diff --git a/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html b/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html
index f794132e6..1b1f74226 100644
--- a/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html
+++ b/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html
@@ -576,7 +576,7 @@ Ecological Interactions
Ecological interaction network for Thalassiosira-Marinobacter Marine Snow Coculture
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, niche partitioning, colonization facilitation).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -584,18 +584,8 @@
Ecological Interactions
-
-
-
-
@@ -603,18 +593,20 @@ Ecological Interactions
-
Photosynthetically active T. weissflogii and specific diatom-attaching bacteria, including M. adhaerens HP15, are required for strong aggregate formation; axenic T. weissflogii did not aggregate in the same assay.
-
+
In the 2011 rolling-tank assay, active T. weissflogii cocultured with attaching bacteria including HP15 formed substantially more aggregates than axenic controls. This is a community aggregation outcome, not a universal bacterial requirement or a separate colonization interaction. The 2014 temperature/pCO2 experiment found no effect of HP15 on total aggregate volume. Inactivated cells in the 2011 Results aggregated much less, not uniformly zero; the inactivation treatment may also have altered exudates and surface properties, so it does not isolate photosynthesis as the sole mediator.
-
Source Taxon: Marinobacter adhaerens HP15
+
Participating Taxa:
-
Target Taxon: Thalassiosira weissflogii
+ Thalassiosira weissflogii,
+
+ Marinobacter adhaerens HP15
+
+
@@ -629,12 +621,6 @@
Bacteria-Dependent Diatom Aggregation
class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419)
-
- biofilm formation
- (GO:0042710 )
-
-
@@ -683,24 +669,39 @@
Evidence
+
+
+
+ "total aggregate volume was independent of the presence of M. adhaerens HP15"
+
+
+
-
M. adhaerens HP15 is linked to transparent exopolymeric particle formation and aggregate formation during interaction with T. weissflogii.
-
+
TEP formation and aggregation were associated with the diatom-HP15 model in earlier work. TEP is a measured community polymer outcome, not proof of directed feeding from the diatom to HP15. The 2014 study found no bacterial effect on total TEP generated; warmer treatments generated more TEP but less aggregation. The 2011 aggregate-free-water measurements and 2014 total-TEP measurements must not be treated as identical endpoints. Chitin-containing fibres in a SEM caption document physical association, not the identity of all TEP or a measured chitin-transfer flux.
-
Source Taxon: Thalassiosira weissflogii
+
Participating Taxa:
-
Target Taxon: Marinobacter adhaerens HP15
+ Thalassiosira weissflogii,
+
+ Marinobacter adhaerens HP15
+
+
@@ -729,9 +730,8 @@
Transparent Exopolymer Particle Enhancement
Downstream Effects:
-
→ Bacteria-Dependent Diatom Aggregation
-
HP15-associated transparent exopolymer particle formation provides the exopolymeric matrix that supports diatom aggregation and marine-snow particle formation.
-
+
→ Condition-Dependent Diatom Aggregation
+
PARTIAL: TEP can provide an adhesive matrix enabling diatom aggregation, but the amount-aggregation relationship is condition dependent. The 2011 association is not a selective mediation test; the 2014 higher-TEP/lower-aggregation result rules out a universal monotonic effect, and polymer stickiness was not directly resolved.
Evidence
+
+
+
+ "had no effect on the amount of TEP generated"
+
+
+
@@ -787,10 +800,8 @@ Evidence
-
Chemotaxis and surface attachment functions in M. adhaerens contribute to physical association with diatom cells and TEP aggregates, providing a mechanistic basis for initiation of the two-member interaction.
-
+
Diatom homogenate or culture supernatant attracted HP15, and chemotaxis-associated mutants had a smaller attached bacterial fraction in coculture than wild type. These perturbations support HP15 chemotaxis/motility contributions to bacterial attachment to the diatom, not a demonstrated growth or colonization benefit to the diatom. Mutant biofilm impairment was assayed on abiotic surfaces and is distinct from diatom aggregation.
Source Taxon: Marinobacter adhaerens HP15
@@ -826,9 +837,8 @@
Chemotaxis-Mediated Attachment
Downstream Effects:
-
→ Bacteria-Dependent Diatom Aggregation
-
M. adhaerens chemotaxis and surface attachment support physical association with diatom cells and TEP aggregates before aggregate formation.
-
+
→ Condition-Dependent Diatom Aggregation
+
HYPOTHESIZED: chemotaxis-dependent attachment may enable the close association underlying the earlier HP15 aggregation phenotype. The reviewed chemotaxis abstract demonstrates reduced attachment, not selective mediation of the aggregation endpoint; aggregation effects cannot be assumed in every environmental treatment.
Evidence
-
The coculture is used to model microbial control of diatom aggregation and sinking particles, a process connected to export of particulate organic carbon and the biological carbon pump.
-
+
The existing marine-snow model interpretation concerns measured aggregate sinking and possible carbon export, not ecological niche partitioning. In the 2011 assay, aggregate size predicted sinking velocity while bacterial presence did not change the size-sinking relationship. Warmer 2014 treatments had depressed aggregation and sinking, especially with acidification. A resulting reduction in ocean carbon sequestration is an extrapolation, not a measured field flux or a demonstrated universal HP15 benefit.
+
+
+
Participating Taxa:
+ Thalassiosira weissflogii,
+
+ Marinobacter adhaerens HP15
+
+
@@ -921,7 +937,7 @@
Evidence
PMID:20827289
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"may enhance the efficiency of the biological pump"
@@ -934,7 +950,7 @@ Evidence
PMID:25375640
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"potentially reduced carbon sequestration after diatom blooms"
@@ -1020,6 +1036,45 @@ Associated Datasets
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which attachment and polymer properties causally control HP15-associated aggregation under each assay condition?
+
+
Mutant attachment, aggregate-free TEP, total TEP, aggregation and sinking are distinct measurements. Polymer chemistry/stickiness and exact mediation remain unresolved; the 2014 null bacterial effects and inverse temperature response constrain the earlier model. Full chemotaxis and MEPS bodies were not available for this review. Non-graph overstatements are tracked in #1884.
+
+
Attaches to: ecological_interactions#Condition-Dependent Diatom Aggregation, ecological_interactions#Condition-Dependent TEP Formation, ecological_interactions#Chemotaxis-Mediated Attachment, ecological_interactions#Aggregate Sinking and Carbon Export Interpretation
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
aggregation rates and sinking velocity of aggregates were depressed in warmer treatments
+
The abstract supplies a direct counterexample to universally increased aggregation with increased TEP.
+
+
+
+
@@ -1242,7 +1297,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1250,14 +1305,12 @@ Evidence
processes.push("biological process involved in interspecies interaction between organisms");
- processes.push("biofilm formation");
-
- var evidenceCount = 3;
+ var evidenceCount = 4;
nodes.push({
id: intId,
- label: "Bacteria-Dependent Diatom Aggregation",
+ label: "Condition-Dependent Diatom Aggregation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1266,23 +1319,26 @@ Evidence
});
- var srcKey = "Marinobacter adhaerens HP15";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Thalassiosira weissflogii";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Thalassiosira weissflogii",
+
+ "Marinobacter adhaerens HP15"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1293,11 +1349,11 @@ Evidence
processes.push("extracellular matrix organization");
- var evidenceCount = 3;
+ var evidenceCount = 4;
nodes.push({
id: intId,
- label: "Transparent Exopolymer Particle Enhancement",
+ label: "Condition-Dependent TEP Formation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1306,23 +1362,26 @@ Evidence
});
- var srcKey = "Thalassiosira weissflogii";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Marinobacter adhaerens HP15";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Thalassiosira weissflogii",
+
+ "Marinobacter adhaerens HP15"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1362,7 +1421,7 @@ Evidence
(function() {
var intId = "interaction:3";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1381,7 +1440,7 @@ Evidence
nodes.push({
id: intId,
- label: "Marine Snow Carbon Flux Model",
+ label: "Aggregate Sinking and Carbon Export Interpretation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1392,6 +1451,19 @@ Evidence
+ var participantKeys = [
+
+ "Thalassiosira weissflogii",
+
+ "Marinobacter adhaerens HP15"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html b/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html
index b033fc5a5..1eff397f4 100644
--- a/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html
+++ b/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html
@@ -598,7 +598,7 @@ Ecological Interactions
Ecological interaction network for Thalassiosira-Ruegeria Phycosphere Coculture
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, colonization facilitation).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding).
@@ -611,8 +611,8 @@
Ecological Interactions
@@ -620,10 +620,9 @@ Ecological Interactions
-
T. pseudonana changes gene expression in response to R. pomeroyi DSS-3, indicating a recognition response in the two-member model system.
+
In the 2017 B12-limited coculture experiment, T. pseudonana CCMP1335 differentially expressed genes with annotations consistent with recognition and signaling in response to R. pomeroyi DSS-3. The proposed plant-like cascade is inferred from homology and transcript patterns, not selectively demonstrated. Little attachment was observed during exponential growth. This is a directed diatom response to bacterial presence, not a measured colonization benefit or proof that recognition causes the separate chitin/lipid transcriptional response.
Source Taxon: Ruegeria pomeroyi DSS-3
@@ -655,17 +654,6 @@
Diatom Recognition of Ruegeria
-
-
Downstream Effects:
-
-
-
→ Diatom Chitin and Lipid Response During Coculture
-
Ruegeria-triggered diatom recognition is reflected in the downstream T. pseudonana transcriptional response affecting chitin metabolism and lipid biosynthesis during coculture.
-
-
-
-
-
Evidence
@@ -693,7 +681,7 @@
Evidence
Phytoplankton Metabolite Transfer to Ruegeria
CROSS_FEEDING
T. pseudonana provides organic substrates that support R. pomeroyi growth, including sulfonates, sugar derivatives, and organic nitrogen compounds inferred from multi-omics measurements.
+ Diatom-derived organic compounds support R. pomeroyi growth when the diatom is the only organic-carbon source. Individual substrate assignments have different evidence strengths: in the 2020 R. pomeroyi column of Table 1, DMSP and N-acetyl-D-glucosamine are supported by gene expression, whereas proline and guanosine have net exometabolite-drawdown evidence. These are three separate bacterial pair cultures, not a mixed three-bacterium competition experiment. Neither transcript induction nor net concentration changes alone trace a compound-specific transfer flux or demonstrate that bacterial consumption causes the diatom chitin response.
Source Taxon: Thalassiosira pseudonana CCMP1335
@@ -757,17 +745,6 @@ Phytoplankton Metabolite Transfer to Ruegeria
-
-
Downstream Effects:
-
-
-
→ Diatom Chitin and Lipid Response During Coculture
-
Diatom-derived substrates consumed by Ruegeria include chitin-related sugar derivatives, linking the transfer node to the chitin-metabolism component of the diatom transcriptional response.
-
-
-
-
Evidence
@@ -779,7 +756,7 @@ Evidence
PMID:28631440
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"we hypothesize that nine diatom metabolites supported the majority of bacterial growth, among them sulfonates, sugar derivatives and organic nitrogen compounds"
@@ -806,9 +783,8 @@ Evidence
-
Coculture with R. pomeroyi is associated with T. pseudonana transcriptional shifts in lipid biosynthesis and chitin metabolism, linking the interaction to diatom cell-surface and carbon allocation processes.
+
In the 2017 study, cocultured diatoms downregulated lipid biosynthesis and upregulated chitin metabolism genes relative to B12-replete axenic controls. These are measured transcriptional changes, not demonstrated Ruegeria-to-diatom substrate feeding, polymer production fluxes or selectively established outputs of a recognition cascade. The bacterium also supported B12-limited diatom growth, a distinct relationship missing from the present topology and tracked in #1883; it must not be inferred from this chitin/lipid node. The later L1 substrate-partitioning assay does not negate the earlier B12-limited benefit.
Source Taxon: Ruegeria pomeroyi DSS-3
@@ -950,6 +926,45 @@
Associated Datasets
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which signaling steps mediate the transcript response, and how should B12-dependent growth support be represented separately?
+
+
The 2017 PDF Figure 1 and Results support rescue of B12-limited diatom growth; that reciprocal interaction is missing from the current graph. Edison dry run completed, but the authorized real invocation stopped before submission because the configured key loader returned no key. New topology remains #1883, not silently replaced by the chitin response. Two existing arrows were removed because co-occurring transcript changes and shared substrate names do not establish those directions. Receptor/cue identity and causal mediation require further evidence; assay-metadata reconciliation is #1885.
+
+
Attaches to: ecological_interactions#Putative Diatom Recognition Response to Ruegeria, ecological_interactions#Phytoplankton Metabolite Transfer to Ruegeria, ecological_interactions#Diatom Chitin and Lipid Response During Coculture
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
induced a potential recognition cascade
+
The abstract explicitly qualifies the recognition cascade; the full paper separately reports B12-limited growth support.
+
+
+
+
@@ -1197,7 +1212,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1212,7 +1227,7 @@ Evidence
nodes.push({
id: intId,
- label: "Diatom Recognition of Ruegeria",
+ label: "Putative Diatom Recognition Response to Ruegeria",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1291,7 +1306,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
diff --git a/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html b/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html
index 2054c0d3c..27f01140f 100644
--- a/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html
+++ b/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html
@@ -603,7 +603,7 @@ Ecological Interactions
Ecological interaction network for Trichodesmium-Alteromonas Marine Consortium
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, mutualism, commensalism).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -611,18 +611,8 @@
Ecological Interactions
-
-
-
-
@@ -631,16 +621,19 @@ Ecological Interactions
-
Trichodesmium colonies provide nutrient-rich physical substrates that are colonized by heterotrophic bacteria, linking diazotrophic primary production to associated heterotrophic metabolism.
+
Trichodesmium colonies provide physical and nutrient-rich habitats associated with heterotrophs. The 2017 study recovered an A. macleodii representative genome from an IMS101 laboratory enrichment and found a conserved association across culture and environmental samples. This establishes association, not commensal neutrality, universal mutualism or a causal explanation of the separate 2018 field day-night transcript patterns. Named participants here identify the laboratory association, not an assertion that the field host was the IMS101 strain.
+
+
-
Source Taxon: Trichodesmium erythraeum IMS101
+
Participating Taxa:
+ Trichodesmium erythraeum IMS101,
+ Alteromonas macleodii Trichodesmium associate
-
Target Taxon: Trichodesmium-associated heterotrophic microbiome
+
@@ -659,16 +652,6 @@
Colony Substrate Colonization by Heterotrophs
-
-
Downstream Effects:
-
-
-
→ Diel Coordinated Resource Cycling
-
Trichodesmium colony colonization provides the host-microbiome setting in which diel nitrogen, carbon, iron, and B12 expression patterns were observed.
-
-
-
-
Evidence
@@ -693,10 +676,9 @@
Evidence
-
Comparative genomics suggests that Alteromonas macleodii contributes functions that may support Trichodesmium-associated community maintenance, including nutrient acquisition, vitamin exchange, catabolism of small carbon compounds, and reactive oxygen detoxification.
+
HYPOTHESIZED: comparative genomics and transcription identify candidate A. macleodii contributions to Trichodesmium nutrient acquisition, small-carbon recycling and ROS detoxification. The study also assayed siderophore production in isolates and reported Trichodesmium DMSP production; those measurements do not establish complete interpartner fluxes or reciprocal fitness effects. The proposed B12 direction is host-to-epibiont, not Alteromonas-to-Trichodesmium, and the 2017 genome permits facultative B12 use. These candidates are not demonstrated causes of the later field co-expression phenotype.
Source Taxon: Alteromonas macleodii Trichodesmium associate
@@ -742,16 +724,6 @@
Alteromonas Helper Functions in Trichodesmium Colonies
-
-
Downstream Effects:
-
-
-
→ Diel Coordinated Resource Cycling
-
Alteromonas Fe, P, B12, carbon-catabolism, and ROS-detoxification gene complements are candidate mechanisms for resource-linked diel coordination in Trichodesmium colonies.
-
-
-
-
Evidence
@@ -763,7 +735,7 @@
Evidence
PMID:28440800
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"iron and phosphorus acquisition, vitamin B12 exchange"
@@ -776,7 +748,7 @@
Evidence
PMID:28440800
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"detoxification of reactive oxygen species"
@@ -789,17 +761,18 @@ Evidence
-
Field metatranscriptomes show coordinated day-night gene expression between Trichodesmium and its microbiome, with co-expressed functions linked to nitrogen, carbon, iron, and vitamin B12 cycling.
+
Sixteen field-colony metatranscriptomes over three day-night transitions in the North Pacific Subtropical Gyre showed coordinated host/microbiome expression, including nitrogen-, carbon-, iron- and B12-related functions. This is coexpression supporting candidate resource interactions, not directly demonstrated cross-feeding, a metabolite flux, or causation by A. macleodii helper genes. The host was field Trichodesmium, not demonstrated to be IMS101; Alteromonas genus transcripts must not be assigned wholesale to A. macleodii. The participant list credits only the record microbiome guild that this field measurement supports. Pseudocobalamin/DMB remodeling and host-to-microbiome provision remain interpretations.
+
-
Source Taxon: Trichodesmium erythraeum IMS101
+
Participating Taxa:
+ Trichodesmium-associated heterotrophic microbiome
-
Target Taxon: Trichodesmium-associated heterotrophic microbiome
+
@@ -899,6 +872,45 @@
Associated Datasets
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which candidate helper activities mediate resource flux or host benefit in the exact association?
+
+
Genomic complementation and field coexpression generate testable hypotheses, not selective mediation or reciprocal-fitness measurements. The removed arrows described habitat context and cross-study candidate explanations. Host-to-microbiome B12 provision, pseudocobalamin remodeling and possible DMB supply are unresolved mechanistic interpretations. Exact laboratory strain, isolate source and field-community identities must remain distinct; non-graph reconciliation is #1886. Existing #297 ROS compound/process and #765 publication-body provenance decisions are preserved.
+
+
Attaches to: ecological_interactions#Colony Substrate Colonization by Heterotrophs, ecological_interactions#Putative Alteromonas Helper Functions in Trichodesmium Colonies, ecological_interactions#Field Host-Microbiome Diel Coexpression
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
Evidence of microbiome reliance on Trichodesmium-derived vitamin B12
+
The abstract gives the proposed host-to-microbiome direction as an inference from coexpression, not a traced flux.
