Invasion of Sclerotia by SynCom Members
+ rationale: Retain measured spatial timing and scoped participants, without niche-partitioning or colonization-causality
+ claims.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id007
+ source: Trinickia MC Key Contribution to Sclerotia Mortality
+ target: Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
+ description: Trinickia sp. MC is the strongest member-level contributor resolved by the dropout series.
+ edges_after:
+ - &id008
+ source: Trinickia MC Key Contribution to Sclerotia Mortality
+ target: Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
+ description: The decrease in mortality following MC removal supports a causal contribution to the full-community
+ outcome over the measured time course. This is not an additive decomposition of member effects or proof of
+ universal necessity; other-member effects can attenuate MC and later reach the same endpoint.
+ retained_edge_decisions:
+ - before: *id007
+ after: *id008
+ rationale: Existing direction retained with conditional resource, PARTIAL mediation or dropout/nonadditivity
+ limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:42523014
+ issues:
+ - 1787
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 2
+ history_files:
+ - history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T203745Z-codex-dc367a.yaml
+ - history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T204135Z-codex-cb916b.yaml
+adversarial_prepublication_fix:
+ findings:
+ - issue: 1787
+ finding: Pairwise scope incorrectly applied consortium-member validation to an external fungal challenge.
+ disposition: Keep the MC dropout result at community-contribution scope with only MC as participant and the
+ fungal challenge as external context; do not assert a pairwise consortium-membership relation.
+ preserved_initial_histories:
+ history/records/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism/2026-10-07T203744Z-codex-e34e15.yaml: e66b28def57972ffacf422722d2ad0ed50bb01b0b59326b8fc9d25ae53ccf755
+ history/records/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture/2026-10-07T203744Z-codex-d0f5ea.yaml: ee532658b263d5c3d448f8c0fa3f45d313fd9994c609131a7724067c756cf514
+ history/records/Salar_Atacama_Lithium_Brine_Community/2026-10-07T203744Z-codex-599245.yaml: 0bbbb168df42120949b0ff42f876ec87516d8f854947d7449463930a5d294a03
+ history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T203745Z-codex-dc367a.yaml: 5b2a6839c615e4dd3bdf58871236580ef7dee4eeff93cc61a95d52c49bb0cac4
+ correction_history: history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T204135Z-codex-cb916b.yaml
+ preflight:
+ command:
+ - /Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3
+ - -m
+ - communitymech.cli
+ - audit-network
+ - --json
+ exit_code: 3
+ log: /private/tmp/communitymech-batch99/preflight-network.json
+ log_sha256: ae22e472a4cdd0a7ab551479ebaa0be0b5cbd0228e91e51872d638ea217856a3
+ status: Corrected before final full verification; no audit severity rule changed.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index b00ed70f8..c22b883b6 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -356,10 +356,10 @@ kb/communities/SPRUCE_Peatland_Methane_Cycling_Community.yaml CommunityMech:0001
kb/communities/SPRUCE_Peatland_Warming_Community.yaml CommunityMech:000319 ffa1825a97b4437efcf9b037aef5464113db4243c49a2c3b9a371274339ea0c5 4 2 86.2 reports/causal_graph_review/decisions/20261007-four-records-batch98.yaml reviewed
kb/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.yaml CommunityMech:000140 2c2b466385e645988ee3833bc3ca4fc428d3feb8a67c9d063e564f32560971d0 3 2 93.3 reports/causal_graph_review/decisions/20261007-four-records-batch98.yaml reviewed
kb/communities/Saccharomyces_Acinetobacter_Lignocellulose_Detox_Coculture.yaml CommunityMech:000263 27f8794dbd947ba51b80c9fb76c107fb0acd83ba630902a2e920bf2155f58dd8 3 2 93.3 reports/causal_graph_review/decisions/20261007-four-records-batch98.yaml reviewed
-kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml CommunityMech:000165 0b5b1da00631c5b9362a6c2b4cb62039c03243a81fe9ef5caf03f5f83f7ef12d 3 2 93.3 pending
-kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml CommunityMech:000445 3a73be2842af7b380749e576dcdd2c679c415d9622e6c03dfce714674b94c6f1 3 1 86.7 pending
-kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml CommunityMech:000062 42d4efc5aebcc1f985d41206a50a60d09525c1c60997dd99ce987ba5e88f056b 5 2 100.0 pending
-kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml CommunityMech:000364 d2978fd118d536e0ee1f0a687081fb2e9bba71aa795a1ad8feeb1e5457ddec72 3 1 88.3 pending
+kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml CommunityMech:000165 fec7e6a58cc17fca35752ff7a4d5c8bbd012cde000682fabef435f0f0e55f80d 2 2 95.0 reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml reviewed
+kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml CommunityMech:000445 d7f617d83df5d01dc2dafc8d7944fe482f4c9046d78337fd6c19040c95ec6baa 3 1 83.3 reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml reviewed
+kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml CommunityMech:000062 4e9934084bc572a4f98d5f209c5b21d853e5e3405d5ba5059be0f05cd18f00dd 1 0 50.0 reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml reviewed
+kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml CommunityMech:000364 b76f915e08d08faf1516698a67c53bb6e25f912bd8d4803dfe55412f1a100a3e 3 1 75.0 reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml reviewed
kb/communities/Sedimenting_Arabinose_Glucose_Saccharomyces_Coculture.yaml CommunityMech:000329 f02ff46ba4cc7b5e7e599fdb12f317244d7b141b2c6caf1a0829609890d37fe8 3 2 100.0 pending
kb/communities/Shewanella_Anammox_Delta_nrfA_Nitrite_Coupled_Consortium.yaml CommunityMech:000402 902be815782c5149408e8f197cd5dc452cce7656fc8794112f327bbd676e13f0 2 0 70.0 pending
kb/communities/Shewanella_Denitrifying_Richness_SynComs.yaml CommunityMech:000114 45c1af6b91f53afec157c8da9a28e0e5f13b6226ab4da6567ba21479dc5ce003 6 1 90.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 33df592ef..051bd9e3d 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -2,14 +2,14 @@
"scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
- "nodes": 1410,
- "edges": 572,
+ "nodes": 1405,
+ "edges": 570,
"records_without_nodes": 8,
- "records_without_edges": 175,
+ "records_without_edges": 176,
"review_status_counts": {
"needs_research": 48,
- "pending": 104,
- "reviewed": 308
+ "pending": 100,
+ "reviewed": 312
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261007-batch99.json b/reports/causal_graph_review/validation-20261007-batch99.json
new file mode 100644
index 000000000..e5732cb53
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261007-batch99.json
@@ -0,0 +1,1133 @@
+{
+ "base_commit": "af0cc46dc2b6438010297cea796110a22ed78771",
+ "scope": [
+ "kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml",
+ "kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml",
+ "kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml",
+ "kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch99.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/focused.log",
+ "log_sha256": "0736b0d0d05bbe15a95e77677baef49a38cf862fa0a7f81131e74e3256879f16",
+ "output_tail": "........ [100%]\n8 passed in 3.39s\n"
+ },
+ {
+ "check": "Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch99/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-strict.tsv",
+ "kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-strict.log",
+ "log_sha256": "b386eb7b03f5d63b0f6059c727e478f91c926e2a4df8dd229d2ece00a1ce4232",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch99/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-batch99/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-strict.tsv\n"
+ },
+ {
+ "check": "Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-references.log",
+ "log_sha256": "8e034926fd88916745c34eb0efefd4e725556cd2bf0c3935f19d41de96cdbe22",
+ "output_tail": "Validating kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.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/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.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": "Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-snippets.log",
+ "log_sha256": "c701a14a68be45219232ec1037f210e46fb14d49e54b85702ad029b20c3f0666",
+ "output_tail": "# 6 evidence snippets scanned across 1 files\n MATCH 6\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": "Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism-rank.log",
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
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+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
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+ "data",