+
+
+
+
@@ -1109,7 +1121,7 @@
(function() {
var intId = "interaction:0";
- var intType = "COMMENSALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1131,23 +1143,26 @@
});
- var srcKey = "Trichodesmium erythraeum IMS101";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Trichodesmium-associated heterotrophic microbiome";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Trichodesmium erythraeum IMS101",
+
+ "Alteromonas macleodii Trichodesmium associate"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1170,7 +1185,7 @@
nodes.push({
id: intId,
- label: "Alteromonas Helper Functions in Trichodesmium Colonies",
+ label: "Putative Alteromonas Helper Functions in Trichodesmium Colonies",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1195,7 +1210,7 @@
(function() {
var intId = "interaction:2";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1210,7 +1225,7 @@
nodes.push({
id: intId,
- label: "Diel Coordinated Resource Cycling",
+ label: "Field Host-Microbiome Diel Coexpression",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1219,17 +1234,18 @@
});
- var srcKey = "Trichodesmium erythraeum IMS101";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Trichodesmium-associated heterotrophic microbiome";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Trichodesmium-associated heterotrophic microbiome"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/history/records/Thalassiosira_Marinobacter_Marine_Snow_Coculture/2026-10-08T083138Z-codex-825172.yaml b/history/records/Thalassiosira_Marinobacter_Marine_Snow_Coculture/2026-10-08T083138Z-codex-825172.yaml
new file mode 100644
index 000000000..714918f0f
--- /dev/null
+++ b/history/records/Thalassiosira_Marinobacter_Marine_Snow_Coculture/2026-10-08T083138Z-codex-825172.yaml
@@ -0,0 +1,29 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml
+ slug: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+session:
+ id: 2026-10-08T083138Z-codex-825172
+ timestamp: '2026-10-08T08:31:38Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1880
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve the positive 2011 aggregation phenotype and the 2014 null effect without
+ universal dependence or colonization typing.; Replace TEP cross-feeding with an assay-bounded
+ polymer outcome and qualify the existing aggregation direction.; Preserve mutant attachment
+ evidence but distinguish bacterial attachment from diatom benefit and downstream mediation.;
+ Keep the existing sinking/export interpretation, remove niche-partitioning typing and
+ separate measurements from extrapolation.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
diff --git a/history/records/Thalassiosira_Ruegeria_Phycosphere_Coculture/2026-10-08T083139Z-codex-dd87e7.yaml b/history/records/Thalassiosira_Ruegeria_Phycosphere_Coculture/2026-10-08T083139Z-codex-dd87e7.yaml
new file mode 100644
index 000000000..d66819c90
--- /dev/null
+++ b/history/records/Thalassiosira_Ruegeria_Phycosphere_Coculture/2026-10-08T083139Z-codex-dd87e7.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml
+ slug: Thalassiosira_Ruegeria_Phycosphere_Coculture
+session:
+ id: 2026-10-08T083139Z-codex-dd87e7
+ timestamp: '2026-10-08T08:31:39Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1881
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain a putative recognition response without colonization typing or a restatement
+ arrow to other transcript changes.; Preserve supported organic-carbon feeding, grade metabolite
+ evidence and remove the shared-substrate-to-transcript arrow.; Retain the chitin/lipid
+ response as transcription, not reverse cross-feeding; preserve the separate B12 growth-benefit
+ boundary.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
diff --git a/history/records/Trichodesmium_Alteromonas_Marine_Consortium/2026-10-08T083139Z-codex-a37037.yaml b/history/records/Trichodesmium_Alteromonas_Marine_Consortium/2026-10-08T083139Z-codex-a37037.yaml
new file mode 100644
index 000000000..5842145fb
--- /dev/null
+++ b/history/records/Trichodesmium_Alteromonas_Marine_Consortium/2026-10-08T083139Z-codex-a37037.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml
+ slug: Trichodesmium_Alteromonas_Marine_Consortium
+session:
+ id: 2026-10-08T083139Z-codex-a37037
+ timestamp: '2026-10-08T08:31:39Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1882
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Represent colony association without commensal neutrality or a habitat-setting
+ arrow; distinguish laboratory and field identities.; Bound helper functions to hypotheses,
+ preserve ROS compound/process grounding and correct the B12 direction and facultative-use
+ distinction.; Retain field coexpression without cross-feeding typing or exact IMS101 attribution;
+ narrow connectivity to the supported guild.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
diff --git a/kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml b/kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml
index e59ff7c2c..8e2547838 100644
--- a/kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml
+++ b/kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml
@@ -106,67 +106,62 @@ taxonomy:
snippet: Marinobacter adhaerens HP15 has been demonstrated to attach to the diatom Thalassiosira weissflogii
explanation: Supports M. adhaerens HP15 as the bacterial member in the exact model.
ecological_interactions:
-- name: Bacteria-Dependent Diatom Aggregation
- description: >
- Photosynthetically active T. weissflogii and specific diatom-attaching
- bacteria, including M. adhaerens HP15, are required for strong aggregate
- formation; axenic T. weissflogii did not aggregate in the same assay.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Marinobacter adhaerens HP15
- term:
- id: NCBITaxon:225937
- label: Marinobacter adhaerens HP15
- target_taxon:
- preferred_term: Thalassiosira weissflogii
- term:
- id: NCBITaxon:1577725
- label: Conticribra weissflogii
+- name: Condition-Dependent Diatom Aggregation
+ description: In the 2011 rolling-tank assay, active T. weissflogii cocultured with attaching bacteria including
+ HP15 formed substantially more aggregates than axenic controls. This is a community aggregation outcome, not
+ a universal bacterial requirement or a separate colonization interaction. The 2014 temperature/pCO2 experiment
+ found no effect of HP15 on total aggregate volume. Inactivated cells in the 2011 Results aggregated much less,
+ not uniformly zero; the inactivation treatment may also have altered exudates and surface properties, so it
+ does not isolate photosynthesis as the sole mediator.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biological process involved in interspecies interaction between organisms
term:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
- - preferred_term: biofilm formation
- term:
- id: GO:0042710
- label: biofilm formation
evidence:
- reference: PMID:20827289
supports: SUPPORT
evidence_source: IN_VITRO
snippet: specific diatom-attaching bacteria were required for aggregation
- explanation: Supports the requirement for attaching bacteria in T. weissflogii aggregation.
+ explanation: The 2011 abstract supports the assay-specific requirement, not universal HP15 dependence across
+ studies.
- reference: PMID:20827289
supports: SUPPORT
evidence_source: IN_VITRO
snippet: T. weissflogii did not aggregate in axenic culture
- explanation: Supports the contrast between axenic diatom controls and bacteria-containing treatments.
+ explanation: Axenic active-diatom controls in the 2011 assay lacked aggregation; this is not the result of every
+ later experiment.
- reference: doi:10.4056/sigs.922139
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: it showed specific attachment to diatom cells. In vitro it led to exopolymer
- formation and aggregation of these algal cells to form marine snow particles
- explanation: HP15 type-strain genome paper directly describes HP15's diatom-cell
- attachment and resulting exopolymer-mediated aggregation into marine snow particles,
- supporting the bacteria-dependent aggregation phenotype.
-- name: Transparent Exopolymer Particle Enhancement
- description: >
- M. adhaerens HP15 is linked to transparent exopolymeric particle formation
- and aggregate formation during interaction with T. weissflogii.
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Thalassiosira weissflogii
+ snippet: it showed specific attachment to diatom cells. In vitro it led to exopolymer formation and aggregation
+ of these algal cells to form marine snow particles
+ explanation: The HP15 genome paper independently identifies the exact attaching strain and its reported aggregation
+ phenotype; it does not establish universal dependence.
+ - reference: PMID:25375640
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: total aggregate volume was independent of the presence of M. adhaerens HP15
+ explanation: The 2014 paper explicitly reports a null bacterial effect under that experiment; this bounds the
+ earlier phenotype.
+ participating_taxa:
+ - preferred_term: Thalassiosira weissflogii
term:
id: NCBITaxon:1577725
label: Conticribra weissflogii
- target_taxon:
- preferred_term: Marinobacter adhaerens HP15
+ - preferred_term: Marinobacter adhaerens HP15
term:
id: NCBITaxon:225937
label: Marinobacter adhaerens HP15
+- name: Condition-Dependent TEP Formation
+ description: TEP formation and aggregation were associated with the diatom-HP15 model in earlier work. TEP is
+ a measured community polymer outcome, not proof of directed feeding from the diatom to HP15. The 2014 study
+ found no bacterial effect on total TEP generated; warmer treatments generated more TEP but less aggregation.
+ The 2011 aggregate-free-water measurements and 2014 total-TEP measurements must not be treated as identical
+ endpoints. Chitin-containing fibres in a SEM caption document physical association, not the identity of all
+ TEP or a measured chitin-transfer flux.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: photosynthesis
term:
@@ -177,38 +172,48 @@ ecological_interactions:
id: GO:0030198
label: extracellular matrix organization
downstream:
- - target: Bacteria-Dependent Diatom Aggregation
- description: >
- HP15-associated transparent exopolymer particle formation provides the
- exopolymeric matrix that supports diatom aggregation and marine-snow
- particle formation.
+ - target: Condition-Dependent Diatom Aggregation
+ description: 'PARTIAL: TEP can provide an adhesive matrix enabling diatom aggregation, but the amount-aggregation
+ relationship is condition dependent. The 2011 association is not a selective mediation test; the 2014 higher-TEP/lower-aggregation
+ result rules out a universal monotonic effect, and polymer stickiness was not directly resolved.'
evidence:
- reference: PMID:22820333
supports: SUPPORT
evidence_source: IN_VITRO
snippet: induce transparent exopolymeric particle and aggregate formation
- explanation: Supports HP15-associated TEP and aggregate formation in the exact model.
+ explanation: The chemotaxis abstract recounts the model aggregation/TEP phenotype; it does not measure TEP uptake
+ as food.
- reference: PMID:20827289
supports: SUPPORT
evidence_source: IN_VITRO
snippet: TEP formation and phytoplankton aggregation
- explanation: Supports TEP formation and aggregation as measured outcomes in the interaction.
+ explanation: Supports the two measured outcomes, not a demonstration that TEP quantity alone causes aggregation.
- reference: doi:10.3354/meps09894
supports: PARTIAL
evidence_source: IN_VITRO
- snippet: a co-incubation sample containing the diatom Thalassiosira weissflogii (left)
- and Marinobacter adhaerens HP15 embedded in a network of chitincontaining fibres
- extruding from the diatom cell
- explanation: SEM evidence of HP15 attaching to T. weissflogii within a chitin-containing
- fibre network during co-incubation - direct visual documentation of the exopolymer
- matrix this interaction is built around. Partial because the publicly available
- excerpt is the figure caption rather than the methods/quantitative results.
+ snippet: a co-incubation sample containing the diatom Thalassiosira weissflogii (left) and Marinobacter adhaerens
+ HP15 embedded in a network of chitincontaining fibres extruding from the diatom cell
+ explanation: 'PARTIAL: retained caption documents HP15 in chitin-containing fibres. The full paper was not accessible;
+ this does not identify all TEP or establish polymer-feeding causality.'
+ - reference: PMID:25375640
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: had no effect on the amount of TEP generated
+ explanation: The later experiment bounds general claims of HP15 enhancement of TEP.
+ participating_taxa:
+ - preferred_term: Thalassiosira weissflogii
+ term:
+ id: NCBITaxon:1577725
+ label: Conticribra weissflogii
+ - preferred_term: Marinobacter adhaerens HP15
+ term:
+ id: NCBITaxon:225937
+ label: Marinobacter adhaerens HP15
- name: Chemotaxis-Mediated Attachment
- description: >
- Chemotaxis and surface attachment functions in M. adhaerens contribute to
- physical association with diatom cells and TEP aggregates, providing a
- mechanistic basis for initiation of the two-member interaction.
- interaction_type: COLONIZATION_FACILITATION
+ description: Diatom homogenate or culture supernatant attracted HP15, and chemotaxis-associated mutants had a
+ smaller attached bacterial fraction in coculture than wild type. These perturbations support HP15 chemotaxis/motility
+ contributions to bacterial attachment to the diatom, not a demonstrated growth or colonization benefit to the
+ diatom. Mutant biofilm impairment was assayed on abiotic surfaces and is distinct from diatom aggregation.
scope: PAIRWISE
source_taxon:
preferred_term: Marinobacter adhaerens HP15
@@ -230,11 +235,11 @@ ecological_interactions:
id: GO:0042710
label: biofilm formation
downstream:
- - target: Bacteria-Dependent Diatom Aggregation
- description: >
- M. adhaerens chemotaxis and surface attachment support physical
- association with diatom cells and TEP aggregates before aggregate
- formation.
+ - target: Condition-Dependent Diatom Aggregation
+ description: 'HYPOTHESIZED: chemotaxis-dependent attachment may enable the close association underlying the
+ earlier HP15 aggregation phenotype. The reviewed chemotaxis abstract demonstrates reduced attachment, not
+ selective mediation of the aggregation endpoint; aggregation effects cannot be assumed in every environmental
+ treatment.'
evidence:
- reference: PMID:22820333
supports: SUPPORT
@@ -246,18 +251,20 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: the fraction of bacteria attaching to the diatom decreased significantly for mutants
explanation: Supports attachment impairment in chemotaxis mutants relative to wild-type HP15.
-- name: Marine Snow Carbon Flux Model
- description: >
- The coculture is used to model microbial control of diatom aggregation and
- sinking particles, a process connected to export of particulate organic
- carbon and the biological carbon pump.
- interaction_type: NICHE_PARTITIONING
+- name: Aggregate Sinking and Carbon Export Interpretation
+ description: The existing marine-snow model interpretation concerns measured aggregate sinking and possible carbon
+ export, not ecological niche partitioning. In the 2011 assay, aggregate size predicted sinking velocity while
+ bacterial presence did not change the size-sinking relationship. Warmer 2014 treatments had depressed aggregation
+ and sinking, especially with acidification. A resulting reduction in ocean carbon sequestration is an extrapolation,
+ not a measured field flux or a demonstrated universal HP15 benefit.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: carbon dioxide
term:
id: CHEBI:16526
label: carbon dioxide
+ notes: CO2/pCO2 is a photosynthetic substrate and imposed environmental condition, not a demonstrated exchanged
+ product of this outcome.
biological_processes:
- preferred_term: photosynthesis
term:
@@ -269,15 +276,24 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
evidence:
- reference: PMID:20827289
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: may enhance the efficiency of the biological pump
- explanation: Supports the carbon-export relevance of bacteria-enhanced aggregation and sinking.
+ explanation: The abstract proposes biological-pump relevance; it does not report measured ocean carbon export.
- reference: PMID:25375640
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: potentially reduced carbon sequestration after diatom blooms
- explanation: Supports use of the exact system to test future-ocean effects on carbon sequestration.
+ explanation: Carbon sequestration is explicitly a conditional extrapolation of laboratory aggregate measurements.
+ participating_taxa:
+ - preferred_term: Thalassiosira weissflogii
+ term:
+ id: NCBITaxon:1577725
+ label: Conticribra weissflogii
+ - preferred_term: Marinobacter adhaerens HP15
+ term:
+ id: NCBITaxon:225937
+ label: Marinobacter adhaerens HP15
environmental_factors:
- name: Photosynthetic activity
value: photosynthetically active versus inactivated diatom cells
@@ -399,3 +415,36 @@ metal_relevance: NOT_APPLICABLE
metal_notes: >
No metal or rare earth processing role is curated for this marine
diatom-bacterium aggregation model.
+discussions:
+- discussion_id: hp15-aggregation-mediation-and-conditions
+ prompt: Which attachment and polymer properties causally control HP15-associated aggregation under each assay
+ condition?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: 'Mutant attachment, aggregate-free TEP, total TEP, aggregation and sinking are distinct measurements.
+ Polymer chemistry/stickiness and exact mediation remain unresolved; the 2014 null bacterial effects and inverse
+ temperature response constrain the earlier model. Full chemotaxis and MEPS bodies were not available for this
+ review. Non-graph overstatements are tracked in #1884.'
+ attaches_to:
+ - ecological_interactions#Condition-Dependent Diatom Aggregation
+ - ecological_interactions#Condition-Dependent TEP Formation
+ - ecological_interactions#Chemotaxis-Mediated Attachment
+ - ecological_interactions#Aggregate Sinking and Carbon Export Interpretation
+ evidence:
+ - reference: PMID:25375640
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: aggregation rates and sinking velocity of aggregates were depressed in warmer treatments
+ explanation: The abstract supplies a direct counterexample to universally increased aggregation with increased
+ TEP.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-08T08:31:37Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Preserve the positive 2011 aggregation phenotype and the 2014 null effect without universal dependence
+ or colonization typing.; Replace TEP cross-feeding with an assay-bounded polymer outcome and qualify the existing
+ aggregation direction.; Preserve mutant attachment evidence but distinguish bacterial attachment from diatom
+ benefit and downstream mediation.; Keep the existing sinking/export interpretation, remove niche-partitioning
+ typing and separate measurements from extrapolation. Issue#1880; reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
+ llm_assisted: true
diff --git a/kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml b/kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml
index ad15fb968..d0ef9adf8 100644
--- a/kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml
+++ b/kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml
@@ -98,11 +98,13 @@ taxonomy:
snippet: bacteria pre-grown in YTSS medium were washed five times in sterile L1 medium and inoculated into three replicate diatom cultures
explanation: Supports the bacterial inoculation step used to assemble the pairwise coculture.
ecological_interactions:
-- name: Diatom Recognition of Ruegeria
- description: T. pseudonana changes gene expression in response to R. pomeroyi DSS-3, indicating a
- recognition response in the two-member model system.
+- name: Putative Diatom Recognition Response to Ruegeria
+ description: In the 2017 B12-limited coculture experiment, T. pseudonana CCMP1335 differentially expressed genes
+ with annotations consistent with recognition and signaling in response to R. pomeroyi DSS-3. The proposed plant-like
+ cascade is inferred from homology and transcript patterns, not selectively demonstrated. Little attachment was
+ observed during exponential growth. This is a directed diatom response to bacterial presence, not a measured
+ colonization benefit or proof that recognition causes the separate chitin/lipid transcriptional response.
scope: PAIRWISE
- interaction_type: COLONIZATION_FACILITATION
source_taxon:
preferred_term: Ruegeria pomeroyi DSS-3
term:
@@ -118,25 +120,27 @@ ecological_interactions:
term:
id: GO:0007154
label: cell communication
+ notes: Putative communication inferred from transcription and annotation; the chemical cue and pathway mediation
+ are unresolved.
- preferred_term: biological process involved in interspecies interaction between organisms
term:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Diatom Chitin and Lipid Response During Coculture
- description: >
- Ruegeria-triggered diatom recognition is reflected in the downstream
- T. pseudonana transcriptional response affecting chitin metabolism and
- lipid biosynthesis during coculture.
evidence:
- reference: PMID:28631440
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Bacterium Ruegeria pomeroyi DSS-3 triggered differential expression of >80 genes in diatom Thalassiosira pseudonana CCMP1335
- explanation: Supports Ruegeria-triggered diatom recognition or response in the exact two-member system.
+ snippet: Bacterium Ruegeria pomeroyi DSS-3 triggered differential expression of >80 genes in diatom Thalassiosira
+ pseudonana CCMP1335
+ explanation: Supports differential transcription; recognition-pathway function is a hypothesis, not a colonization
+ or mediation assay.
- name: Phytoplankton Metabolite Transfer to Ruegeria
- description: T. pseudonana provides organic substrates that support R. pomeroyi growth, including
- sulfonates, sugar derivatives, and organic nitrogen compounds inferred from multi-omics measurements.
+ description: 'Diatom-derived organic compounds support R. pomeroyi growth when the diatom is the only organic-carbon
+ source. Individual substrate assignments have different evidence strengths: in the 2020 R. pomeroyi column of
+ Table 1, DMSP and N-acetyl-D-glucosamine are supported by gene expression, whereas proline and guanosine have
+ net exometabolite-drawdown evidence. These are three separate bacterial pair cultures, not a mixed three-bacterium
+ competition experiment. Neither transcript induction nor net concentration changes alone trace a compound-specific
+ transfer flux or demonstrate that bacterial consumption causes the diatom chitin response.'
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -154,18 +158,26 @@ ecological_interactions:
term:
id: CHEBI:16457
label: S,S-dimethyl-beta-propiothetin
+ notes: Gene-expression inference (G; functionally verified genes for DMSP) in the R. pomeroyi pair in 2020 Table
+ 1; candidate uptake, not an individually traced transfer flux.
- preferred_term: N-acetyl-D-glucosamine
term:
id: CHEBI:506227
label: N-acetyl-D-glucosamine
+ notes: Gene-expression inference (G) in the R. pomeroyi pair in 2020 Table 1; candidate uptake, not an individually
+ traced transfer flux.
- preferred_term: proline
term:
id: CHEBI:26271
label: proline
+ notes: Net metabolite drawdown (M) in the R. pomeroyi pair in 2020 Table 1; candidate uptake, not an individually
+ traced transfer flux.
- preferred_term: guanosine
term:
id: CHEBI:16750
label: guanosine
+ notes: Net metabolite drawdown (M) in the R. pomeroyi pair in 2020 Table 1; candidate uptake, not an individually
+ traced transfer flux.
biological_processes:
- preferred_term: photosynthesis
term:
@@ -183,29 +195,28 @@ ecological_interactions:
term:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Diatom Chitin and Lipid Response During Coculture
- description: >
- Diatom-derived substrates consumed by Ruegeria include chitin-related
- sugar derivatives, linking the transfer node to the chitin-metabolism
- component of the diatom transcriptional response.
evidence:
- reference: PMID:28631440
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: we hypothesize that nine diatom metabolites supported the majority of bacterial growth, among them sulfonates, sugar derivatives and organic nitrogen compounds
- explanation: Supports diatom-to-Ruegeria metabolite transfer and candidate metabolite classes.
+ snippet: we hypothesize that nine diatom metabolites supported the majority of bacterial growth, among them
+ sulfonates, sugar derivatives and organic nitrogen compounds
+ explanation: The 2017 abstract explicitly hypothesizes compound identities; it does not directly measure all
+ nine transfer fluxes.
- reference: PMID:33097854
supports: SUPPORT
evidence_source: IN_VITRO
snippet: marine phytoplankter T. pseudonana CCMP1335 served as the sole carbon source for three bacterial strains
- explanation: Supports the experimental premise that diatom products served as the bacterial carbon source, including in the R. pomeroyi pairwise coculture.
+ explanation: The 2020 sole-carbon-source design supports diatom-to-bacterium feeding in separate pair cultures,
+ not simultaneous competition.
- name: Diatom Chitin and Lipid Response During Coculture
- description: Coculture with R. pomeroyi is associated with T. pseudonana transcriptional shifts in
- lipid biosynthesis and chitin metabolism, linking the interaction to diatom cell-surface and carbon
- allocation processes.
+ description: 'In the 2017 study, cocultured diatoms downregulated lipid biosynthesis and upregulated chitin metabolism
+ genes relative to B12-replete axenic controls. These are measured transcriptional changes, not demonstrated
+ Ruegeria-to-diatom substrate feeding, polymer production fluxes or selectively established outputs of a recognition
+ cascade. The bacterium also supported B12-limited diatom growth, a distinct relationship missing from the present
+ topology and tracked in #1883; it must not be inferred from this chitin/lipid node. The later L1 substrate-partitioning
+ assay does not negate the earlier B12-limited benefit.'
scope: PAIRWISE
- interaction_type: CROSS_FEEDING
source_taxon:
preferred_term: Ruegeria pomeroyi DSS-3
term:
@@ -388,3 +399,36 @@ associated_datasets:
snippet: Raw data, peak lists, and analysis scripts are available at MetaboLights under accession MTBLS1544.
explanation: Supports the exometabolomics data and analysis resource for the coculture study.
metal_relevance: NOT_APPLICABLE
+discussions:
+- discussion_id: ruegeria-recognition-mediation-and-b12-extension
+ prompt: Which signaling steps mediate the transcript response, and how should B12-dependent growth support be
+ represented separately?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: 'The 2017 PDF Figure 1 and Results support rescue of B12-limited diatom growth; that reciprocal interaction
+ is missing from the current graph. Edison dry run completed, but the authorized real invocation stopped before
+ submission because the configured key loader returned no key. New topology remains #1883, not silently replaced
+ by the chitin response. Two existing arrows were removed because co-occurring transcript changes and shared
+ substrate names do not establish those directions. Receptor/cue identity and causal mediation require further
+ evidence; assay-metadata reconciliation is #1885.'
+ attaches_to:
+ - ecological_interactions#Putative Diatom Recognition Response to Ruegeria
+ - ecological_interactions#Phytoplankton Metabolite Transfer to Ruegeria
+ - ecological_interactions#Diatom Chitin and Lipid Response During Coculture
+ evidence:
+ - reference: PMID:28631440
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: induced a potential recognition cascade
+ explanation: The abstract explicitly qualifies the recognition cascade; the full paper separately reports B12-limited
+ growth support.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-08T08:31:38Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain a putative recognition response without colonization typing or a restatement arrow to other transcript
+ changes.; Preserve supported organic-carbon feeding, grade metabolite evidence and remove the shared-substrate-to-transcript
+ arrow.; Retain the chitin/lipid response as transcription, not reverse cross-feeding; preserve the separate
+ B12 growth-benefit boundary. Issue#1881; reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
+ llm_assisted: true
diff --git a/kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml b/kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml
index 8bea140e9..75ce78c75 100644
--- a/kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml
+++ b/kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml
@@ -94,42 +94,42 @@ taxonomy:
explanation: Supports inclusion of a broader heterotrophic microbiome in addition to Alteromonas.
ecological_interactions:
- name: Colony Substrate Colonization by Heterotrophs
- description: Trichodesmium colonies provide nutrient-rich physical substrates that are colonized by
- heterotrophic bacteria, linking diazotrophic primary production to associated heterotrophic metabolism.
- interaction_type: COMMENSALISM
+ description: Trichodesmium colonies provide physical and nutrient-rich habitats associated with heterotrophs.
+ The 2017 study recovered an A. macleodii representative genome from an IMS101 laboratory enrichment and found
+ a conserved association across culture and environmental samples. This establishes association, not commensal
+ neutrality, universal mutualism or a causal explanation of the separate 2018 field day-night transcript patterns.
+ Named participants here identify the laboratory association, not an assertion that the field host was the IMS101
+ strain.
scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: Trichodesmium erythraeum IMS101
- term:
- id: NCBITaxon:203124
- label: Trichodesmium erythraeum IMS101
- target_taxon:
- preferred_term: Trichodesmium-associated heterotrophic microbiome
- term:
- id: NCBITaxon:2
- label: Bacteria
biological_processes:
- preferred_term: nitrogen fixation
term:
id: GO:0009399
label: nitrogen fixation
notes: Trichodesmium fixes nitrogen in oligotrophic marine environments.
- downstream:
- - target: Diel Coordinated Resource Cycling
- description: Trichodesmium colony colonization provides the host-microbiome
- setting in which diel nitrogen, carbon, iron, and B12 expression patterns
- were observed.
evidence:
- reference: PMID:28440800
supports: SUPPORT
evidence_source: COMPUTATIONAL
snippet: macroscopic colonies that serve as relatively nutrient-rich substrates
- explanation: Supports a colony habitat effect that enables heterotrophic colonization.
-- name: Alteromonas Helper Functions in Trichodesmium Colonies
- description: Comparative genomics suggests that Alteromonas macleodii contributes functions that may
- support Trichodesmium-associated community maintenance, including nutrient acquisition, vitamin exchange,
- catabolism of small carbon compounds, and reactive oxygen detoxification.
- interaction_type: MUTUALISM
+ explanation: Supports nutrient-rich colony habitat context; neither fitness neutrality nor mediation of field
+ expression was established.
+ participating_taxa:
+ - preferred_term: Trichodesmium erythraeum IMS101
+ term:
+ id: NCBITaxon:203124
+ label: Trichodesmium erythraeum IMS101
+ - preferred_term: Alteromonas macleodii Trichodesmium associate
+ term:
+ id: NCBITaxon:28108
+ label: Alteromonas macleodii
+- name: Putative Alteromonas Helper Functions in Trichodesmium Colonies
+ description: 'HYPOTHESIZED: comparative genomics and transcription identify candidate A. macleodii contributions
+ to Trichodesmium nutrient acquisition, small-carbon recycling and ROS detoxification. The study also assayed
+ siderophore production in isolates and reported Trichodesmium DMSP production; those measurements do not establish
+ complete interpartner fluxes or reciprocal fitness effects. The proposed B12 direction is host-to-epibiont,
+ not Alteromonas-to-Trichodesmium, and the 2017 genome permits facultative B12 use. These candidates are not
+ demonstrated causes of the later field co-expression phenotype.'
scope: PAIRWISE
source_taxon:
preferred_term: Alteromonas macleodii Trichodesmium associate
@@ -146,71 +146,61 @@ ecological_interactions:
term:
id: CHEBI:18367
label: phosphate(3-)
- notes: Phosphorus acquisition was one inferred interaction axis.
+ notes: Phosphate release is a proposed APase-mediated nutrient-acquisition mechanism (2017 Figure 3), not a
+ measured interpartner phosphate flux.
- preferred_term: iron(2+)
term:
id: CHEBI:29033
label: iron(2+)
- notes: Iron acquisition was one inferred interaction axis; ferrous iron is used as a conservative
- CHEBI grounding for iron availability.
+ notes: The 2017 Fe-acquisition model includes siderophore-bound Fe(III), photoreduction and Fe(II) availability;
+ this term is one proposed species, not a generic or measured iron-transfer grounding.
- preferred_term: vitamin B12
term:
id: CHEBI:176843
label: vitamin B12
- notes: Cobalamin exchange was an inferred interaction axis and later a
- detected diel co-expression dependency.
+ notes: Proposed Trichodesmium-to-Alteromonas provision, opposite to the helper node taxon direction. The 2017
+ genome supports facultative vitamin use; the 2018 field co-expression inference does not prove exact-strain
+ dependence or transfer flux.
- preferred_term: reactive oxygen species
term:
id: CHEBI:26523
label: reactive oxygen species
- notes: The compound. What the consortium does with it is the sibling biological_processes
- entry - ROS is involved in the interaction, and its detoxification is the process
- (#297).
+ notes: The compound. What the consortium does with it is the sibling biological_processes entry - ROS is involved
+ in the interaction, and its detoxification is the process (#297).
biological_processes:
- preferred_term: reactive oxygen species detoxification
term:
id: GO:0098869
label: cellular oxidant detoxification
- notes: 'Modelled as both compound and process, which is what the note this replaces
- described: "reactive oxygen species detoxification is an inferred interaction process".
- CHEBI:26523 is the species; GO:0098869 is what is done to it. Its definition -
- "reduces or removes the toxicity of superoxide radicals or hydrogen peroxide" - is
- the general oxidant case, chosen over GO:0141082 "symbiont-mediated detoxification
- of host-generated reactive oxygen species", which would assert a host-symbiont
- relation this consortium does not have, and over GO:0061692, which is hydrogen
- peroxide only. Inherits the interaction''s COMPUTATIONAL evidence: this is the
+ notes: 'Modelled as both compound and process, which is what the note this replaces described: "reactive oxygen
+ species detoxification is an inferred interaction process". CHEBI:26523 is the species; GO:0098869 is what
+ is done to it. Its definition - "reduces or removes the toxicity of superoxide radicals or hydrogen peroxide"
+ - is the general oxidant case, chosen over GO:0141082 "symbiont-mediated detoxification of host-generated
+ reactive oxygen species", which would assert a host-symbiont relation this consortium does not have, and over
+ GO:0061692, which is hydrogen peroxide only. Inherits the interaction''s COMPUTATIONAL evidence: this is the
inferred axis the source names, not a measured one (#297).'
- downstream:
- - target: Diel Coordinated Resource Cycling
- description: Alteromonas Fe, P, B12, carbon-catabolism, and
- ROS-detoxification gene complements are candidate mechanisms for
- resource-linked diel coordination in Trichodesmium colonies.
evidence:
- reference: PMID:28440800
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: iron and phosphorus acquisition, vitamin B12 exchange
- explanation: Supports inferred nutrient and vitamin exchange between Alteromonas and Trichodesmium.
+ explanation: Names genomic candidate axes, not measured mutualistic fitness or a demonstrated direction for
+ every compound. B12 provision is proposed in the reverse taxon direction.
- reference: PMID:28440800
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
snippet: detoxification of reactive oxygen species
- explanation: Supports an oxidative-stress helper mechanism in the association.
-- name: Diel Coordinated Resource Cycling
- description: Field metatranscriptomes show coordinated day-night gene expression between Trichodesmium
- and its microbiome, with co-expressed functions linked to nitrogen, carbon, iron, and vitamin B12 cycling.
- interaction_type: CROSS_FEEDING
+ explanation: Names a candidate oxidative-stress helper function; the exact association was not subjected to
+ a selective ROS-rescue test in this study.
+- name: Field Host-Microbiome Diel Coexpression
+ description: Sixteen field-colony metatranscriptomes over three day-night transitions in the North Pacific Subtropical
+ Gyre showed coordinated host/microbiome expression, including nitrogen-, carbon-, iron- and B12-related functions.
+ This is coexpression supporting candidate resource interactions, not directly demonstrated cross-feeding, a
+ metabolite flux, or causation by A. macleodii helper genes. The host was field Trichodesmium, not demonstrated
+ to be IMS101; Alteromonas genus transcripts must not be assigned wholesale to A. macleodii. The participant
+ list credits only the record microbiome guild that this field measurement supports. Pseudocobalamin/DMB remodeling
+ and host-to-microbiome provision remain interpretations.
scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: Trichodesmium erythraeum IMS101
- term:
- id: NCBITaxon:203124
- label: Trichodesmium erythraeum IMS101
- target_taxon:
- preferred_term: Trichodesmium-associated heterotrophic microbiome
- term:
- id: NCBITaxon:2
- label: Bacteria
biological_processes:
- preferred_term: photosynthesis
term:
@@ -221,18 +211,26 @@ ecological_interactions:
term:
id: GO:0009399
label: nitrogen fixation
- notes: Diel expression patterns can affect nitrogen fixation and resource cycling.
+ notes: Nitrogen-fixation-related expression is coordinated with microbiome transcripts; feedback on fixation
+ rates is proposed, not measured by coexpression.
evidence:
- reference: PMID:29382945
supports: SUPPORT
evidence_source: COMPUTATIONAL
snippet: significantly coordinated patterns of gene expression between host and microbiome
- explanation: Supports coordinated diel activity between Trichodesmium and associated bacteria.
+ explanation: Supports the measured field coexpression phenotype, not exact-strain field membership or demonstrated
+ causal coupling.
- reference: PMID:29382945
supports: SUPPORT
evidence_source: COMPUTATIONAL
snippet: linked to key resources including nitrogen, carbon, and iron
- explanation: Supports resource-linked functional coordination in the holobiont.
+ explanation: Supports functional resource annotations of correlated genes; it does not measure transfers of
+ these resources.
+ participating_taxa:
+ - preferred_term: Trichodesmium-associated heterotrophic microbiome
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
environmental_factors:
- name: oligotrophic warm ocean habitat
value: warm oligotrophic oceans
@@ -365,8 +363,39 @@ curation_history:
- timestamp: '2026-09-13T01:01:48Z'
curator: codex
action: REMOVE_UNVERIFIABLE_PUBLICATION_EVIDENCE
- changes: "Removed 1 evidence items that no longer match the retained abstracts after PR #766's publication-body
- policy caught newer main caches. Preserved all scientific claims, taxonomy and interaction topology;
- these claims require re-evidencing where support was removed. See the linked publication-text-removal
- history for license/version uncertainty."
+ changes: 'Removed 1 evidence items that no longer match the retained abstracts after PR #766''s publication-body
+ policy caught newer main caches. Preserved all scientific claims, taxonomy and interaction topology; these claims
+ require re-evidencing where support was removed. See the linked publication-text-removal history for license/version
+ uncertainty.'
llm_assisted: true
+- timestamp: '2026-10-08T08:31:38Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Represent colony association without commensal neutrality or a habitat-setting arrow; distinguish laboratory
+ and field identities.; Bound helper functions to hypotheses, preserve ROS compound/process grounding and correct
+ the B12 direction and facultative-use distinction.; Retain field coexpression without cross-feeding typing or
+ exact IMS101 attribution; narrow connectivity to the supported guild. Issue#1882; reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
+ llm_assisted: true
+discussions:
+- discussion_id: trichodesmium-helper-flux-and-field-identity
+ prompt: Which candidate helper activities mediate resource flux or host benefit in the exact association?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: 'Genomic complementation and field coexpression generate testable hypotheses, not selective mediation
+ or reciprocal-fitness measurements. The removed arrows described habitat context and cross-study candidate explanations.
+ Host-to-microbiome B12 provision, pseudocobalamin remodeling and possible DMB supply are unresolved mechanistic
+ interpretations. Exact laboratory strain, isolate source and field-community identities must remain distinct;
+ non-graph reconciliation is #1886. Existing #297 ROS compound/process and #765 publication-body provenance decisions
+ are preserved.'
+ attaches_to:
+ - ecological_interactions#Colony Substrate Colonization by Heterotrophs
+ - ecological_interactions#Putative Alteromonas Helper Functions in Trichodesmium Colonies
+ - ecological_interactions#Field Host-Microbiome Diel Coexpression
+ evidence:
+ - reference: PMID:29382945
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: Evidence of microbiome reliance on Trichodesmium-derived vitamin B12
+ explanation: The abstract gives the proposed host-to-microbiome direction as an inference from coexpression,
+ not a traced flux.
+ posed_by: codex
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index c03e6320c..8be3361ed 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,36 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch113: Marine Assay And Causal Boundaries
+
+[Decisions](decisions/20261008-three-records-batch113.yaml),
+[provenance](cache-provenance-20261008-batch113.json),
+[validation](validation-20261008-batch113.json), and
+[self-adversarial review](adversarial-review-20261008-batch113.yaml) cover
+the diatom-HP15, diatom-Ruegeria and Trichodesmium-Alteromonas records.
+All ten existing nodes remain; four unsupported arrows are removed and two
+condition-bounded HP15 directions remain. Positive growth and attachment
+findings are preserved without promoting transcript correlations or genomic
+candidates to demonstrated mechanisms.
+
+Three fresh extracted primary main bodies and three complete primary PDF
+text extractions were read, with selected PDF figures visually inspected.
+The 2018 diel main body was read from existing curator text; chemotaxis is
+abstract-bounded and the MEPS fibre evidence remains caption-only. Of 24
+graph/discussion quotations, 23 match fresh primary text and one matches
+the existing MEPS caption. No publication bodies or PDFs were added.
+Three append-only histories preserve all non-graph blocks, 457 other records
+and 923 caches. Explicit participant lists change in two records while the
+measured connectivity census and connectivity rules remain unchanged.
+
+Repairs #1880-#1882 await protected-main merge. Ruegeria remains
+`needs_research`: its distinct B12 growth-support extension (#1883) needs
+the skill-required Edison step. The one-community dry run completed; the
+authorized real invocation stopped before submission because its configured
+key loader found no key. No provider credits were spent. Non-graph metadata
+follow-ups #1884-#1886 remain open. Self-review is not independent approval
+or completion of the corpus review.
+
## Batch112: Syntrophic Feedback And Assay Boundaries
[Decisions](decisions/20261008-seven-records-batch112.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch113.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch113.yaml
new file mode 100644
index 000000000..cb24480fd
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch113.yaml
@@ -0,0 +1,337 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 7a920570e99167cd0e97083f1dbc32cc20c317b9
+scope:
+- kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml
+- kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml
+- kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch113.json
+findings:
+- issue: 1880
+ severity: P2
+ finding: Bound HP15 marine-snow graph to assay-specific aggregation and TEP evidence
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1881
+ severity: P2
+ finding: Separate Ruegeria transcript responses from colonization and reverse cross-feeding
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1882
+ severity: P2
+ finding: Bound Trichodesmium helper hypotheses and remove cross-study causal arrows
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1883
+ severity: P2
+ finding: Complete the missing Ruegeria B12 growth-support graph after Edison authentication
+ status: open_research_extension
+ disposition: Remain open until separately verified.