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+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch99/verification-final/Salar_Atacama_Lithium_Brine_Community-references.log",
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+ "explained_output_tail": "Validating kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Salar_Atacama_Lithium_Brine_Community-snippets",
+ "command": [
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+ "scripts/evidence_snippet_audit.py",
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+ "log": "/private/tmp/communitymech-batch99/verification-final/Salar_Atacama_Lithium_Brine_Community-snippets.log",
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+ "command": [
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+ "command": [
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
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+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch99/verification-final/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom-snippets.log",
+ "log_sha256": "a8367fb81c0fa16fe2af40c09dcb67e1d2e9bb1982d1546f4a07b2530efb4ab4",
+ "output_tail": "# 34 evidence snippets scanned across 1 files\n MATCH 34\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": "Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom-rank.log",
+ "log_sha256": "bf50c1c05cf98f24c894e80dc418af620c6efd24e4cd64f4c36292d8009ea91f",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000364\",\n \"name\": \"Sclerotinia Sclerotia 12-Strain Biocontrol SynCom\",\n \"score\": 75.0,\n \"taxonomy\": 12,\n \"connected_taxa\": 12,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T203745Z-codex-dc367a.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom-history-1",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T204135Z-codex-cb916b.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom-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-batch99/verification-final/inventory.log",
+ "log_sha256": "6d8ff9d3d6dcab418bf97dac6ce1a873ca7c96ae4a98d9235a7beb073c4b39db",
+ "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\": 1405,\n \"edges\": 570,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 176,\n \"review_status_counts\": {\n \"needs_research\": 48,\n \"pending\": 100,\n \"reviewed\": 312\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-batch99/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-batch99/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-batch99/verification-final/rank-all.log",
+ "log_sha256": "b3aed5d3e64c3673d78ca645d80d70c256dae72db553d8e10992a69d5c89b0a7",
+ "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"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch99/verification-final/render.log",
+ "log_sha256": "ea379671fd8ddfe567686abc42b37c1811bacec9662554d627e6d7f1748fdf46",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch99/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch99/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch99/docs/index.html\n"
+ },
+ {
+ "check": "render-repeat",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
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+ "log": "/private/tmp/communitymech-batch99/verification-final/render-repeat.log",
+ "log_sha256": "ea379671fd8ddfe567686abc42b37c1811bacec9662554d627e6d7f1748fdf46",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch99/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch99/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch99/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch99/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-batch98')),('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-batch99/verification-final/connectivity-survey.log",
+ "log_sha256": "337f0da9e356f80f3cffcb497a4625b6a0c605a209cfd6eab1ce6926f15d8160",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 402, \"mixed\": 128, \"community_level_only\": 274, \"taxa\": 1542, \"credited_solely_by_the_rule\": 1268}, \"current\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1548, \"credited_solely_by_the_rule\": 1274}}\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_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/verification-final/regressions.log",
+ "log_sha256": "eb167a7dd7d4c3501c88fbda76e1e583723c1e0b6333c44299e90c8a64477c3b",