+- issue: 1884
+ severity: P2
+ finding: Reconcile HP15 non-graph photosynthesis, pCO2 and chitin claims with source limits
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1885
+ severity: P2
+ finding: Keep Ruegeria assay media and metabolite evidence grades distinct outside the graph
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1886
+ severity: P2
+ finding: Separate IMS101 enrichment, epibiont isolation and field-community metadata
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+adversarial_checks:
+- 'Every original node and direction has a disposition: ten nodes retained, six renamed, two existing directions
+ qualified and four unsupported arrows removed. No new topology. Renamed targets and discussion anchors resolve
+ exactly.'
+- 'Overcorrection check: preserve positive 2011 aggregation, mutant attachment impairment, diatom-supported Ruegeria
+ growth, the 2017 B12-limited growth rescue and conserved Trichodesmium association. Qualification does not erase
+ observed benefits.'
+- 'HP15: later null bacterial effects on total TEP, aggregate volume and the size-sinking relation constrain universal
+ claims. Aggregate-free-water TEP and total TEP are different endpoints. Inactivation did not produce uniformly
+ zero aggregation and may change surface chemistry. The caption documents chitin fibres, not all TEP chemistry
+ or feeding. The two retained arrows remain conditional or hypothetical; ocean export is an extrapolation.'
+- 'Ruegeria: recognition is inferred from gene homology and transcription, not a colonization benefit. Chitin/lipid
+ transcription is not reverse feeding. Neither removed arrow demonstrates mediation. Structured 2020 Table 1 cells
+ distinguish DMSP/GlcNAc expression from proline/guanosine net drawdown; neither is a traced compound-specific
+ flux. Separate pair cultures are not a mixed consortium.'
+- 'B12 check: the 2017 growth rescue must not be erased by later L1 assay results or substituted for the chitin
+ node. Missing topology remains #1883 and needs_research. One authorized real invocation stopped at authentication
+ before submission. No report, task or spend is claimed; previously denied scopes were not retried.'
+- 'Trichodesmium: association is not commensal neutrality and genomic complementarity is not mutualistic fitness.
+ The 2017 mechanism figure is a model; siderophore and DMSP measurements do not prove full interpartner fluxes.
+ Proposed B12 provision runs host-to-epibiont, with facultative use in the 2017 genome. Preserve #297 ROS compound/process
+ distinctions and proposed iron chemistry without treating Fe(II) as generic iron. Remove the two unsupported explanatory
+ arrows.'
+- 'Field identity: the 2018 host was not demonstrated to be IMS101, and Alteromonas genus transcripts are not automatically
+ A. macleodii. The field node credits only the canonical microbiome guild. Laboratory association retains the canonical
+ pair. Non-graph identity and medium issues remain #1886 and #765; restricted publication bodies are not restored.'
+- 'Source scope: three fresh extracted main bodies, three complete primary PDF text extractions and selected figure
+ images were reviewed. Diel main text came from existing curator text; chemotaxis is abstract-bounded and MEPS
+ remains caption-only after HTTP 401. Of 24 quotations, 23 match fresh primary text and one matches the existing
+ caption. No new publication bodies or caches. Supplements, raw data and other figure pixels were not reviewed.'
+- Three guarded records and append-only histories preserve 457 other records, 923 caches, all non-graph blocks and
+ prior history/decision artifacts. Two explicit participant-list users are added to the exact test expectation.
+ Census remains 412 community-level, 136 mixed, 276 community-only, 1563 taxa and 1273 solely credited. Connectivity
+ logic and share guards are unchanged.
+- Five real in-memory control/mutation/restored-control probes reject TEP feeding, proven attachment mediation,
+ reverse transcript feeding, genomic SUPPORT inflation and exact IMS101 field attribution. Actual mutations and
+ rejecting assertions are recorded. Canonical hashes are unchanged; probes are not counted as additional pytest
+ tests.
+- Ten focused tests and 1024 combined regressions pass. All three edited records pass schema, strict, terms, full-record
+ references, snippets and history checks. The 56 network warnings are unchanged, with zero structural defects.
+ Deterministic rendering and exact HTML descriptions cover 456 pages, 1366 nodes and 531 arrows, not UI screenshots.
+ Full-corpus snippets remain informational. Local reference passes are not Linux certification.
+- 'Repairs #1880-#1882 await protected-main merge; research #1883 and metadata #1884-#1886 remain open. Self-review
+ is not independent approval. Exact-head publication and postcommit docs-current are separate gates. Root CI blocker
+ #1836 is not bypassed and dependent branches are not deleted.'
+- 'Corpus: 364 reviewed, 42 pending and 54 needs_research across 460 records. The overall goal remains incomplete.'
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: TEP restored as directed feeding
+ test: test_tep_is_not_directed_feeding_or_a_universal_aggregation_driver
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 32
+ assertion: assert tep["scope"] == "COMMUNITY_LEVEL" and "interaction_type" not in tep
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/1/interaction_type
+ before: null
+ after: CROSS_FEEDING
+ - mutation: Attachment promoted to demonstrated aggregation mediation
+ test: test_attachment_perturbation_does_not_demonstrate_aggregation_mediation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 49
+ assertion: assert attachment["downstream"][0]["description"].startswith("HYPOTHESIZED:")
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/2/downstream/0/description
+ before: 'HYPOTHESIZED: chemotaxis-dependent attachment may enable the close association underlying the earlier
+ HP15 aggregation phenotype. The reviewed chemotaxis abstract demonstrates reduced attachment, not selective
+ mediation of the aggregation endpoint; aggregation effects cannot be assumed in every environmental treatment.'
+ after: Attachment demonstrably causes aggregation in every condition.
+ - mutation: Transcript response restored as reverse cross-feeding
+ test: test_ruegeria_recognition_and_chitin_response_are_not_exchange_or_mediation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 65
+ assertion: assert "interaction_type" not in recognition and "interaction_type" not in response
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/2/interaction_type
+ before: null
+ after: CROSS_FEEDING
+ - mutation: Candidate genomic helper mechanisms promoted to proven support
+ test: test_trichodesmium_helpers_remain_hypotheses_with_host_to_epibiont_b12
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 97
+ assertion: assert all(e["supports"] == "PARTIAL" for e in helper["evidence"])
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/1/evidence/0/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Exact laboratory strain added to the field-expression participants
+ test: test_field_expression_does_not_credit_the_exact_laboratory_strain
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 106
+ assertion: assert [p["preferred_term"] for p in diel["participating_taxa"]] == [
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/2/participating_taxa
+ before:
+ - preferred_term: Trichodesmium-associated heterotrophic microbiome
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+ after:
+ - preferred_term: Trichodesmium-associated heterotrophic microbiome
+ term:
+ id: NCBITaxon:2
+ label: Bacteria
+ - preferred_term: Trichodesmium erythraeum IMS101
+ term:
+ id: NCBITaxon:203124
+ label: Trichodesmium erythraeum IMS101
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml: 8b79efb0b04a43548b3c73ac280ac987b83c4e97f2531b55da5c940f29485eae
+ kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml: f1e51614a8c4a7856a2669afe12574d1c982f12dcebf9f53f49c65d470f747d6
+ kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml: 0d2e03b468366edc434574c18f28c80e5f3ce5ebf4a69d31169fa647f6edcdd0
+ tests/test_causal_review_batch113.py: 84a0d66a0b217512ecca6a4988cd20009a0924f90a68eadce3da56c0aa7868d0
+ probe_script_sha256: 975019454558d57378233c5069eff106cfd4ce15499def3fe2aec65a7d5a0cec
+ scope: In-memory control/mutation/restored-control; no canonical writes and not additional pytest tests.
+ artifact: /private/tmp/communitymech-batch113/adversarial-regression-proof.json
+ sha256: 8a500d7db1c016637ddfd9bf517d6d60537735f8dc5c648c5d1a9222f752b8d8
+verification:
+ combined_regressions: 1024 passed in 306.57s (0:05:06)
+ new_regression_tests: 10
+ total_recorded_gate_outputs: 34
+ primary_graph_snippet_proof:
+ graph_quotations: 21
+ discussion_quotations: 3
+ fresh_primary_literal_matches: 23
+ existing_caption_only: 1
+ all_cached_literal_matches: 24
+ retained_nodes: 10
+ removed_nodes: 0
+ renamed_nodes: 6
+ retained_arrows: 2
+ removed_arrows: 4
+ new_nodes_or_directions: 0
+ references: Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment.
+ Total checks in the reference CLI counts issues, not examined snippets.
+ snippet_counts_by_record:
+ kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml:
+ MATCH: 24
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml:
+ MATCH: 24
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml:
+ MATCH: 19
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9017
+ categories:
+ MATCH: 8872
+ RENDERING: 28
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 76
+ caveat: Informational audit exit0 is not clean-corpus or entailment certification.
+ network:
+ existing_findings_preserved: 56
+ added_findings: {}
+ removed_findings: {}
+ structural_defects: 0
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml: 37a32697693f1a6298e472ddb74f6b9688b9d08b2902f4830c975c9f4f9b0f39
+ tests/test_causal_review_batch113.py: 84a0d66a0b217512ecca6a4988cd20009a0924f90a68eadce3da56c0aa7868d0
+ tests/test_participating_taxa.py: a7daf71d4b29c7849293647ab82e6dbf828a42c88b26130eb0e39e9ffd3ee6ca
+ reports/causal_graph_review/cache-provenance-20261008-batch113.json: 6287cbceda5407c04d63c12b9739b6041e3824a6de5013ddde13f614796bfc09
+ kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml: 8b79efb0b04a43548b3c73ac280ac987b83c4e97f2531b55da5c940f29485eae
+ kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml: f1e51614a8c4a7856a2669afe12574d1c982f12dcebf9f53f49c65d470f747d6
+ kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml: 0d2e03b468366edc434574c18f28c80e5f3ce5ebf4a69d31169fa647f6edcdd0
+ history_sha256:
+ history/records/Thalassiosira_Marinobacter_Marine_Snow_Coculture/2026-10-08T083138Z-codex-825172.yaml: 96367c9ae4fb2b219fbfac915bea44ac4d74db35d15cb9ae5b0917ff72d5ccad
+ history/records/Thalassiosira_Ruegeria_Phycosphere_Coculture/2026-10-08T083139Z-codex-dd87e7.yaml: b2db268516d72edbf9bbba6d801a1ff52239842f2c153a824dbcbfdfd00ec9f5
+ history/records/Trichodesmium_Alteromonas_Marine_Consortium/2026-10-08T083139Z-codex-a37037.yaml: ef36a5df8e56897ef7b0d50f5dac1d6c9384ad7ecec866f7ccf662bdb7934d51
+ unchanged_records: 457
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 858
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - target: CommunityMech:000162
+ artifact: /private/tmp/communitymech-batch113/edison-dry-run/Thalassiosira_Ruegeria_Phycosphere_Coculture-edison-literature-causal-meta.yaml
+ sha256: 4e371d688d522e5288bf5f0ed47abf41785e62199d53466e58d450627fdd90b1
+ query_sha256: 1b2797a8920505adf873e50a02f8827e5aa23ac5e5aa8387603ef7310bb42e67
+ authorized_invocations: 1
+ invocation_exit_code: 1
+ blocked_stage: load_api_key before client creation
+ task_id: null
+ blocker: Configured Edison key unavailable; no other credential locations inspected.
+ issue: 1883
+ repair_scope: Existing-node evidence/scope corrections and removal of four unsupported arrows; no added nodes
+ or directions.
+ post_commit_docs_current: Separate publication gate, not preasserted.
+participant_census:
+ current:
+ records: 460
+ with_community_level: 412
+ mixed: 136
+ community_level_only: 276
+ taxa: 1563
+ credited_solely_by_the_rule: 1273
+ delta_from_batch112:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ explanation: Two new explicit participant-list users; overall connectivity census unchanged. No connectivity rule
+ or share-guard changes.
+corpus:
+ records: 460
+ nodes: 1380
+ edges: 539
+ review_status_counts:
+ needs_research: 54
+ pending: 42
+ reviewed: 364
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary established Python3.13 lint environment; project dependencies unchanged.
+limitations:
+- Fresh pre-source baseline across both roots:460 records,923 caches,56 warnings,zero structural defects. All10
+ existing nodes/6directions reviewed;10nodes/2directions retained,4unsupported arrows removed. No new topology.
+- Three whole canonical records and existing snippet evidence read. Fresh primary metadata/abstracts and Crossref
+ identities for nine sources; MEPS has no retrieved abstract. Full fresh extracted main bodies:2014future-ocean1-167,HP15genome1-89,2020partitioning1-163.
+ Table1 of the 2020 paper also parsed as structured XML to confirm the Ruegeria column.
+- Full PDF extracted text read:2011aggregation pages1-10 from existing user PDF,2017recognition pages1-14 from WHOI,2017Trichodesmium
+ pages1-12 from author research site. Visual review:aggregation pages5/6/8(Figs1/2/3/5),recognition pages2/3/8(Figs1/2/4),Trichodesmium
+ pages7/9(text and Fig3). Other figure pixels, separate supplements and raw data not reviewed.
+- 2018diel existing curator TXT read lines1-810, including abstract,complete main body and beginning references;
+ reference-list tail not read. Fresh primary abstract independently retrieved. FullTextXML attempts failed for
+ aggregation,chemotaxis,Trichodesmium2017 and diel2018. Chemotaxis graph is abstract-bounded; MEPS public PDF returned401
+ twice, no bypass or full-paper claim. Existing caption retained PARTIAL and not treated as proof of all TEP chemistry.
+- No PDFs or publication bodies added to the repository;923 existing caches untouched. Graph/discussion quote matches
+ are independently checked against fresh primary texts except one existing MEPS caption-only quote. Cache matching
+ is not entailment or Linux reference-loader certification. Some long cache bodies were not read in full; the independent
+ primary bodies and existing target snippets were reviewed.
+- HP15 preserves positive2011and null2014assay effects; no universal attachment/TEP/aggregation/sinking chain, no
+ measured ocean sequestration. Inactivation has possible surface/exudate confounding. Mutant attachment and abiotic
+ biofilm phenotypes are not selective aggregation mediation.
+- Ruegeria preserves supported organic-carbon feeding and transcript responses. DMSP/GlcNAc expression and proline/guanosine
+ net drawdown have distinct evidence grades; net depletion is not a traced transfer flux.2017B12-limited growth
+ rescue is distinct from laterL1assay. Missing reciprocal B12topology remains needs_research in1883.
+- Trichodesmium association,genomic complementation and field coexpression are distinct evidence levels. Preserve
+ potential helper mechanisms andROScompound/process#297; vitamin provision is proposed host-to-epibiont and2017facultativeuse
+ must not become obligatory dependence. Field node does not assert exactIMS101orA.macleodii membership; only canonical
+ microbiome guild is credited there. Non-graph identity issues remain1886.
+- Issue-title/body dedup covered all1124existing issues initially and a fresh pre-creation sweep; nine matching
+ issue bodies read. Ignored/hidden-inclusive local path index covers128files,excluding.git/docs/site/references_cache/.env,not
+ all historical file bodies. Historical PR comments were not exhaustively searched.
+- Edison one-community dry run completed. Scope-specific credit-spending invocation authorized by execution approval,
+ then stopped in load_api_key before client creation:configured key unavailable. No task submitted,report received
+ or provider credit spent. User asked to configure key securely. Previous denied and unanswered scopes not retried.
+ No absence claim about credentials elsewhere.
+- Non-graph blocks,457otherrecords,923caches and prior histories preserved. No runtime/schema/validator changes.
+ Required validation and measured census are recorded separately; self-review is not independent approval. Issues
+ remain open until protected-main merge or separately verified followup. RootCI blocker1836 forbids invented CI
+ or premature merge/branch cleanup.
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch113.json b/reports/causal_graph_review/cache-provenance-20261008-batch113.json
new file mode 100644
index 000000000..204dca7ce
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch113.json
@@ -0,0 +1,784 @@
+{
+ "changes": [],
+ "unchanged_cache_files": 923,
+ "primary_artifacts": {
+ "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/Mechs/CommunityMech/references_cache/files/PMID_20827289.pdf": "c40b3aae947563128b03f872f642c6536a02e7ee45c4b683eb4378c38dc566de",
+ "/private/tmp/communitymech-batch113/aggregation-abstract.txt": "6602a281735718e8d20d977d6b57a3a44c1b62945737647b86ba339130610273",
+ "/private/tmp/communitymech-batch113/aggregation-crossref.json": "7d98024e3648863fbd53a23c894c640f8b49da36a5cd7e26cb0c742808ce9366",
+ "/private/tmp/communitymech-batch113/aggregation-metadata.json": "042e636f0aa5a0adaee6122d75475f8699d5c77d2bccd0eadbd5e54f41bb418f",
+ "/private/tmp/communitymech-batch113/baseline.json": "e4e0d15e305843d5a7dc342cd390e15fed00e3d022b87656cd9c17c074e5dd9b",
+ "/private/tmp/communitymech-batch113/chemotaxis-abstract.txt": "52802fe41fbc850bf7e3d66dcbd8d25b1b9851c4056cb710a0d0138ddf0baca6",
+ "/private/tmp/communitymech-batch113/chemotaxis-crossref.json": "b8837a95cc8c934ec3f30a92481715d1bf1ae54530f11e91899aa4f536bb5dce",
+ "/private/tmp/communitymech-batch113/chemotaxis-metadata.json": "edd759fb7ae40d70e9250490c0bcd8777e12c0fdb52c9f174968af8b1ad2fa1b",
+ "/private/tmp/communitymech-batch113/chitin_fibres-crossref.json": "b4e2a85dc4026196d90842079c53fd97c4412c6d688d0798fc83b5a4324c97f9",
+ "/private/tmp/communitymech-batch113/chitin_fibres-metadata.json": "46c175c7c1bedf3d5063f4085a81414bf839cc88a7837d5f1e2e3195797962df",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-abstract.txt": "d3f04faaac74cdabf7e42e93a97804f4efae39c8ae31cc5f5031c046399759f5",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-crossref.json": "8fbe1add7e0d17867c975e94ab91e6a35c3dd1e83924c0adcf7eac616ed42e50",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-metadata.json": "ff0c87dcffb15d9a6e073330db0b59ef3e0b7590987b7c97a8ad8765d75e2b81",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-primary.txt": "f06ba6d9c770005c9271e24bd5f89c87eedd34672b874ea147116e43275d125b",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-primary.xml": "1aa91708805c535b3b9363e3510400d97fb1b40c78f93864a93a6f71d47ab502",
+ "/private/tmp/communitymech-batch113/diatom_recognition-abstract.txt": "03ec4e345f442b5d3af2d277174d529850174cc13ebf7f6af18ecabe9ab4d36d",
+ "/private/tmp/communitymech-batch113/diatom_recognition-crossref.json": "e59d76b0c2834c32d634bbe696498138f0b6b8061ebd36fddd1084adc91262e5",
+ "/private/tmp/communitymech-batch113/diatom_recognition-metadata.json": "b5b2825c12c9b91976b88c021b20952abf36464383303350484c43db92cfc79f",
+ "/private/tmp/communitymech-batch113/edison-dry-run/Thalassiosira_Ruegeria_Phycosphere_Coculture-edison-literature-causal-meta.yaml": "4e371d688d522e5288bf5f0ed47abf41785e62199d53466e58d450627fdd90b1",
+ "/private/tmp/communitymech-batch113/future_ocean-abstract.txt": "e9c5914658fcdc16f5b7fa8f590bfabb8c823db78c34d6d4f9222cc308ebd3c2",
+ "/private/tmp/communitymech-batch113/future_ocean-crossref.json": "ca69baa7ea820aad173c3d7367e99167e3167ea10ab09df079ed5610986eb2ae",
+ "/private/tmp/communitymech-batch113/future_ocean-metadata.json": "fdc42361e42c671d2693c8390d07ec17493fbc312eba91175bafba286ec40958",
+ "/private/tmp/communitymech-batch113/future_ocean-primary.txt": "643dcf6d94231c8e5ecb3657a5927876e74f6671e1ab08b79a97f65d36609658",
+ "/private/tmp/communitymech-batch113/future_ocean-primary.xml": "c7a2bd9e1d67cdcce76f95fc965b503964adbfd396c1322b7de99c9ce2db8ee0",
+ "/private/tmp/communitymech-batch113/hp15_genome-abstract.txt": "56b86a60698dc26e66213325e02057af921d875ae053bf2174d5d5da7fe695ae",
+ "/private/tmp/communitymech-batch113/hp15_genome-crossref.json": "49c7c5fa7d8757f1895f0fe25258191e5c0abdd6666636a0eee02e68528638e0",
+ "/private/tmp/communitymech-batch113/hp15_genome-metadata.json": "ffde0cc61de9fb5c78f24c2114510140c1c7afc6769d4b4132309b3fdab4ba53",
+ "/private/tmp/communitymech-batch113/hp15_genome-primary.txt": "927d5b049d31e29a3fe1a743cd900d813c1b0d8552ea792591d0e25ba8604cc8",
+ "/private/tmp/communitymech-batch113/hp15_genome-primary.xml": "0d6d31ae955dc9d1e27bcb5e49006689781a2b431a8fa53d87e0ed618b5f1e44",
+ "/private/tmp/communitymech-batch113/issue-dedup-current.json": "0052884b3bd38111520cbcd972261bce41d6ea21a2d814fd8a12e639a60e3613",
+ "/private/tmp/communitymech-batch113/local-matches.txt": "b002a9b7318d558c6fbba824a6b08e7521cc6b447fdb55ee2dc8e4a1bc125423",
+ "/private/tmp/communitymech-batch113/pdf-manifest.json": "ae11c81da4dec2e934c528b756c2a17ddffb11de6b13ae1ea2d71c5658780cbd",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-01.txt": "3ca0dd5312a023f6faa23e7fd34fbb8760b6b4e92b59f4744c478aa7584ff8ff",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-02.txt": "17502c1554503852058f015da583d68779bb51eb0a7e94c886774222a459401c",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-03.txt": "333425fd1c5fddaa54ee1120b44cca33100f0402d40c3759a800e75961a23a20",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-04.txt": "1592eaa05916cf3cbbd8b8e6d4f1df2d0361060d0b2a1c0f4042d7301b87cf2c",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-05.png": "db0766cda461e14083662eb40a1319d004be9689dd344d9bd005ea8c5e91af87",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-05.txt": "4e68b8ba881ca3cfb3130b477480a0b250b9d0333a8832c3131c627d6314978e",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-06.png": "8be896d575bb77ef4615f9fc3c85ec0859803617fc83e5f1736e04c3081e0115",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-06.txt": "95f842cab62873a04aa9fb666afa751da11ee1c3ac1cfb48306d41ffd98c1b01",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-07.txt": "2f06474d0c9f57ac021b64cb387c98039b501cca2854f3beeb13067b383b706e",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-08.png": "73b0a74b662f43f55efd26c78da9f0866dc3de53da4a030348c8eaf22b00fc50",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-08.txt": "23fd88022c3dae270f937ad15e538b5bb56113f7b1cd375e4aedd79d537c8a1f",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-09.txt": "dab70e059d5078aec9e2298148555596516cbb8e5be0c292ef672d46b5f4fdab",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-10.txt": "b3d0dcd53c62215c225a10113863af68364f29a767e7b421c3ae835ed0cf643b",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-01.txt": "0c322412036dce7d93dd6dae1417e85b2b57a0f9b7fb98d42c9e3564b7dd0254",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-02.png": "4290234ee4fda993cc7973a862c55d4ad9b314ed08163230172e9914d68f1eca",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-02.txt": "736f8995b4e5468e6576acb30251e611bdcd8dcafa136f603f1374bdbaa986a9",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-03.png": "537e9af50077e8009213d2742ca5a9d9f989e74f5eca996deeddb2016f56fb12",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-03.txt": "13961998655e22b08b248dd72c2151a09d04379928eb0e3b14158effbd0b04fe",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-04.txt": "2607cc78a086788a0dab7647197749939fd0c021d52284f1a776dbbfb2e33044",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-05.txt": "30dc900193c467c48cd65cb9e5ac5ed84c9789fb1cd9f724aceae35af70f5ec5",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-06.txt": "99b89945ec9575f42377832689119926ae8bef63c5273a99cb2aac67cbd564e3",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-07.txt": "71fe8010e6b338fffed8a7d2488b76d57eb97762ac8b597489a1b91469c595b2",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-08.png": "4758d41e8d1230f3ddb8a49e9dbfd5da25693b9dd33dadfc20bb6e634812d543",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-08.txt": "385df38e55fdcd0419d68e38a575d7df3fa64bcedd5b1b6fb780eb35769ff8a7",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-09.txt": "7f66b550ad1699c3986f83c4e69a5fa35990918cbc79e7b01df9ee7988cd42c3",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-10.txt": "221790525e2cb7f41d9dfea2a312215ba7a4e95d3bf947e2540cbfb1b4c8fe2f",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-11.txt": "ddae72d484a907acd045f6ba35270b3376faaa3b5b6bbfcc7c98cc07d808ee77",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-12.txt": "b15f9c38c4aa6ae3e9c87c0a2b02bf5ea3e6f369cfc5b41f4417f3dcd1c7717e",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-13.txt": "a3f0e4bf51455bc042687d10069b3b26530a95f5c48b3c042cd927d8a6b19f62",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-14.txt": "aeb41bc3ed63d5079300c1eac128e550afe878c95d70a516e52f594aabe5809f",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition.pdf": "e37b48578e4a79183fb623596dc16fa3b9f3a4b476a537f4a7004f51cf0eedcc",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-01.txt": "ec50ca0d007c60e2150f15bd06150d6110e2dacc6aa6a739d80d8e10186beb40",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-02.txt": "26fe7f54a1936c2e06378014ed292b7e949eaa23e2eb03ae691ddfcdd5ffe10e",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-03.txt": "2986b3409b3dab656003a962431d6df2f97815edf9854bf461c1032b70ad83fe",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-04.txt": "1ceb990e8eb0a10830fc2b964019caa452531a0cb8e2601593be4a2dea0f807a",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-05.txt": "efaa89ffc5ae9f2f893f71ab67695a192cdde1520a32fcebfa12d21994ec3f5b",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-06.txt": "a1b9f112d4960b7e117b73df6a03fbf6ddb240cbe6782e3e51b369b6b04dd47e",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-07.png": "07d75b761276a419f616d8f38309dba1b2bb44d51c240a3f260b7f33a77f5160",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-07.txt": "e2caca889b886984f65492720e90c4c7144fb1a041367906c5a50c78fe384ac8",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-08.txt": "bb835fd938aa03cb04ff3765b650bee0c01fc7f14579c044a00045b8da086b69",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-09.png": "e99752f6f2bb5cc29aa9af074d1f189629f7c7a46caa71aefe21249c40cbb08f",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-09.txt": "51b694b8b6e620ce39ead86279b6dd97660956b1a937b50e0a6cbc8c750d5d1b",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-10.txt": "a18720a2e20dfe3fd30265523de3524a489654a42ff9e0fb0894910e6657f204",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-11.txt": "ce882142f780b31cc942954c34047a4e1259c92954c474d4f41e3f9b4e7fad51",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-12.txt": "c04322725772e971985af10ae271489357e58a19b95e3ffc6e2722cd28191137",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes.pdf": "3f6744880efd09ebfabe7c73682a5ce426575808c0b5c37b9f4dffc839f5da2c",
+ "/private/tmp/communitymech-batch113/primary-manifest.json": "54a487b8908feffa1feeed66fe7a60d59ee199d4755315503570e30299764f0b",
+ "/private/tmp/communitymech-batch113/rendered-figures.json": "7f9d1adf428f3c7ecc9b70cb3596ba4fbe80328036334d1e2adab66554921344",
+ "/private/tmp/communitymech-batch113/tricho_diel-abstract.txt": "991a5c5ccd82ebc4b1cb28a30182531c400708afd1f6c016def1f26764fed644",
+ "/private/tmp/communitymech-batch113/tricho_diel-crossref.json": "47a61b55e624a103901753ca83e8afd6367cbdabd0237ec852d15da8571ee4c1",
+ "/private/tmp/communitymech-batch113/tricho_diel-metadata.json": "cf30eb8d10292d1380ab625e26b77f1a7df7e4bcf3f49376a17b2aa226793136",
+ "/private/tmp/communitymech-batch113/tricho_genomes-abstract.txt": "17cbacbd2658c364b7e40e4a6e49d1107791b1729748f9fb21e147e79132f60a",
+ "/private/tmp/communitymech-batch113/tricho_genomes-crossref.json": "3a57b6801019907afe7a4dce0c16f384b6b76817b82ca70113854da655acc840",
+ "/private/tmp/communitymech-batch113/tricho_genomes-metadata.json": "20b87c1043e018e6f15da964a2419d6330ba35c11c1441bf1db44f8f9d153d7c",
+ "references_cache/PMID_20827289.md": "7886cc9bd5fb04794399faec79365aadb7045538a37bb29cf9cd72f1cf96f19e",
+ "references_cache/PMID_22820333.md": "b5e59d9bd1f234d9e34c96b3ec72f7af9a197633cd7f6abc0d6c5fcb4bad2451",
+ "references_cache/PMID_25375640.md": "b0acc6fc72bf7d22e01ccd22c51600e0ec337f30e91898732cee0875d42d8e16",
+ "references_cache/PMID_28440800.txt": "42d9afaeca8e20c30ceccab47e452631af33fd4c10d8d2e642e74e907598e7fa",
+ "references_cache/PMID_28631440.txt": "a64edc7b5bcf844fd640ad24b402260a7ed7a2f6389325dabe815123fce5f7b8",
+ "references_cache/PMID_29382945.txt": "822a4f5f9029897f4316affee3951d724ea2612862499c05ef30a7c832e27af6",
+ "references_cache/PMID_33097854.md": "a8e47a63b081b28ca3075345c1700e0abea0b46a18b64b4a4337df7781440d89",
+ "references_cache/doi_10.3354_meps09894.md": "b7de73cd4e0d3af39fabf09d998e038348d20305cb6e539f1b183e2d84d0df31",
+ "references_cache/doi_10.4056_sigs.922139.md": "139c13b694456bd96672197ec8d8f0de1b40fbfd561511c2ba850aa2d6a1c2b7"
+ },
+ "source_access": {
+ "retrieval_manifest": {
+ "aggregation": {
+ "pmid": "20827289",
+ "doi": "10.1038/ismej.2010.145",
+ "pmcid": "PMC3105730",
+ "title": "Diatom-associated bacteria are required for aggregation of Thalassiosira weissflogii.",
+ "metadata": "/private/tmp/communitymech-batch113/aggregation-metadata.json",
+ "metadata_sha256": "042e636f0aa5a0adaee6122d75475f8699d5c77d2bccd0eadbd5e54f41bb418f",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A20827289+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3105730/fullTextXML",
+ "status": "retrieval_failed",
+ "error": "HTTP Error 500: "
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch113/aggregation-abstract.txt",
+ "abstract_sha256": "6602a281735718e8d20d977d6b57a3a44c1b62945737647b86ba339130610273",
+ "crossref": "/private/tmp/communitymech-batch113/aggregation-crossref.json",
+ "crossref_sha256": "7d98024e3648863fbd53a23c894c640f8b49da36a5cd7e26cb0c742808ce9366",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2010,
+ 9,
+ 9
+ ]
+ ],
+ "date-time": "2010-09-09T00:00:00Z",
+ "timestamp": 1283990400000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://academic.oup.com/pages/standard-publication-reuse-rights"
+ }
+ ]
+ },
+ "chemotaxis": {
+ "pmid": "22820333",
+ "doi": "10.1128/aem.01790-12",
+ "pmcid": "PMC3457506",
+ "title": "Chemotaxis of Marinobacter adhaerens and its impact on attachment to the diatom Thalassiosira weissflogii.",
+ "metadata": "/private/tmp/communitymech-batch113/chemotaxis-metadata.json",
+ "metadata_sha256": "edd759fb7ae40d70e9250490c0bcd8777e12c0fdb52c9f174968af8b1ad2fa1b",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A22820333+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3457506/fullTextXML",
+ "status": "retrieval_failed",
+ "error": "HTTP Error 500: "
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch113/chemotaxis-abstract.txt",
+ "abstract_sha256": "52802fe41fbc850bf7e3d66dcbd8d25b1b9851c4056cb710a0d0138ddf0baca6",
+ "crossref": "/private/tmp/communitymech-batch113/chemotaxis-crossref.json",
+ "crossref_sha256": "b8837a95cc8c934ec3f30a92481715d1bf1ae54530f11e91899aa4f536bb5dce",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2012,
+ 10,
+ 1
+ ]
+ ],
+ "date-time": "2012-10-01T00:00:00Z",
+ "timestamp": 1349049600000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://journals.asm.org/non-commercial-tdm-license"
+ }
+ ]
+ },
+ "future_ocean": {
+ "pmid": "25375640",
+ "doi": "10.1371/journal.pone.0112379",
+ "pmcid": "PMC4223051",
+ "title": "Aggregation and sedimentation of Thalassiosira weissflogii (diatom) in a warmer and more acidified future ocean.",
+ "metadata": "/private/tmp/communitymech-batch113/future_ocean-metadata.json",
+ "metadata_sha256": "fdc42361e42c671d2693c8390d07ec17493fbc312eba91175bafba286ec40958",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A25375640+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4223051/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch113/future_ocean-abstract.txt",
+ "abstract_sha256": "e9c5914658fcdc16f5b7fa8f590bfabb8c823db78c34d6d4f9222cc308ebd3c2",
+ "xml": "/private/tmp/communitymech-batch113/future_ocean-primary.xml",
+ "xml_sha256": "c7a2bd9e1d67cdcce76f95fc965b503964adbfd396c1322b7de99c9ce2db8ee0",
+ "primary_text": "/private/tmp/communitymech-batch113/future_ocean-primary.txt",
+ "primary_text_sha256": "643dcf6d94231c8e5ecb3657a5927876e74f6671e1ab08b79a97f65d36609658",
+ "license": [
+ "https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited."
+ ],
+ "crossref": "/private/tmp/communitymech-batch113/future_ocean-crossref.json",
+ "crossref_sha256": "ca69baa7ea820aad173c3d7367e99167e3167ea10ab09df079ed5610986eb2ae",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2014,
+ 11,
+ 6
+ ]
+ ],
+ "date-time": "2014-11-06T00:00:00Z",
+ "timestamp": 1415232000000
+ },
+ "content-version": "unspecified",
+ "delay-in-days": 0,
+ "URL": "http://creativecommons.org/licenses/by/4.0/"
+ }
+ ]
+ },
+ "hp15_genome": {
+ "pmid": "21304739",
+ "doi": "10.4056/sigs.922139",
+ "pmcid": "PMC3035377",
+ "title": "Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism.",
+ "metadata": "/private/tmp/communitymech-batch113/hp15_genome-metadata.json",
+ "metadata_sha256": "ffde0cc61de9fb5c78f24c2114510140c1c7afc6769d4b4132309b3fdab4ba53",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.4056%2Fsigs.922139%22+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3035377/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch113/hp15_genome-abstract.txt",
+ "abstract_sha256": "56b86a60698dc26e66213325e02057af921d875ae053bf2174d5d5da7fe695ae",
+ "xml": "/private/tmp/communitymech-batch113/hp15_genome-primary.xml",
+ "xml_sha256": "0d6d31ae955dc9d1e27bcb5e49006689781a2b431a8fa53d87e0ed618b5f1e44",
+ "primary_text": "/private/tmp/communitymech-batch113/hp15_genome-primary.txt",
+ "primary_text_sha256": "927d5b049d31e29a3fe1a743cd900d813c1b0d8552ea792591d0e25ba8604cc8",
+ "license": [
+ "https://creativecommons.org/licenses/by/2.5/This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited."
+ ],
+ "crossref": "/private/tmp/communitymech-batch113/hp15_genome-crossref.json",
+ "crossref_sha256": "49c7c5fa7d8757f1895f0fe25258191e5c0abdd6666636a0eee02e68528638e0",
+ "crossref_license": []
+ },
+ "chitin_fibres": {
+ "pmid": null,
+ "doi": "10.3354/meps09894",
+ "pmcid": null,
+ "title": [
+ "Effects of Marinobacter adhaerens HP15 on polymer exudation by Thalassiosira weissflogii at different N:P ratios"
+ ],
+ "metadata": "/private/tmp/communitymech-batch113/chitin_fibres-metadata.json",
+ "metadata_sha256": "46c175c7c1bedf3d5063f4085a81414bf839cc88a7837d5f1e2e3195797962df",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.3354%2Fmeps09894%22+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 0
+ }
+ ],
+ "crossref": "/private/tmp/communitymech-batch113/chitin_fibres-crossref.json",
+ "crossref_sha256": "b4e2a85dc4026196d90842079c53fd97c4412c6d688d0798fc83b5a4324c97f9",
+ "crossref_license": []
+ },
+ "diatom_recognition": {
+ "pmid": "28631440",
+ "doi": "10.1111/1462-2920.13834",
+ "pmcid": null,
+ "title": "Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system.",
+ "metadata": "/private/tmp/communitymech-batch113/diatom_recognition-metadata.json",
+ "metadata_sha256": "b5b2825c12c9b91976b88c021b20952abf36464383303350484c43db92cfc79f",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A28631440+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch113/diatom_recognition-abstract.txt",
+ "abstract_sha256": "03ec4e345f442b5d3af2d277174d529850174cc13ebf7f6af18ecabe9ab4d36d",
+ "crossref": "/private/tmp/communitymech-batch113/diatom_recognition-crossref.json",
+ "crossref_sha256": "e59d76b0c2834c32d634bbe696498138f0b6b8061ebd36fddd1084adc91262e5",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2018,
+ 6,
+ 19
+ ]
+ ],
+ "date-time": "2018-06-19T00:00:00Z",
+ "timestamp": 1529366400000
+ },
+ "content-version": "am",
+ "delay-in-days": 333,
+ "URL": "http://onlinelibrary.wiley.com/termsAndConditions#am"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2017,
+ 7,
+ 21
+ ]
+ ],
+ "date-time": "2017-07-21T00:00:00Z",
+ "timestamp": 1500595200000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "http://onlinelibrary.wiley.com/termsAndConditions#vor"
+ }
+ ]
+ },
+ "diatom_partitioning": {
+ "pmid": "33097854",
+ "doi": "10.1038/s41396-020-00811-y",
+ "pmcid": "PMC8027193",
+ "title": "Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy.",
+ "metadata": "/private/tmp/communitymech-batch113/diatom_partitioning-metadata.json",
+ "metadata_sha256": "ff0c87dcffb15d9a6e073330db0b59ef3e0b7590987b7c97a8ad8765d75e2b81",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A33097854+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8027193/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch113/diatom_partitioning-abstract.txt",
+ "abstract_sha256": "d3f04faaac74cdabf7e42e93a97804f4efae39c8ae31cc5f5031c046399759f5",
+ "xml": "/private/tmp/communitymech-batch113/diatom_partitioning-primary.xml",
+ "xml_sha256": "1aa91708805c535b3b9363e3510400d97fb1b40c78f93864a93a6f71d47ab502",
+ "primary_text": "/private/tmp/communitymech-batch113/diatom_partitioning-primary.txt",
+ "primary_text_sha256": "f06ba6d9c770005c9271e24bd5f89c87eedd34672b874ea147116e43275d125b",
+ "license": [
+ "Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article\u2019s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article\u2019s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/."