+ "output_tail": "........................................................................ [ 7%]\n........................................................................ [ 15%]\n........................................................................ [ 23%]\n........................................................................ [ 31%]\n........................................................................ [ 39%]\n........................................................................ [ 47%]\n........................................................................ [ 55%]\n........................................................................ [ 63%]\n........................................................................ [ 71%]\n........................................................................ [ 79%]\n........................................................................ [ 87%]\n........................................................................ [ 95%]\n........................................ [100%]\n904 passed in 453.95s (0:07:33)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch99.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/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_batch99.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_community_level_connectivity_credit.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/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-batch99/verification-final/audit-snippets-all.log",
+ "log_sha256": "30474bb576c69af01dc3f9667511cf3ec734aeb9821691d5fa26faf7708e0c97",
+ "output_tail": "# 8947 evidence snippets scanned across 460 files\n MATCH 8812\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-batch99/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_batch99.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch99/focused-final.log",
+ "log_sha256": "d83a0b00a4d6f860883041eea775759ed79ccc785c0a1d7f2a1390fb7479990c",
+ "output_tail": "........ [100%]\n8 passed in 2.81s\n"
+ }
+ ],
+ "limitations": [
+ "Four whole records and all14originalnodes/6arrows reviewed. Retain9nodes/4arrows, remove5unsupportednodes/2arrows, rename1node. Four changed records; no new topology or Edison submission/spend.",
+ "Yeast-alga: fresh abstract and public PMC author-manuscript main text1-155, including Figure1 caption, read. Reciprocal carbon/nitrogen support retained; oxygen release is not an isolated yeast benefit. EuropePMC XML returnedHTTP500; normal public PMC HTML succeeded. Existing body quotations remain, no new body text cached; issue1789 tracks inconsistent cache provenance and765 broader re-evidencing.",
+ "Resveratrol: fresh primary results227-277/309-389 and discussion391-455 read. Condition-dependent coauxotrophy and titer comparisons retained; no direct transfer-flux claim or inference that increased product titer establishes mutualistic fitness. Precursor accumulation and biomass tradeoff retained.",
+ "Brine: publisher web-rendered abstract163-168, main text190-310 including methods and results read. EuropePMC DOI search returned no record; direct publisher fetch403 stopped, normal public web text was available. Two-brine composition comparison is not a lithium-only perturbation or demonstrated functional exchange. Four unsupported functional nodes removed, not asserted biologically impossible.",
+ "Sclerotia: fresh final primary results385-466 and discussion480-540 read. Three nodes and dropout-supported direction retained; spatial order is not causation or competition relief. Only graph claims changed; no new wet-lab/genetic instructions. Cached accepted-manuscript quotations match directly; two spatial excerpts differ slightly from final article (range rendering and added that of), with both versions recorded and exact normalized final-text checks. Non-graph version differences remain in1788.",
+ "Relevant cache content and graph snippets checked. Flattened resveratrol cache search output was truncated, so complete cache-body review is not claimed. No figure-pixel/supplement/raw-data review. All923caches unchanged; fresh complete papers remain private local artifacts, not published.",
+ "All456otherrecords, canonical taxonomy and non-graph raw blocks preserved; four initial histories plus one append-only scope-correction history. Identity-only participant lists use exact existing members. Brine participant list denotes a curated subset across samples; full biocontrol inoculum does not imply equal contribution. No runtime connectivity semantics changed.",