+ ],
+ "crossref": "/private/tmp/communitymech-batch113/diatom_partitioning-crossref.json",
+ "crossref_sha256": "8fbe1add7e0d17867c975e94ab91e6a35c3dd1e83924c0adcf7eac616ed42e50",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2024,
+ 1,
+ 10
+ ]
+ ],
+ "date-time": "2024-01-10T00:00:00Z",
+ "timestamp": 1704844800000
+ },
+ "content-version": "vor",
+ "delay-in-days": 1174,
+ "URL": "https://creativecommons.org/licenses/by/4.0/"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2020,
+ 10,
+ 23
+ ]
+ ],
+ "date-time": "2020-10-23T00:00:00Z",
+ "timestamp": 1603411200000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2020,
+ 10,
+ 23
+ ]
+ ],
+ "date-time": "2020-10-23T00:00:00Z",
+ "timestamp": 1603411200000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0"
+ }
+ ]
+ },
+ "tricho_genomes": {
+ "pmid": "28440800",
+ "doi": "10.1038/ismej.2017.49",
+ "pmcid": "PMC5520037",
+ "title": "The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions.",
+ "metadata": "/private/tmp/communitymech-batch113/tricho_genomes-metadata.json",
+ "metadata_sha256": "20b87c1043e018e6f15da964a2419d6330ba35c11c1441bf1db44f8f9d153d7c",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A28440800+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5520037/fullTextXML",
+ "status": "retrieval_failed",
+ "error": "HTTP Error 500: "
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch113/tricho_genomes-abstract.txt",
+ "abstract_sha256": "17cbacbd2658c364b7e40e4a6e49d1107791b1729748f9fb21e147e79132f60a",
+ "crossref": "/private/tmp/communitymech-batch113/tricho_genomes-crossref.json",
+ "crossref_sha256": "3a57b6801019907afe7a4dce0c16f384b6b76817b82ca70113854da655acc840",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2017,
+ 4,
+ 25
+ ]
+ ],
+ "date-time": "2017-04-25T00:00:00Z",
+ "timestamp": 1493078400000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://academic.oup.com/pages/standard-publication-reuse-rights"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2017,
+ 4,
+ 25
+ ]
+ ],
+ "date-time": "2017-04-25T00:00:00Z",
+ "timestamp": 1493078400000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "http://www.springer.com/tdm"
+ }
+ ]
+ },
+ "tricho_diel": {
+ "pmid": "29382945",
+ "doi": "10.1038/s41396-017-0041-5",
+ "pmcid": "PMC5864210",
+ "title": "Coordinated gene expression between Trichodesmium and its microbiome over day-night cycles in the North Pacific Subtropical Gyre.",
+ "metadata": "/private/tmp/communitymech-batch113/tricho_diel-metadata.json",
+ "metadata_sha256": "cf30eb8d10292d1380ab625e26b77f1a7df7e4bcf3f49376a17b2aa226793136",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A29382945+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5864210/fullTextXML",
+ "status": "retrieval_failed",
+ "error": "HTTP Error 500: "
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch113/tricho_diel-abstract.txt",
+ "abstract_sha256": "991a5c5ccd82ebc4b1cb28a30182531c400708afd1f6c016def1f26764fed644",
+ "crossref": "/private/tmp/communitymech-batch113/tricho_diel-crossref.json",
+ "crossref_sha256": "47a61b55e624a103901753ca83e8afd6367cbdabd0237ec852d15da8571ee4c1",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2018,
+ 1,
+ 30
+ ]
+ ],
+ "date-time": "2018-01-30T00:00:00Z",
+ "timestamp": 1517270400000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://academic.oup.com/pages/standard-publication-reuse-rights"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2018,
+ 1,
+ 30
+ ]
+ ],
+ "date-time": "2018-01-30T00:00:00Z",
+ "timestamp": 1517270400000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "http://www.springer.com/tdm"
+ }
+ ]
+ }
+ },
+ "pdf_manifest": {
+ "aggregation": {
+ "doi": "10.1038/ismej.2010.145",
+ "pdf": "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/Mechs/CommunityMech/references_cache/files/PMID_20827289.pdf",
+ "pdf_sha256": "c40b3aae947563128b03f872f642c6536a02e7ee45c4b683eb4378c38dc566de",
+ "url": null,
+ "pages": [
+ {
+ "page": 1,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-01.txt",
+ "text_sha256": "3ca0dd5312a023f6faa23e7fd34fbb8760b6b4e92b59f4744c478aa7584ff8ff"
+ },
+ {
+ "page": 2,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-02.txt",
+ "text_sha256": "17502c1554503852058f015da583d68779bb51eb0a7e94c886774222a459401c"
+ },
+ {
+ "page": 3,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-03.txt",
+ "text_sha256": "333425fd1c5fddaa54ee1120b44cca33100f0402d40c3759a800e75961a23a20"
+ },
+ {
+ "page": 4,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-04.txt",
+ "text_sha256": "1592eaa05916cf3cbbd8b8e6d4f1df2d0361060d0b2a1c0f4042d7301b87cf2c"
+ },
+ {
+ "page": 5,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-05.txt",
+ "text_sha256": "4e68b8ba881ca3cfb3130b477480a0b250b9d0333a8832c3131c627d6314978e"
+ },
+ {
+ "page": 6,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-06.txt",
+ "text_sha256": "95f842cab62873a04aa9fb666afa751da11ee1c3ac1cfb48306d41ffd98c1b01"
+ },
+ {
+ "page": 7,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-07.txt",
+ "text_sha256": "2f06474d0c9f57ac021b64cb387c98039b501cca2854f3beeb13067b383b706e"
+ },
+ {
+ "page": 8,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-08.txt",
+ "text_sha256": "23fd88022c3dae270f937ad15e538b5bb56113f7b1cd375e4aedd79d537c8a1f"
+ },
+ {
+ "page": 9,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-09.txt",
+ "text_sha256": "dab70e059d5078aec9e2298148555596516cbb8e5be0c292ef672d46b5f4fdab"
+ },
+ {
+ "page": 10,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-10.txt",
+ "text_sha256": "b3d0dcd53c62215c225a10113863af68364f29a767e7b421c3ae835ed0cf643b"
+ }
+ ],
+ "page_count": 10,
+ "text_read": false,
+ "figures_reviewed": [],
+ "repository_copy": false,
+ "license_scope": "Read-only research; no publication body or PDF added to repository."
+ },
+ "diatom_recognition": {
+ "doi": "10.1111/1462-2920.13834",
+ "pdf": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition.pdf",
+ "pdf_sha256": "e37b48578e4a79183fb623596dc16fa3b9f3a4b476a537f4a7004f51cf0eedcc",
+ "url": "https://website.whoi.edu/gfd/wp-content/uploads/sites/14/2018/10/Durham_et_al_2017_262208.pdf",
+ "pages": [
+ {
+ "page": 1,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-01.txt",
+ "text_sha256": "0c322412036dce7d93dd6dae1417e85b2b57a0f9b7fb98d42c9e3564b7dd0254"
+ },
+ {
+ "page": 2,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-02.txt",
+ "text_sha256": "736f8995b4e5468e6576acb30251e611bdcd8dcafa136f603f1374bdbaa986a9"
+ },
+ {
+ "page": 3,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-03.txt",
+ "text_sha256": "13961998655e22b08b248dd72c2151a09d04379928eb0e3b14158effbd0b04fe"
+ },
+ {
+ "page": 4,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-04.txt",
+ "text_sha256": "2607cc78a086788a0dab7647197749939fd0c021d52284f1a776dbbfb2e33044"
+ },
+ {
+ "page": 5,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-05.txt",
+ "text_sha256": "30dc900193c467c48cd65cb9e5ac5ed84c9789fb1cd9f724aceae35af70f5ec5"
+ },
+ {
+ "page": 6,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-06.txt",
+ "text_sha256": "99b89945ec9575f42377832689119926ae8bef63c5273a99cb2aac67cbd564e3"
+ },
+ {
+ "page": 7,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-07.txt",
+ "text_sha256": "71fe8010e6b338fffed8a7d2488b76d57eb97762ac8b597489a1b91469c595b2"
+ },
+ {
+ "page": 8,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-08.txt",
+ "text_sha256": "385df38e55fdcd0419d68e38a575d7df3fa64bcedd5b1b6fb780eb35769ff8a7"
+ },
+ {
+ "page": 9,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-09.txt",
+ "text_sha256": "7f66b550ad1699c3986f83c4e69a5fa35990918cbc79e7b01df9ee7988cd42c3"
+ },
+ {
+ "page": 10,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-10.txt",
+ "text_sha256": "221790525e2cb7f41d9dfea2a312215ba7a4e95d3bf947e2540cbfb1b4c8fe2f"
+ },
+ {
+ "page": 11,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-11.txt",
+ "text_sha256": "ddae72d484a907acd045f6ba35270b3376faaa3b5b6bbfcc7c98cc07d808ee77"
+ },
+ {
+ "page": 12,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-12.txt",
+ "text_sha256": "b15f9c38c4aa6ae3e9c87c0a2b02bf5ea3e6f369cfc5b41f4417f3dcd1c7717e"
+ },
+ {
+ "page": 13,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-13.txt",
+ "text_sha256": "a3f0e4bf51455bc042687d10069b3b26530a95f5c48b3c042cd927d8a6b19f62"
+ },
+ {
+ "page": 14,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-14.txt",
+ "text_sha256": "aeb41bc3ed63d5079300c1eac128e550afe878c95d70a516e52f594aabe5809f"
+ }
+ ],
+ "page_count": 14,
+ "text_read": false,
+ "figures_reviewed": [],
+ "repository_copy": false,
+ "license_scope": "Read-only research; no publication body or PDF added to repository."
+ },
+ "chitin_fibres": {
+ "doi": "10.3354/meps09894",
+ "url": "https://www.int-res.com/articles/feature/m461p001.pdf",
+ "status": "retrieval_failed",
+ "error": "HTTP Error 401: Unauthorized",
+ "repository_copy": false
+ },
+ "tricho_genomes": {
+ "doi": "10.1038/ismej.2017.49",
+ "pdf": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes.pdf",
+ "pdf_sha256": "3f6744880efd09ebfabe7c73682a5ce426575808c0b5c37b9f4dffc839f5da2c",
+ "url": "https://astrobiomike.github.io/research/Lee_et_al_2017_ISME.pdf",
+ "pages": [
+ {
+ "page": 1,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-01.txt",
+ "text_sha256": "ec50ca0d007c60e2150f15bd06150d6110e2dacc6aa6a739d80d8e10186beb40"
+ },
+ {
+ "page": 2,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-02.txt",
+ "text_sha256": "26fe7f54a1936c2e06378014ed292b7e949eaa23e2eb03ae691ddfcdd5ffe10e"
+ },
+ {
+ "page": 3,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-03.txt",
+ "text_sha256": "2986b3409b3dab656003a962431d6df2f97815edf9854bf461c1032b70ad83fe"
+ },
+ {
+ "page": 4,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-04.txt",
+ "text_sha256": "1ceb990e8eb0a10830fc2b964019caa452531a0cb8e2601593be4a2dea0f807a"
+ },
+ {
+ "page": 5,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-05.txt",
+ "text_sha256": "efaa89ffc5ae9f2f893f71ab67695a192cdde1520a32fcebfa12d21994ec3f5b"
+ },
+ {
+ "page": 6,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-06.txt",
+ "text_sha256": "a1b9f112d4960b7e117b73df6a03fbf6ddb240cbe6782e3e51b369b6b04dd47e"
+ },
+ {
+ "page": 7,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-07.txt",
+ "text_sha256": "e2caca889b886984f65492720e90c4c7144fb1a041367906c5a50c78fe384ac8"
+ },
+ {
+ "page": 8,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-08.txt",
+ "text_sha256": "bb835fd938aa03cb04ff3765b650bee0c01fc7f14579c044a00045b8da086b69"
+ },
+ {
+ "page": 9,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-09.txt",
+ "text_sha256": "51b694b8b6e620ce39ead86279b6dd97660956b1a937b50e0a6cbc8c750d5d1b"
+ },
+ {
+ "page": 10,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-10.txt",
+ "text_sha256": "a18720a2e20dfe3fd30265523de3524a489654a42ff9e0fb0894910e6657f204"
+ },
+ {
+ "page": 11,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-11.txt",
+ "text_sha256": "ce882142f780b31cc942954c34047a4e1259c92954c474d4f41e3f9b4e7fad51"
+ },
+ {
+ "page": 12,
+ "text": "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-12.txt",
+ "text_sha256": "c04322725772e971985af10ae271489357e58a19b95e3ffc6e2722cd28191137"
+ }
+ ],
+ "page_count": 12,
+ "text_read": false,
+ "figures_reviewed": [],
+ "repository_copy": false,
+ "license_scope": "Read-only research; no publication body or PDF added to repository."
+ }
+ },
+ "actual_read_scope": [
+ "Three whole canonical records and existing snippet evidence read. Fresh primary metadata/abstracts and Crossref identities for nine sources; MEPS has no retrieved abstract. Full fresh extracted main bodies:2014future-ocean1-167,HP15genome1-89,2020partitioning1-163. Table1 of the 2020 paper also parsed as structured XML to confirm the Ruegeria column.",
+ "Full PDF extracted text read:2011aggregation pages1-10 from existing user PDF,2017recognition pages1-14 from WHOI,2017Trichodesmium pages1-12 from author research site. Visual review:aggregation pages5/6/8(Figs1/2/3/5),recognition pages2/3/8(Figs1/2/4),Trichodesmium pages7/9(text and Fig3). Other figure pixels, separate supplements and raw data not reviewed.",
+ "2018diel existing curator TXT read lines1-810, including abstract,complete main body and beginning references; reference-list tail not read. Fresh primary abstract independently retrieved. FullTextXML attempts failed for aggregation,chemotaxis,Trichodesmium2017 and diel2018. Chemotaxis graph is abstract-bounded; MEPS public PDF returned401 twice, no bypass or full-paper claim. Existing caption retained PARTIAL and not treated as proof of all TEP chemistry.",
+ "No PDFs or publication bodies added to the repository;923 existing caches untouched. Graph/discussion quote matches are independently checked against fresh primary texts except one existing MEPS caption-only quote. Cache matching is not entailment or Linux reference-loader certification. Some long cache bodies were not read in full; the independent primary bodies and existing target snippets were reviewed."
+ ]
+ },
+ "limitations": [
+ "Fresh pre-source baseline across both roots:460 records,923 caches,56 warnings,zero structural defects. All10 existing nodes/6directions reviewed;10nodes/2directions retained,4unsupported arrows removed. No new topology.",
+ "Three whole canonical records and existing snippet evidence read. Fresh primary metadata/abstracts and Crossref identities for nine sources; MEPS has no retrieved abstract. Full fresh extracted main bodies:2014future-ocean1-167,HP15genome1-89,2020partitioning1-163. Table1 of the 2020 paper also parsed as structured XML to confirm the Ruegeria column.",
+ "Full PDF extracted text read:2011aggregation pages1-10 from existing user PDF,2017recognition pages1-14 from WHOI,2017Trichodesmium pages1-12 from author research site. Visual review:aggregation pages5/6/8(Figs1/2/3/5),recognition pages2/3/8(Figs1/2/4),Trichodesmium pages7/9(text and Fig3). Other figure pixels, separate supplements and raw data not reviewed.",
+ "2018diel existing curator TXT read lines1-810, including abstract,complete main body and beginning references; reference-list tail not read. Fresh primary abstract independently retrieved. FullTextXML attempts failed for aggregation,chemotaxis,Trichodesmium2017 and diel2018. Chemotaxis graph is abstract-bounded; MEPS public PDF returned401 twice, no bypass or full-paper claim. Existing caption retained PARTIAL and not treated as proof of all TEP chemistry.",
+ "No PDFs or publication bodies added to the repository;923 existing caches untouched. Graph/discussion quote matches are independently checked against fresh primary texts except one existing MEPS caption-only quote. Cache matching is not entailment or Linux reference-loader certification. Some long cache bodies were not read in full; the independent primary bodies and existing target snippets were reviewed.",
+ "HP15 preserves positive2011and null2014assay effects; no universal attachment/TEP/aggregation/sinking chain, no measured ocean sequestration. Inactivation has possible surface/exudate confounding. Mutant attachment and abiotic biofilm phenotypes are not selective aggregation mediation.",
+ "Ruegeria preserves supported organic-carbon feeding and transcript responses. DMSP/GlcNAc expression and proline/guanosine net drawdown have distinct evidence grades; net depletion is not a traced transfer flux.2017B12-limited growth rescue is distinct from laterL1assay. Missing reciprocal B12topology remains needs_research in1883.",
+ "Trichodesmium association,genomic complementation and field coexpression are distinct evidence levels. Preserve potential helper mechanisms andROScompound/process#297; vitamin provision is proposed host-to-epibiont and2017facultativeuse must not become obligatory dependence. Field node does not assert exactIMS101orA.macleodii membership; only canonical microbiome guild is credited there. Non-graph identity issues remain1886.",
+ "Issue-title/body dedup covered all1124existing issues initially and a fresh pre-creation sweep; nine matching issue bodies read. Ignored/hidden-inclusive local path index covers128files,excluding.git/docs/site/references_cache/.env,not all historical file bodies. Historical PR comments were not exhaustively searched.",
+ "Edison one-community dry run completed. Scope-specific credit-spending invocation authorized by execution approval, then stopped in load_api_key before client creation:configured key unavailable. No task submitted,report received or provider credit spent. User asked to configure key securely. Previous denied and unanswered scopes not retried. No absence claim about credentials elsewhere.",
+ "Non-graph blocks,457otherrecords,923caches and prior histories preserved. No runtime/schema/validator changes. Required validation and measured census are recorded separately; self-review is not independent approval. Issues remain open until protected-main merge or separately verified followup. RootCI blocker1836 forbids invented CI or premature merge/branch cleanup."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml b/reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
new file mode 100644
index 000000000..b4028e85b
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
@@ -0,0 +1,1095 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 7a920570e99167cd0e97083f1dbc32cc20c317b9
+baseline_commit: 7a920570e99167cd0e97083f1dbc32cc20c317b9
+base_tree: 9b2e9b908db769aa738f4a1358c20ec30433c1c3
+pre_source_baseline_sha256: e4e0d15e305843d5a7dc342cd390e15fed00e3d022b87656cd9c17c074e5dd9b
+issues:
+- 1880
+- 1881
+- 1882
+unresolved_research_issues:
+- 1883
+unresolved_non_graph_issues:
+- 1884
+- 1885
+- 1886
+source_access:
+ retrieval_manifest:
+ aggregation:
+ pmid: '20827289'
+ doi: 10.1038/ismej.2010.145
+ pmcid: PMC3105730
+ title: Diatom-associated bacteria are required for aggregation of Thalassiosira weissflogii.
+ metadata: /private/tmp/communitymech-batch113/aggregation-metadata.json
+ metadata_sha256: 042e636f0aa5a0adaee6122d75475f8699d5c77d2bccd0eadbd5e54f41bb418f
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A20827289+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3105730/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch113/aggregation-abstract.txt
+ abstract_sha256: 6602a281735718e8d20d977d6b57a3a44c1b62945737647b86ba339130610273
+ crossref: /private/tmp/communitymech-batch113/aggregation-crossref.json
+ crossref_sha256: 7d98024e3648863fbd53a23c894c640f8b49da36a5cd7e26cb0c742808ce9366
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2010
+ - 9
+ - 9
+ date-time: '2010-09-09T00:00:00Z'
+ timestamp: 1283990400000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://academic.oup.com/pages/standard-publication-reuse-rights
+ chemotaxis:
+ pmid: '22820333'
+ doi: 10.1128/aem.01790-12
+ pmcid: PMC3457506
+ title: Chemotaxis of Marinobacter adhaerens and its impact on attachment to the diatom Thalassiosira weissflogii.