+ "Six matching all-state issue bodies read; fresh ignored/hidden-inclusive local dedup excluded .git/docs/site/references_cache, with relevant caches separately inspected. Comments/PRs not exhaustive. Graph1784-1787 await protected-main merge. Non-graph1788, provenance1789 and broader765 remain open.",
+ "Self-adversarial review is not independent approval or corpus completion. Loader1703 and DOI-cache1091 not certified. Denied/unanswered Edison scopes unchanged. Validation and publication not preasserted."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml": {
+ "MATCH": 6,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml": {
+ "MATCH": 17,
+ "RENDERING": 1,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml": {
+ "MATCH": 23,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml": {
+ "MATCH": 34,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 64,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [],
+ "repair_scope": "Remove unsupported existing claims and bound retained directions; no new mechanisms or topology."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch99/alga-metadata.json": "41994c41d3bd406f73cbdcc1899ecae4d2ce2d9b79d692dd7edfabce21b8b6fd",
+ "/private/tmp/communitymech-batch99/alga-primary.txt": "0be25d355cea62fa7f1e432c574d856800de7a7e65bbcae625c464f5aca4be80",
+ "/private/tmp/communitymech-batch99/alga-publisher.html": "a191336a4c3a3d971730a4677b8fcfba7ed2ed7851b73789d7a76274d0529a70",
+ "/private/tmp/communitymech-batch99/alga-publisher.txt": "a08a42133516b75bc2689f07e5eddabb454553dc031298cec957cb2ae06a9bb9",
+ "/private/tmp/communitymech-batch99/baseline.json": "4eddccbe3aa2e4e320075b23c20d8a9445e8ee97cb71cae93c5e0e91de8854e5",
+ "/private/tmp/communitymech-batch99/brine-metadata.json": "19321c8455a193df9af12f73b5515a4d819bce83427f6ab62650e3fbef9aa299",
+ "/private/tmp/communitymech-batch99/brine-web-abstract.txt": "4dfba6f1c5b8f8e86dd738360c9577f69f0b0e74a03f0e4b1495d21ba05787d2",
+ "/private/tmp/communitymech-batch99/brine-web-results.txt": "62b63b393d1b49670d6df0dc62381ffad3dc99815f8d6fc01050c99c8190afff",
+ "/private/tmp/communitymech-batch99/dedup-local-current.txt": "e0cb4682ed93c311d852861d4d0e16a8967c8ad40d520a3cb7f7c279acb35771",
+ "/private/tmp/communitymech-batch99/issue-dedup-current.json": "190eac11304d9cbb1a197a5dcc231433e4b8380e6476c04509e2a3d41d5c561c",
+ "/private/tmp/communitymech-batch99/primary-manifest.json": "f2f6341b0ea3cfee4fac868de770fcd6ce1daffc85fc038736e994155f601f09",
+ "/private/tmp/communitymech-batch99/publisher-manifest.json": "5c03d4a06bbff29c5b0b48e83ffd79f644a0c50781c6456670b28cc508604dca",
+ "/private/tmp/communitymech-batch99/resveratrol-metadata.json": "d0caa58e82f39474ff1d0d69364b54daa85b394f0c3309ef752fc6aa5a9a0f5b",
+ "/private/tmp/communitymech-batch99/resveratrol-primary.txt": "86a4878aae9d9ea2c1f5bb66f05bcf8e2a6fe02fbbd8ed2ac0e06f6afd090f09",
+ "/private/tmp/communitymech-batch99/resveratrol-primary.xml": "b603906b52fd2447de1c1b976b993f1207ec08097555fec421da5d83fec1f0ee",
+ "/private/tmp/communitymech-batch99/sclerotia-metadata.json": "7c479d9940c422a9b5492eb4e1de43bfb75deca4457de9802afbd9d4ad1265a5",
+ "/private/tmp/communitymech-batch99/sclerotia-primary.txt": "480b73f04ffb591f059c609a34040c1681cfbacd8ca171e4a859b0f3d4768b48",
+ "/private/tmp/communitymech-batch99/sclerotia-primary.xml": "36927d702d7a5d7d1ce17db154250d5bebc57c3c1ed63d51230648a7e530a7ae",
+ "references_cache/PMID_24994654.md": "f6df25b9f7b415ad865d97134556f6bcd18ca1e36ab91f290cc2d525e35e08f9",
+ "references_cache/PMID_41491832.txt": "6860bca7ce19e9f4f9f187f2fd09c3dc064e4152e42152510e52fef19a8a8135",
+ "references_cache/PMID_42523014.txt": "78e19019cf62c0b4314eb190b977aa9202c75bf07da7e559eef3f14bf692acbd",
+ "references_cache/doi_10.1029_2018JG004621.md": "43e8953e1ca352c98c64d0ed00d504b97e6a7b3a0eb6db090989665f50b2b0e3"
+ },
+ "immutable_prior_history_and_decision_files": 782,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 12,
+ "new_discussion_quotations": 4,
+ "fresh_primary_literal_matches": 14,
+ "documented_manuscript_version_equivalents": 2,
+ "all_cached_literal_matches": 16,
+ "retained_nodes": 9,
+ "removed_nodes": 5,
+ "retained_arrows": 4,
+ "removed_arrows": 2,
+ "new_nodes_or_directions": 0,
+ "scope": "Two sclerotia spatial excerpts differ between accepted manuscript and final article, with exact final wording separately matched. All other reviewed quotations match fresh primary text literally after normalization; entailment is a separate review."
+ },
+ "network_delta": {
+ "existing_findings_preserved": 56,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "Five unsupported nodes/two arrows removed; all56pre-existing warnings unchanged,zero structural defects. Initial external-target scope error corrected without changing audit rules."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1391,
+ "arrows": 562
+ },
+ "render_scope": "Deterministic rendering and exact HTML-description parser, not browser screenshots; postcommit docs-current separately required.",
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 402,
+ "mixed": 128,
+ "community_level_only": 274,
+ "taxa": 1542,
+ "credited_solely_by_the_rule": 1268
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 403,
+ "mixed": 128,
+ "community_level_only": 275,
+ "taxa": 1548,
+ "credited_solely_by_the_rule": 1274
+ }
+ },
+ "delta": {
+ "records": 0,
+ "with_community_level": 1,
+ "mixed": 0,
+ "community_level_only": 1,
+ "taxa": 6,
+ "credited_solely_by_the_rule": 6
+ },
+ "interpretation": "Atacama becomes a community-profile node with six named existing taxa. MC remains a one-participant community contribution, with external fungal challenge not made a consortium member. Community-level count402->403 and solely community-credited taxa1268->1274 reflect this scope correction, not a runtime-rule change. Exact participant allowlist adds one stem; only the community-level census ceiling increases by one."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 8947,
+ "categories": {
+ "MATCH": 8812,
+ "RENDERING": 20,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 38,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Both-root informational audit exit0 is not clean-corpus certification; literal matches are not entailment.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1405,
+ "edges": 570,
+ "records_without_nodes": 8,
+ "records_without_edges": 176,
+ "review_status_counts": {
+ "needs_research": 48,
+ "pending": 100,
+ "reviewed": 312
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261007-four-records-batch99.yaml": "d074d1dd6b8e027bb5c8174d73c1d3c9493e80fe254a5326386369fb6ebd4167",
+ "tests/test_causal_review_batch99.py": "bbf33fc0ee37a4dcf83afbb4bbceada82f22d68db28ffb0e7df2c5c9dc388470",
+ "tests/test_participating_taxa.py": "66913594c22331ac6cb551eef0a2ca8cf6c468875ae38e1dc98c1a1af21af9f3",
+ "tests/test_community_level_connectivity_credit.py": "b758fe7bfd3428e33fbc9c6ac1cf363747bcad39cac1a28dc659bfbbd6532512",
+ "reports/causal_graph_review/README.md": "87d16c9a996950f759d8b0a2fe8560f3f00daa895f01fbd5b0fbfa6e97223685",
+ "reports/causal_graph_review/cache-provenance-20261007-batch99.json": "a1739bef0423fe4536237e3bbd3828e3b60acbd3e18fae08f8e33819a7348cac",
+ "kb/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.yaml": "fec7e6a58cc17fca35752ff7a4d5c8bbd012cde000682fabef435f0f0e55f80d",
+ "kb/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml": "d7f617d83df5d01dc2dafc8d7944fe482f4c9046d78337fd6c19040c95ec6baa",
+ "kb/communities/Salar_Atacama_Lithium_Brine_Community.yaml": "4e9934084bc572a4f98d5f209c5b21d853e5e3405d5ba5059be0f05cd18f00dd",
+ "kb/communities/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml": "b76f915e08d08faf1516698a67c53bb6e25f912bd8d4803dfe55412f1a100a3e"
+ },
+ "pre_research_baseline": {
+ "base_commit": "af0cc46dc2b6438010297cea796110a22ed78771",
+ "base_tree": "afcdcd4ca8a24c7deb82e3e48eea85e9564fc48f",
+ "research_worktree": "/private/tmp/communitymech-causal-batch98",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch99/baseline-rank.log",
+ "sha256": "de73c3267a438df4f39ac0ea6e1f1b2035a2d571d8ccf5c912c0bdbbc8bc46bf"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch99/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch99/baseline-network.log",
+ "sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch99/baseline-downstream.log",
+ "sha256": "dc1542020c3bb712e894e0758277adeed7eb54b80cd8abfdefd5d3f454933dee"
+ }
+ ],
+ "baseline_sha256": "4eddccbe3aa2e4e320075b23c20d8a9445e8ee97cb71cae93c5e0e91de8854e5"
+ },
+ "reference_validator_caveat": "Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; primary access and section limits are recorded in the ledger. CLI Total checks counts issues,not executed checks. Loader1703 not certified.",
+ "status": "verified_existing_graph_repairs_with_source_access_limits",
+ "adversarial_prepublication_fix": {
+ "findings": [
+ {
+ "issue": 1787,
+ "finding": "Pairwise scope incorrectly applied consortium-member validation to an external fungal challenge.",
+ "disposition": "Keep the MC dropout result at community-contribution scope with only MC as participant and the fungal challenge as external context; do not assert a pairwise consortium-membership relation.",
+ "preserved_initial_histories": {
+ "history/records/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism/2026-10-07T203744Z-codex-e34e15.yaml": "e66b28def57972ffacf422722d2ad0ed50bb01b0b59326b8fc9d25ae53ccf755",
+ "history/records/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture/2026-10-07T203744Z-codex-d0f5ea.yaml": "ee532658b263d5c3d448f8c0fa3f45d313fd9994c609131a7724067c756cf514",
+ "history/records/Salar_Atacama_Lithium_Brine_Community/2026-10-07T203744Z-codex-599245.yaml": "0bbbb168df42120949b0ff42f876ec87516d8f854947d7449463930a5d294a03",
+ "history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T203745Z-codex-dc367a.yaml": "5b2a6839c615e4dd3bdf58871236580ef7dee4eeff93cc61a95d52c49bb0cac4"
+ },
+ "correction_history": "history/records/Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom/2026-10-07T204135Z-codex-cb916b.yaml"
+ }
+ ],
+ "preflight": {
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 3,
+ "log": "/private/tmp/communitymech-batch99/preflight-network.json",
+ "log_sha256": "ae22e472a4cdd0a7ab551479ebaa0be0b5cbd0228e91e51872d638ea217856a3",
+ "status": "Corrected before final full verification; no audit severity rule changed."