+ metadata: /private/tmp/communitymech-batch113/chemotaxis-metadata.json
+ metadata_sha256: edd759fb7ae40d70e9250490c0bcd8777e12c0fdb52c9f174968af8b1ad2fa1b
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A22820333+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3457506/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch113/chemotaxis-abstract.txt
+ abstract_sha256: 52802fe41fbc850bf7e3d66dcbd8d25b1b9851c4056cb710a0d0138ddf0baca6
+ crossref: /private/tmp/communitymech-batch113/chemotaxis-crossref.json
+ crossref_sha256: b8837a95cc8c934ec3f30a92481715d1bf1ae54530f11e91899aa4f536bb5dce
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2012
+ - 10
+ - 1
+ date-time: '2012-10-01T00:00:00Z'
+ timestamp: 1349049600000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://journals.asm.org/non-commercial-tdm-license
+ future_ocean:
+ pmid: '25375640'
+ doi: 10.1371/journal.pone.0112379
+ pmcid: PMC4223051
+ title: Aggregation and sedimentation of Thalassiosira weissflogii (diatom) in a warmer and more acidified
+ future ocean.
+ metadata: /private/tmp/communitymech-batch113/future_ocean-metadata.json
+ metadata_sha256: fdc42361e42c671d2693c8390d07ec17493fbc312eba91175bafba286ec40958
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A25375640+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4223051/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch113/future_ocean-abstract.txt
+ abstract_sha256: e9c5914658fcdc16f5b7fa8f590bfabb8c823db78c34d6d4f9222cc308ebd3c2
+ xml: /private/tmp/communitymech-batch113/future_ocean-primary.xml
+ xml_sha256: c7a2bd9e1d67cdcce76f95fc965b503964adbfd396c1322b7de99c9ce2db8ee0
+ primary_text: /private/tmp/communitymech-batch113/future_ocean-primary.txt
+ primary_text_sha256: 643dcf6d94231c8e5ecb3657a5927876e74f6671e1ab08b79a97f65d36609658
+ license:
+ - https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of
+ the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction
+ in any medium, provided the original author and source are properly credited.
+ crossref: /private/tmp/communitymech-batch113/future_ocean-crossref.json
+ crossref_sha256: ca69baa7ea820aad173c3d7367e99167e3167ea10ab09df079ed5610986eb2ae
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2014
+ - 11
+ - 6
+ date-time: '2014-11-06T00:00:00Z'
+ timestamp: 1415232000000
+ content-version: unspecified
+ delay-in-days: 0
+ URL: http://creativecommons.org/licenses/by/4.0/
+ hp15_genome:
+ pmid: '21304739'
+ doi: 10.4056/sigs.922139
+ pmcid: PMC3035377
+ title: Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine
+ microorganism.
+ metadata: /private/tmp/communitymech-batch113/hp15_genome-metadata.json
+ metadata_sha256: ffde0cc61de9fb5c78f24c2114510140c1c7afc6769d4b4132309b3fdab4ba53
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.4056%2Fsigs.922139%22+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3035377/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch113/hp15_genome-abstract.txt
+ abstract_sha256: 56b86a60698dc26e66213325e02057af921d875ae053bf2174d5d5da7fe695ae
+ xml: /private/tmp/communitymech-batch113/hp15_genome-primary.xml
+ xml_sha256: 0d6d31ae955dc9d1e27bcb5e49006689781a2b431a8fa53d87e0ed618b5f1e44
+ primary_text: /private/tmp/communitymech-batch113/hp15_genome-primary.txt
+ primary_text_sha256: 927d5b049d31e29a3fe1a743cd900d813c1b0d8552ea792591d0e25ba8604cc8
+ license:
+ - https://creativecommons.org/licenses/by/2.5/This is an open-access article distributed under the terms of
+ the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction
+ in any medium, provided the original work is properly cited.
+ crossref: /private/tmp/communitymech-batch113/hp15_genome-crossref.json
+ crossref_sha256: 49c7c5fa7d8757f1895f0fe25258191e5c0abdd6666636a0eee02e68528638e0
+ crossref_license: []
+ chitin_fibres:
+ pmid: null
+ doi: 10.3354/meps09894
+ pmcid: null
+ title:
+ - Effects of Marinobacter adhaerens HP15 on polymer exudation by Thalassiosira weissflogii at different N:P
+ ratios
+ metadata: /private/tmp/communitymech-batch113/chitin_fibres-metadata.json
+ metadata_sha256: 46c175c7c1bedf3d5063f4085a81414bf839cc88a7837d5f1e2e3195797962df
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.3354%2Fmeps09894%22+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 0
+ crossref: /private/tmp/communitymech-batch113/chitin_fibres-crossref.json
+ crossref_sha256: b4e2a85dc4026196d90842079c53fd97c4412c6d688d0798fc83b5a4324c97f9
+ crossref_license: []
+ diatom_recognition:
+ pmid: '28631440'
+ doi: 10.1111/1462-2920.13834
+ pmcid: null
+ title: Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system.
+ metadata: /private/tmp/communitymech-batch113/diatom_recognition-metadata.json
+ metadata_sha256: b5b2825c12c9b91976b88c021b20952abf36464383303350484c43db92cfc79f
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A28631440+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ abstract: /private/tmp/communitymech-batch113/diatom_recognition-abstract.txt
+ abstract_sha256: 03ec4e345f442b5d3af2d277174d529850174cc13ebf7f6af18ecabe9ab4d36d
+ crossref: /private/tmp/communitymech-batch113/diatom_recognition-crossref.json
+ crossref_sha256: e59d76b0c2834c32d634bbe696498138f0b6b8061ebd36fddd1084adc91262e5
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2018
+ - 6
+ - 19
+ date-time: '2018-06-19T00:00:00Z'
+ timestamp: 1529366400000
+ content-version: am
+ delay-in-days: 333
+ URL: http://onlinelibrary.wiley.com/termsAndConditions#am
+ - start:
+ date-parts:
+ - - 2017
+ - 7
+ - 21
+ date-time: '2017-07-21T00:00:00Z'
+ timestamp: 1500595200000
+ content-version: vor
+ delay-in-days: 0
+ URL: http://onlinelibrary.wiley.com/termsAndConditions#vor
+ diatom_partitioning:
+ pmid: '33097854'
+ doi: 10.1038/s41396-020-00811-y
+ pmcid: PMC8027193
+ title: Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy.
+ metadata: /private/tmp/communitymech-batch113/diatom_partitioning-metadata.json
+ metadata_sha256: ff0c87dcffb15d9a6e073330db0b59ef3e0b7590987b7c97a8ad8765d75e2b81
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A33097854+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8027193/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch113/diatom_partitioning-abstract.txt
+ abstract_sha256: d3f04faaac74cdabf7e42e93a97804f4efae39c8ae31cc5f5031c046399759f5
+ xml: /private/tmp/communitymech-batch113/diatom_partitioning-primary.xml
+ xml_sha256: 1aa91708805c535b3b9363e3510400d97fb1b40c78f93864a93a6f71d47ab502
+ primary_text: /private/tmp/communitymech-batch113/diatom_partitioning-primary.txt
+ primary_text_sha256: f06ba6d9c770005c9271e24bd5f89c87eedd34672b874ea147116e43275d125b
+ license:
+ - "Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which\
+ \ permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you\
+ \ give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons\
+ \ license, and indicate if changes were made. The images or other third party material in this article are\
+ \ included in the article\u2019s Creative Commons license, unless indicated otherwise in a credit line to\
+ \ the material. If material is not included in the article\u2019s Creative Commons license and your intended\
+ \ use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission\
+ \ directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/."
+ crossref: /private/tmp/communitymech-batch113/diatom_partitioning-crossref.json
+ crossref_sha256: 8fbe1add7e0d17867c975e94ab91e6a35c3dd1e83924c0adcf7eac616ed42e50
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2024
+ - 1
+ - 10
+ date-time: '2024-01-10T00:00:00Z'
+ timestamp: 1704844800000
+ content-version: vor
+ delay-in-days: 1174
+ URL: https://creativecommons.org/licenses/by/4.0/
+ - start:
+ date-parts:
+ - - 2020
+ - 10
+ - 23
+ date-time: '2020-10-23T00:00:00Z'
+ timestamp: 1603411200000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0
+ - start:
+ date-parts:
+ - - 2020
+ - 10
+ - 23
+ date-time: '2020-10-23T00:00:00Z'
+ timestamp: 1603411200000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0
+ tricho_genomes:
+ pmid: '28440800'
+ doi: 10.1038/ismej.2017.49
+ pmcid: PMC5520037
+ title: 'The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential
+ interactions.'
+ metadata: /private/tmp/communitymech-batch113/tricho_genomes-metadata.json
+ metadata_sha256: 20b87c1043e018e6f15da964a2419d6330ba35c11c1441bf1db44f8f9d153d7c
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A28440800+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5520037/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch113/tricho_genomes-abstract.txt
+ abstract_sha256: 17cbacbd2658c364b7e40e4a6e49d1107791b1729748f9fb21e147e79132f60a
+ crossref: /private/tmp/communitymech-batch113/tricho_genomes-crossref.json
+ crossref_sha256: 3a57b6801019907afe7a4dce0c16f384b6b76817b82ca70113854da655acc840
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2017
+ - 4
+ - 25
+ date-time: '2017-04-25T00:00:00Z'
+ timestamp: 1493078400000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://academic.oup.com/pages/standard-publication-reuse-rights
+ - start:
+ date-parts:
+ - - 2017
+ - 4
+ - 25
+ date-time: '2017-04-25T00:00:00Z'
+ timestamp: 1493078400000
+ content-version: tdm
+ delay-in-days: 0
+ URL: http://www.springer.com/tdm
+ tricho_diel:
+ pmid: '29382945'
+ doi: 10.1038/s41396-017-0041-5
+ pmcid: PMC5864210
+ title: Coordinated gene expression between Trichodesmium and its microbiome over day-night cycles in the North
+ Pacific Subtropical Gyre.
+ metadata: /private/tmp/communitymech-batch113/tricho_diel-metadata.json
+ metadata_sha256: cf30eb8d10292d1380ab625e26b77f1a7df7e4bcf3f49376a17b2aa226793136
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A29382945+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5864210/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch113/tricho_diel-abstract.txt
+ abstract_sha256: 991a5c5ccd82ebc4b1cb28a30182531c400708afd1f6c016def1f26764fed644
+ crossref: /private/tmp/communitymech-batch113/tricho_diel-crossref.json
+ crossref_sha256: 47a61b55e624a103901753ca83e8afd6367cbdabd0237ec852d15da8571ee4c1
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2018
+ - 1
+ - 30
+ date-time: '2018-01-30T00:00:00Z'
+ timestamp: 1517270400000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://academic.oup.com/pages/standard-publication-reuse-rights
+ - start:
+ date-parts:
+ - - 2018
+ - 1
+ - 30
+ date-time: '2018-01-30T00:00:00Z'
+ timestamp: 1517270400000
+ content-version: tdm
+ delay-in-days: 0
+ URL: http://www.springer.com/tdm
+ pdf_manifest:
+ aggregation:
+ doi: 10.1038/ismej.2010.145
+ pdf: /Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/Mechs/CommunityMech/references_cache/files/PMID_20827289.pdf
+ pdf_sha256: c40b3aae947563128b03f872f642c6536a02e7ee45c4b683eb4378c38dc566de
+ url: null
+ pages:
+ - page: 1
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-01.txt
+ text_sha256: 3ca0dd5312a023f6faa23e7fd34fbb8760b6b4e92b59f4744c478aa7584ff8ff
+ - page: 2
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-02.txt
+ text_sha256: 17502c1554503852058f015da583d68779bb51eb0a7e94c886774222a459401c
+ - page: 3
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-03.txt
+ text_sha256: 333425fd1c5fddaa54ee1120b44cca33100f0402d40c3759a800e75961a23a20
+ - page: 4
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-04.txt
+ text_sha256: 1592eaa05916cf3cbbd8b8e6d4f1df2d0361060d0b2a1c0f4042d7301b87cf2c
+ - page: 5
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-05.txt
+ text_sha256: 4e68b8ba881ca3cfb3130b477480a0b250b9d0333a8832c3131c627d6314978e
+ - page: 6
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-06.txt
+ text_sha256: 95f842cab62873a04aa9fb666afa751da11ee1c3ac1cfb48306d41ffd98c1b01
+ - page: 7
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-07.txt
+ text_sha256: 2f06474d0c9f57ac021b64cb387c98039b501cca2854f3beeb13067b383b706e
+ - page: 8
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-08.txt
+ text_sha256: 23fd88022c3dae270f937ad15e538b5bb56113f7b1cd375e4aedd79d537c8a1f
+ - page: 9
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-09.txt
+ text_sha256: dab70e059d5078aec9e2298148555596516cbb8e5be0c292ef672d46b5f4fdab
+ - page: 10
+ text: /private/tmp/communitymech-batch113/pdf-review/aggregation-page-10.txt
+ text_sha256: b3d0dcd53c62215c225a10113863af68364f29a767e7b421c3ae835ed0cf643b
+ page_count: 10
+ text_read: false
+ figures_reviewed: []
+ repository_copy: false
+ license_scope: Read-only research; no publication body or PDF added to repository.
+ diatom_recognition:
+ doi: 10.1111/1462-2920.13834
+ pdf: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition.pdf
+ pdf_sha256: e37b48578e4a79183fb623596dc16fa3b9f3a4b476a537f4a7004f51cf0eedcc
+ url: https://website.whoi.edu/gfd/wp-content/uploads/sites/14/2018/10/Durham_et_al_2017_262208.pdf
+ pages:
+ - page: 1
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-01.txt
+ text_sha256: 0c322412036dce7d93dd6dae1417e85b2b57a0f9b7fb98d42c9e3564b7dd0254
+ - page: 2
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-02.txt
+ text_sha256: 736f8995b4e5468e6576acb30251e611bdcd8dcafa136f603f1374bdbaa986a9
+ - page: 3
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-03.txt
+ text_sha256: 13961998655e22b08b248dd72c2151a09d04379928eb0e3b14158effbd0b04fe
+ - page: 4
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-04.txt
+ text_sha256: 2607cc78a086788a0dab7647197749939fd0c021d52284f1a776dbbfb2e33044
+ - page: 5
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-05.txt
+ text_sha256: 30dc900193c467c48cd65cb9e5ac5ed84c9789fb1cd9f724aceae35af70f5ec5
+ - page: 6
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-06.txt
+ text_sha256: 99b89945ec9575f42377832689119926ae8bef63c5273a99cb2aac67cbd564e3
+ - page: 7
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-07.txt
+ text_sha256: 71fe8010e6b338fffed8a7d2488b76d57eb97762ac8b597489a1b91469c595b2
+ - page: 8
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-08.txt
+ text_sha256: 385df38e55fdcd0419d68e38a575d7df3fa64bcedd5b1b6fb780eb35769ff8a7
+ - page: 9
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-09.txt
+ text_sha256: 7f66b550ad1699c3986f83c4e69a5fa35990918cbc79e7b01df9ee7988cd42c3
+ - page: 10
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-10.txt
+ text_sha256: 221790525e2cb7f41d9dfea2a312215ba7a4e95d3bf947e2540cbfb1b4c8fe2f
+ - page: 11
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-11.txt
+ text_sha256: ddae72d484a907acd045f6ba35270b3376faaa3b5b6bbfcc7c98cc07d808ee77
+ - page: 12
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-12.txt
+ text_sha256: b15f9c38c4aa6ae3e9c87c0a2b02bf5ea3e6f369cfc5b41f4417f3dcd1c7717e
+ - page: 13
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-13.txt
+ text_sha256: a3f0e4bf51455bc042687d10069b3b26530a95f5c48b3c042cd927d8a6b19f62
+ - page: 14
+ text: /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-14.txt
+ text_sha256: aeb41bc3ed63d5079300c1eac128e550afe878c95d70a516e52f594aabe5809f
+ page_count: 14
+ text_read: false
+ figures_reviewed: []
+ repository_copy: false
+ license_scope: Read-only research; no publication body or PDF added to repository.
+ chitin_fibres:
+ doi: 10.3354/meps09894
+ url: https://www.int-res.com/articles/feature/m461p001.pdf
+ status: retrieval_failed
+ error: 'HTTP Error 401: Unauthorized'
+ repository_copy: false
+ tricho_genomes:
+ doi: 10.1038/ismej.2017.49
+ pdf: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes.pdf
+ pdf_sha256: 3f6744880efd09ebfabe7c73682a5ce426575808c0b5c37b9f4dffc839f5da2c
+ url: https://astrobiomike.github.io/research/Lee_et_al_2017_ISME.pdf
+ pages:
+ - page: 1
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-01.txt
+ text_sha256: ec50ca0d007c60e2150f15bd06150d6110e2dacc6aa6a739d80d8e10186beb40
+ - page: 2
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-02.txt
+ text_sha256: 26fe7f54a1936c2e06378014ed292b7e949eaa23e2eb03ae691ddfcdd5ffe10e
+ - page: 3
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-03.txt
+ text_sha256: 2986b3409b3dab656003a962431d6df2f97815edf9854bf461c1032b70ad83fe
+ - page: 4
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-04.txt
+ text_sha256: 1ceb990e8eb0a10830fc2b964019caa452531a0cb8e2601593be4a2dea0f807a
+ - page: 5
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-05.txt
+ text_sha256: efaa89ffc5ae9f2f893f71ab67695a192cdde1520a32fcebfa12d21994ec3f5b
+ - page: 6
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-06.txt
+ text_sha256: a1b9f112d4960b7e117b73df6a03fbf6ddb240cbe6782e3e51b369b6b04dd47e
+ - page: 7
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-07.txt
+ text_sha256: e2caca889b886984f65492720e90c4c7144fb1a041367906c5a50c78fe384ac8
+ - page: 8
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-08.txt
+ text_sha256: bb835fd938aa03cb04ff3765b650bee0c01fc7f14579c044a00045b8da086b69
+ - page: 9
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-09.txt
+ text_sha256: 51b694b8b6e620ce39ead86279b6dd97660956b1a937b50e0a6cbc8c750d5d1b
+ - page: 10
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-10.txt
+ text_sha256: a18720a2e20dfe3fd30265523de3524a489654a42ff9e0fb0894910e6657f204
+ - page: 11
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-11.txt
+ text_sha256: ce882142f780b31cc942954c34047a4e1259c92954c474d4f41e3f9b4e7fad51
+ - page: 12
+ text: /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-12.txt
+ text_sha256: c04322725772e971985af10ae271489357e58a19b95e3ffc6e2722cd28191137
+ page_count: 12
+ text_read: false
+ figures_reviewed: []
+ repository_copy: false
+ license_scope: Read-only research; no publication body or PDF added to repository.
+ actual_read_scope:
+ - Three whole canonical records and existing snippet evidence read. Fresh primary metadata/abstracts and Crossref
+ identities for nine sources; MEPS has no retrieved abstract. Full fresh extracted main bodies:2014future-ocean1-167,HP15genome1-89,2020partitioning1-163.
+ Table1 of the 2020 paper also parsed as structured XML to confirm the Ruegeria column.
+ - Full PDF extracted text read:2011aggregation pages1-10 from existing user PDF,2017recognition pages1-14 from
+ WHOI,2017Trichodesmium pages1-12 from author research site. Visual review:aggregation pages5/6/8(Figs1/2/3/5),recognition
+ pages2/3/8(Figs1/2/4),Trichodesmium pages7/9(text and Fig3). Other figure pixels, separate supplements and raw
+ data not reviewed.