+ }
+ },
+ "total_recorded_gate_outputs": 43
+}
diff --git a/tests/test_causal_review_batch99.py b/tests/test_causal_review_batch99.py
new file mode 100644
index 000000000..581b92b17
--- /dev/null
+++ b/tests/test_causal_review_batch99.py
@@ -0,0 +1,143 @@
+"""Keep resource loops, production endpoints and compositional evidence 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-batch99.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_resource_loop_retains_two_directions_without_oxygen_benefit():
+ _, _, docs = records()
+ carbon, nitrogen = docs[0]["ecological_interactions"]
+ assert [n["name"] for n in [carbon, nitrogen]] == [
+ "Yeast Carbon Dioxide Provisioning",
+ "Algal Reduced Nitrogen Provisioning",
+ ]
+ assert carbon["downstream"][0]["target"] == nitrogen["name"]
+ assert nitrogen["downstream"][0]["target"] == carbon["name"]
+ assert all(n["downstream"][0]["description"].startswith("PARTIAL:") for n in [carbon, nitrogen])
+ assert all(n["interaction_type"] == "CROSS_FEEDING" for n in [carbon, nitrogen])
+ assert "(14)" in nitrogen["evidence"][0]["snippet"]
+ assert all(p["term"]["id"] != "GO:0006113" for p in carbon["biological_processes"])
+
+
+def test_resveratrol_titer_is_not_mutualistic_fitness_or_isolated_transfer():
+ _, _, docs = records()
+ mutualism, pathway, outcome = docs[1]["ecological_interactions"]
+ assert mutualism["interaction_type"] == "MUTUALISM"
+ assert pathway["interaction_type"] == "CROSS_FEEDING"
+ assert "downstream" not in mutualism
+ assert pathway["downstream"][0]["description"].startswith("PARTIAL:")
+ assert "interaction_type" not in outcome
+ assert "precursor accumulation and lower biomass" in outcome["description"]
+ assert "not by itself a mutualistic fitness measurement" in outcome["description"]
+
+
+def test_brine_profile_does_not_assert_a_metabolic_chain():
+ _, _, docs = records()
+ nodes = docs[2]["ecological_interactions"]
+ assert len(nodes) == 1
+ node = nodes[0]
+ assert node["scope"] == "COMMUNITY_LEVEL"
+ assert node["name"] == "Community Composition Across Natural and Concentrated Brines"
+ assert not any(
+ k in node
+ for k in [
+ "source_taxon",
+ "target_taxon",
+ "interaction_type",
+ "downstream",
+ "metabolites",
+ "biological_processes",
+ ]
+ )
+ assert "not a controlled lithium-only effect" in node["description"]
+ assert "not the concentrated sample" in node["description"]
+
+
+def test_sclerotia_dropout_effect_is_not_essentiality_or_niche_partitioning():
+ _, _, docs = records()
+ full, mc, spatial = docs[3]["ecological_interactions"]
+ assert all(
+ "interaction_type" not in n and "biological_processes" not in n for n in [full, mc, spatial]
+ )
+ assert mc["scope"] == "COMMUNITY_LEVEL" and "source_taxon" not in mc
+ assert len(mc["participating_taxa"]) == 1
+ assert mc["participating_taxa"][0]["preferred_term"] == "Trinickia sclerotiorum sp. nov. MC"
+ assert mc["target_taxon"]["term"]["id"] == "NCBITaxon:5180"
+ assert mc["downstream"][0]["target"] == full["name"]
+ assert "not an additive decomposition" in mc["downstream"][0]["description"]
+ assert "not demonstrated competition-reducing niche partitioning" in spatial["description"]
+ assert "downstream" not in spatial
+
+
+def test_participant_lists_are_scoped_canonical_identities():
+ _, _, docs = records()
+ for doc, index, members in [
+ (docs[2], 0, range(6)),
+ (docs[3], 0, range(12)),
+ (docs[3], 2, [3, 2, 10, 11]),
+ ]:
+ expected = [
+ {k: doc["taxonomy"][i]["taxon_term"][k] for k in ["preferred_term", "term"]}
+ for i in members
+ ]
+ assert doc["ecological_interactions"][index]["participating_taxa"] == expected
+ assert all(t["taxon_term"]["term"]["id"] != "NCBITaxon:5180" for t in docs[3]["taxonomy"])
+
+
+def test_dispositions_and_append_only_histories_cover_every_original_node():
+ ledger, rows, docs = records()
+ assert sum(len(r["node_decisions"]) for r in rows) == 9
+ assert sum(len(r["removed_node_decisions"]) for r in rows) == 5
+ assert sum(len(r["renamed_nodes"]) for r in rows) == 1
+ assert sum(len(r["retained_edge_decisions"]) for r in rows) == 4
+ assert sum(len(r["removed_edge_decisions"]) for r in rows) == 2
+ assert len(ledger["snippet_checks"]) == ledger["primary_graph_snippet_count"] == 12
+ assert len(ledger["discussion_snippet_checks"]) == 4
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert row["curation_events_added"] == len(row["history_files"])
+ assert row["curation_events_added"] == (2 if doc["id"] == "CommunityMech:000364" else 1)
+ assert doc["curation_history"][-1]["llm_assisted"]
+ assert (ROOT / row["history_files"][0]).is_file()
+ for e in row["retained_edge_decisions"]:
+ assert all(
+ row["renamed_nodes"].get(e["before"][k], e["before"][k]) == e["after"][k]
+ for k in ["source", "target"]
+ )
+
+
+def test_manuscript_version_differences_are_explicit_not_claimed_literal():
+ ledger, _, _ = records()
+ checks = ledger["snippet_checks"] + ledger["discussion_snippet_checks"]
+ assert all(c["cache_matched"] for c in checks)
+ variants = [c for c in checks if not c["independent_primary_match"]]
+ assert len(variants) == 2
+ assert {c["evidence_index"] for c in variants} == {0, 2}
+ assert all(
+ c["final_version_equivalent"]
+ and c["reference"] == "PMID:42523014"
+ and c["node"] == "Spatial Invasion of Sclerotia by SynCom Members"
+ for c in variants
+ )
+ assert "exceeded that of all other" in variants[1]["final_version_snippet"]
+
+
+def test_open_scope_and_provider_boundaries_are_preserved():
+ ledger, _, _ = records()
+ assert ledger["issues"] == [1784, 1785, 1786, 1787]
+ assert ledger["unresolved_non_graph_issues"] == [1788, 1789]
+ assert ledger["cache_changes"] == [] and not ledger["independent_approval"]
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert any("403" in s for s in ledger["limitations"])
+ assert any("HTTP500" 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 c74daee6f..84ed7f7f4 100644
--- a/tests/test_community_level_connectivity_credit.py
+++ b/tests/test_community_level_connectivity_credit.py
@@ -104,7 +104,8 @@ def test_most_records_carry_a_community_level_interaction(survey):
"""The rule's reach. #312 measured 156; ongoing curation reached 381."""
# #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
+ # #1786 re-scopes Atacama's six-member subset as a community profile (402 -> 403).
+ assert 130 <= survey["with_community_level"] <= 403, survey
def test_the_mixed_records_are_where_the_coarseness_bites(survey):
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index cd61f0214..48b098a5c 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -396,6 +396,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"SPRUCE_Peatland_Warming_Community.yaml",
"Saccharomyces_Acinetobacter_Lignocellulose_Detox_Coculture.yaml",
"Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.yaml",
+ "Salar_Atacama_Lithium_Brine_Community.yaml",
"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom.yaml",
"Shewanella_Anammox_Delta_nrfA_Nitrite_Coupled_Consortium.yaml",
"Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.yaml",