+ - 2018diel existing curator TXT read lines1-810, including abstract,complete main body and beginning references;
+ reference-list tail not read. Fresh primary abstract independently retrieved. FullTextXML attempts failed for
+ aggregation,chemotaxis,Trichodesmium2017 and diel2018. Chemotaxis graph is abstract-bounded; MEPS public PDF
+ returned401 twice, no bypass or full-paper claim. Existing caption retained PARTIAL and not treated as proof
+ of all TEP chemistry.
+ - No PDFs or publication bodies added to the repository;923 existing caches untouched. Graph/discussion quote
+ matches are independently checked against fresh primary texts except one existing MEPS caption-only quote. Cache
+ matching is not entailment or Linux reference-loader certification. Some long cache bodies were not read in
+ full; the independent primary bodies and existing target snippets were reviewed.
+primary_artifacts:
+ /Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/Mechs/CommunityMech/references_cache/files/PMID_20827289.pdf: c40b3aae947563128b03f872f642c6536a02e7ee45c4b683eb4378c38dc566de
+ /private/tmp/communitymech-batch113/aggregation-abstract.txt: 6602a281735718e8d20d977d6b57a3a44c1b62945737647b86ba339130610273
+ /private/tmp/communitymech-batch113/aggregation-crossref.json: 7d98024e3648863fbd53a23c894c640f8b49da36a5cd7e26cb0c742808ce9366
+ /private/tmp/communitymech-batch113/aggregation-metadata.json: 042e636f0aa5a0adaee6122d75475f8699d5c77d2bccd0eadbd5e54f41bb418f
+ /private/tmp/communitymech-batch113/baseline.json: e4e0d15e305843d5a7dc342cd390e15fed00e3d022b87656cd9c17c074e5dd9b
+ /private/tmp/communitymech-batch113/chemotaxis-abstract.txt: 52802fe41fbc850bf7e3d66dcbd8d25b1b9851c4056cb710a0d0138ddf0baca6
+ /private/tmp/communitymech-batch113/chemotaxis-crossref.json: b8837a95cc8c934ec3f30a92481715d1bf1ae54530f11e91899aa4f536bb5dce
+ /private/tmp/communitymech-batch113/chemotaxis-metadata.json: edd759fb7ae40d70e9250490c0bcd8777e12c0fdb52c9f174968af8b1ad2fa1b
+ /private/tmp/communitymech-batch113/chitin_fibres-crossref.json: b4e2a85dc4026196d90842079c53fd97c4412c6d688d0798fc83b5a4324c97f9
+ /private/tmp/communitymech-batch113/chitin_fibres-metadata.json: 46c175c7c1bedf3d5063f4085a81414bf839cc88a7837d5f1e2e3195797962df
+ /private/tmp/communitymech-batch113/diatom_partitioning-abstract.txt: d3f04faaac74cdabf7e42e93a97804f4efae39c8ae31cc5f5031c046399759f5
+ /private/tmp/communitymech-batch113/diatom_partitioning-crossref.json: 8fbe1add7e0d17867c975e94ab91e6a35c3dd1e83924c0adcf7eac616ed42e50
+ /private/tmp/communitymech-batch113/diatom_partitioning-metadata.json: ff0c87dcffb15d9a6e073330db0b59ef3e0b7590987b7c97a8ad8765d75e2b81
+ /private/tmp/communitymech-batch113/diatom_partitioning-primary.txt: f06ba6d9c770005c9271e24bd5f89c87eedd34672b874ea147116e43275d125b
+ /private/tmp/communitymech-batch113/diatom_partitioning-primary.xml: 1aa91708805c535b3b9363e3510400d97fb1b40c78f93864a93a6f71d47ab502
+ /private/tmp/communitymech-batch113/diatom_recognition-abstract.txt: 03ec4e345f442b5d3af2d277174d529850174cc13ebf7f6af18ecabe9ab4d36d
+ /private/tmp/communitymech-batch113/diatom_recognition-crossref.json: e59d76b0c2834c32d634bbe696498138f0b6b8061ebd36fddd1084adc91262e5
+ /private/tmp/communitymech-batch113/diatom_recognition-metadata.json: b5b2825c12c9b91976b88c021b20952abf36464383303350484c43db92cfc79f
+ ? /private/tmp/communitymech-batch113/edison-dry-run/Thalassiosira_Ruegeria_Phycosphere_Coculture-edison-literature-causal-meta.yaml
+ : 4e371d688d522e5288bf5f0ed47abf41785e62199d53466e58d450627fdd90b1
+ /private/tmp/communitymech-batch113/future_ocean-abstract.txt: e9c5914658fcdc16f5b7fa8f590bfabb8c823db78c34d6d4f9222cc308ebd3c2
+ /private/tmp/communitymech-batch113/future_ocean-crossref.json: ca69baa7ea820aad173c3d7367e99167e3167ea10ab09df079ed5610986eb2ae
+ /private/tmp/communitymech-batch113/future_ocean-metadata.json: fdc42361e42c671d2693c8390d07ec17493fbc312eba91175bafba286ec40958
+ /private/tmp/communitymech-batch113/future_ocean-primary.txt: 643dcf6d94231c8e5ecb3657a5927876e74f6671e1ab08b79a97f65d36609658
+ /private/tmp/communitymech-batch113/future_ocean-primary.xml: c7a2bd9e1d67cdcce76f95fc965b503964adbfd396c1322b7de99c9ce2db8ee0
+ /private/tmp/communitymech-batch113/hp15_genome-abstract.txt: 56b86a60698dc26e66213325e02057af921d875ae053bf2174d5d5da7fe695ae
+ /private/tmp/communitymech-batch113/hp15_genome-crossref.json: 49c7c5fa7d8757f1895f0fe25258191e5c0abdd6666636a0eee02e68528638e0
+ /private/tmp/communitymech-batch113/hp15_genome-metadata.json: ffde0cc61de9fb5c78f24c2114510140c1c7afc6769d4b4132309b3fdab4ba53
+ /private/tmp/communitymech-batch113/hp15_genome-primary.txt: 927d5b049d31e29a3fe1a743cd900d813c1b0d8552ea792591d0e25ba8604cc8
+ /private/tmp/communitymech-batch113/hp15_genome-primary.xml: 0d6d31ae955dc9d1e27bcb5e49006689781a2b431a8fa53d87e0ed618b5f1e44
+ /private/tmp/communitymech-batch113/issue-dedup-current.json: 0052884b3bd38111520cbcd972261bce41d6ea21a2d814fd8a12e639a60e3613
+ /private/tmp/communitymech-batch113/local-matches.txt: b002a9b7318d558c6fbba824a6b08e7521cc6b447fdb55ee2dc8e4a1bc125423
+ /private/tmp/communitymech-batch113/pdf-manifest.json: ae11c81da4dec2e934c528b756c2a17ddffb11de6b13ae1ea2d71c5658780cbd
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-01.txt: 3ca0dd5312a023f6faa23e7fd34fbb8760b6b4e92b59f4744c478aa7584ff8ff
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-02.txt: 17502c1554503852058f015da583d68779bb51eb0a7e94c886774222a459401c
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-03.txt: 333425fd1c5fddaa54ee1120b44cca33100f0402d40c3759a800e75961a23a20
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-04.txt: 1592eaa05916cf3cbbd8b8e6d4f1df2d0361060d0b2a1c0f4042d7301b87cf2c
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-05.png: db0766cda461e14083662eb40a1319d004be9689dd344d9bd005ea8c5e91af87
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-05.txt: 4e68b8ba881ca3cfb3130b477480a0b250b9d0333a8832c3131c627d6314978e
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-06.png: 8be896d575bb77ef4615f9fc3c85ec0859803617fc83e5f1736e04c3081e0115
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-06.txt: 95f842cab62873a04aa9fb666afa751da11ee1c3ac1cfb48306d41ffd98c1b01
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-07.txt: 2f06474d0c9f57ac021b64cb387c98039b501cca2854f3beeb13067b383b706e
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-08.png: 73b0a74b662f43f55efd26c78da9f0866dc3de53da4a030348c8eaf22b00fc50
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-08.txt: 23fd88022c3dae270f937ad15e538b5bb56113f7b1cd375e4aedd79d537c8a1f
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-09.txt: dab70e059d5078aec9e2298148555596516cbb8e5be0c292ef672d46b5f4fdab
+ /private/tmp/communitymech-batch113/pdf-review/aggregation-page-10.txt: b3d0dcd53c62215c225a10113863af68364f29a767e7b421c3ae835ed0cf643b
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-01.txt: 0c322412036dce7d93dd6dae1417e85b2b57a0f9b7fb98d42c9e3564b7dd0254
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-02.png: 4290234ee4fda993cc7973a862c55d4ad9b314ed08163230172e9914d68f1eca
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-02.txt: 736f8995b4e5468e6576acb30251e611bdcd8dcafa136f603f1374bdbaa986a9
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-03.png: 537e9af50077e8009213d2742ca5a9d9f989e74f5eca996deeddb2016f56fb12
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-03.txt: 13961998655e22b08b248dd72c2151a09d04379928eb0e3b14158effbd0b04fe
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-04.txt: 2607cc78a086788a0dab7647197749939fd0c021d52284f1a776dbbfb2e33044
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-05.txt: 30dc900193c467c48cd65cb9e5ac5ed84c9789fb1cd9f724aceae35af70f5ec5
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-06.txt: 99b89945ec9575f42377832689119926ae8bef63c5273a99cb2aac67cbd564e3
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-07.txt: 71fe8010e6b338fffed8a7d2488b76d57eb97762ac8b597489a1b91469c595b2
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-08.png: 4758d41e8d1230f3ddb8a49e9dbfd5da25693b9dd33dadfc20bb6e634812d543
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-08.txt: 385df38e55fdcd0419d68e38a575d7df3fa64bcedd5b1b6fb780eb35769ff8a7
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-09.txt: 7f66b550ad1699c3986f83c4e69a5fa35990918cbc79e7b01df9ee7988cd42c3
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-10.txt: 221790525e2cb7f41d9dfea2a312215ba7a4e95d3bf947e2540cbfb1b4c8fe2f
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-11.txt: ddae72d484a907acd045f6ba35270b3376faaa3b5b6bbfcc7c98cc07d808ee77
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-12.txt: b15f9c38c4aa6ae3e9c87c0a2b02bf5ea3e6f369cfc5b41f4417f3dcd1c7717e
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-13.txt: a3f0e4bf51455bc042687d10069b3b26530a95f5c48b3c042cd927d8a6b19f62
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-14.txt: aeb41bc3ed63d5079300c1eac128e550afe878c95d70a516e52f594aabe5809f
+ /private/tmp/communitymech-batch113/pdf-review/diatom_recognition.pdf: e37b48578e4a79183fb623596dc16fa3b9f3a4b476a537f4a7004f51cf0eedcc
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-01.txt: ec50ca0d007c60e2150f15bd06150d6110e2dacc6aa6a739d80d8e10186beb40
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-02.txt: 26fe7f54a1936c2e06378014ed292b7e949eaa23e2eb03ae691ddfcdd5ffe10e
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-03.txt: 2986b3409b3dab656003a962431d6df2f97815edf9854bf461c1032b70ad83fe
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-04.txt: 1ceb990e8eb0a10830fc2b964019caa452531a0cb8e2601593be4a2dea0f807a
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-05.txt: efaa89ffc5ae9f2f893f71ab67695a192cdde1520a32fcebfa12d21994ec3f5b
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-06.txt: a1b9f112d4960b7e117b73df6a03fbf6ddb240cbe6782e3e51b369b6b04dd47e
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-07.png: 07d75b761276a419f616d8f38309dba1b2bb44d51c240a3f260b7f33a77f5160
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-07.txt: e2caca889b886984f65492720e90c4c7144fb1a041367906c5a50c78fe384ac8
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-08.txt: bb835fd938aa03cb04ff3765b650bee0c01fc7f14579c044a00045b8da086b69
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-09.png: e99752f6f2bb5cc29aa9af074d1f189629f7c7a46caa71aefe21249c40cbb08f
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-09.txt: 51b694b8b6e620ce39ead86279b6dd97660956b1a937b50e0a6cbc8c750d5d1b
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-10.txt: a18720a2e20dfe3fd30265523de3524a489654a42ff9e0fb0894910e6657f204
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-11.txt: ce882142f780b31cc942954c34047a4e1259c92954c474d4f41e3f9b4e7fad51
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-12.txt: c04322725772e971985af10ae271489357e58a19b95e3ffc6e2722cd28191137
+ /private/tmp/communitymech-batch113/pdf-review/tricho_genomes.pdf: 3f6744880efd09ebfabe7c73682a5ce426575808c0b5c37b9f4dffc839f5da2c
+ /private/tmp/communitymech-batch113/primary-manifest.json: 54a487b8908feffa1feeed66fe7a60d59ee199d4755315503570e30299764f0b
+ /private/tmp/communitymech-batch113/rendered-figures.json: 7f9d1adf428f3c7ecc9b70cb3596ba4fbe80328036334d1e2adab66554921344
+ /private/tmp/communitymech-batch113/tricho_diel-abstract.txt: 991a5c5ccd82ebc4b1cb28a30182531c400708afd1f6c016def1f26764fed644
+ /private/tmp/communitymech-batch113/tricho_diel-crossref.json: 47a61b55e624a103901753ca83e8afd6367cbdabd0237ec852d15da8571ee4c1
+ /private/tmp/communitymech-batch113/tricho_diel-metadata.json: cf30eb8d10292d1380ab625e26b77f1a7df7e4bcf3f49376a17b2aa226793136
+ /private/tmp/communitymech-batch113/tricho_genomes-abstract.txt: 17cbacbd2658c364b7e40e4a6e49d1107791b1729748f9fb21e147e79132f60a
+ /private/tmp/communitymech-batch113/tricho_genomes-crossref.json: 3a57b6801019907afe7a4dce0c16f384b6b76817b82ca70113854da655acc840
+ /private/tmp/communitymech-batch113/tricho_genomes-metadata.json: 20b87c1043e018e6f15da964a2419d6330ba35c11c1441bf1db44f8f9d153d7c
+ references_cache/PMID_20827289.md: 7886cc9bd5fb04794399faec79365aadb7045538a37bb29cf9cd72f1cf96f19e
+ references_cache/PMID_22820333.md: b5e59d9bd1f234d9e34c96b3ec72f7af9a197633cd7f6abc0d6c5fcb4bad2451
+ references_cache/PMID_25375640.md: b0acc6fc72bf7d22e01ccd22c51600e0ec337f30e91898732cee0875d42d8e16
+ references_cache/PMID_28440800.txt: 42d9afaeca8e20c30ceccab47e452631af33fd4c10d8d2e642e74e907598e7fa
+ references_cache/PMID_28631440.txt: a64edc7b5bcf844fd640ad24b402260a7ed7a2f6389325dabe815123fce5f7b8
+ references_cache/PMID_29382945.txt: 822a4f5f9029897f4316affee3951d724ea2612862499c05ef30a7c832e27af6
+ references_cache/PMID_33097854.md: a8e47a63b081b28ca3075345c1700e0abea0b46a18b64b4a4337df7781440d89
+ references_cache/doi_10.3354_meps09894.md: b7de73cd4e0d3af39fabf09d998e038348d20305cb6e539f1b183e2d84d0df31
+ references_cache/doi_10.4056_sigs.922139.md: 139c13b694456bd96672197ec8d8f0de1b40fbfd561511c2ba850aa2d6a1c2b7
+reviewed_counts:
+ original_nodes: 10
+ retained_nodes: 10
+ removed_nodes: 0
+ original_arrows: 6
+ retained_arrows: 2
+ removed_arrows: 4
+ renamed_nodes: 6
+ graph_quotations: 21
+ discussion_quotations: 3
+ new_discussions: 3
+primary_graph_snippet_count: 20
+snippet_checks:
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Condition-Dependent Diatom Aggregation
+ evidence_index: 0
+ reference: PMID:20827289
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/aggregation-abstract.txt
+ cache_artifact: references_cache/PMID_20827289.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Condition-Dependent Diatom Aggregation
+ evidence_index: 1
+ reference: PMID:20827289
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/aggregation-abstract.txt
+ cache_artifact: references_cache/PMID_20827289.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Condition-Dependent Diatom Aggregation
+ evidence_index: 2
+ reference: doi:10.4056/sigs.922139
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/hp15_genome-primary.txt
+ cache_artifact: references_cache/doi_10.4056_sigs.922139.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Condition-Dependent Diatom Aggregation
+ evidence_index: 3
+ reference: PMID:25375640
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/future_ocean-primary.txt
+ cache_artifact: references_cache/PMID_25375640.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Condition-Dependent TEP Formation
+ evidence_index: 0
+ reference: PMID:22820333
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/chemotaxis-abstract.txt
+ cache_artifact: references_cache/PMID_22820333.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Condition-Dependent TEP Formation
+ evidence_index: 1
+ reference: PMID:20827289
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/aggregation-abstract.txt
+ cache_artifact: references_cache/PMID_20827289.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Condition-Dependent TEP Formation
+ evidence_index: 2
+ reference: doi:10.3354/meps09894
+ cache_matched: true
+ independent_primary_match: false
+ matched_artifact: references_cache/doi_10.3354_meps09894.md
+ cache_artifact: references_cache/doi_10.3354_meps09894.md
+ scope: Normalized contiguous match, not entailment proof. Existing caption-only cache; publisher PDF HTTP 401.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Condition-Dependent TEP Formation
+ evidence_index: 3
+ reference: PMID:25375640
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/future_ocean-primary.txt
+ cache_artifact: references_cache/PMID_25375640.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Chemotaxis-Mediated Attachment
+ evidence_index: 0
+ reference: PMID:22820333
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/chemotaxis-abstract.txt
+ cache_artifact: references_cache/PMID_22820333.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Chemotaxis-Mediated Attachment
+ evidence_index: 1
+ reference: PMID:22820333
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/chemotaxis-abstract.txt
+ cache_artifact: references_cache/PMID_22820333.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Aggregate Sinking and Carbon Export Interpretation
+ evidence_index: 0
+ reference: PMID:20827289
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/aggregation-abstract.txt
+ cache_artifact: references_cache/PMID_20827289.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: Aggregate Sinking and Carbon Export Interpretation
+ evidence_index: 1
+ reference: PMID:25375640
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/future_ocean-primary.txt
+ cache_artifact: references_cache/PMID_25375640.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Ruegeria_Phycosphere_Coculture
+ node: Putative Diatom Recognition Response to Ruegeria
+ evidence_index: 0
+ reference: PMID:28631440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/diatom_recognition-abstract.txt
+ cache_artifact: references_cache/PMID_28631440.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Ruegeria_Phycosphere_Coculture
+ node: Phytoplankton Metabolite Transfer to Ruegeria
+ evidence_index: 0
+ reference: PMID:28631440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/diatom_recognition-abstract.txt
+ cache_artifact: references_cache/PMID_28631440.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Ruegeria_Phycosphere_Coculture
+ node: Phytoplankton Metabolite Transfer to Ruegeria
+ evidence_index: 1
+ reference: PMID:33097854
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/diatom_partitioning-primary.txt
+ cache_artifact: references_cache/PMID_33097854.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Ruegeria_Phycosphere_Coculture
+ node: Diatom Chitin and Lipid Response During Coculture
+ evidence_index: 0
+ reference: PMID:28631440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/diatom_recognition-abstract.txt
+ cache_artifact: references_cache/PMID_28631440.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Trichodesmium_Alteromonas_Marine_Consortium
+ node: Colony Substrate Colonization by Heterotrophs
+ evidence_index: 0
+ reference: PMID:28440800
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/tricho_genomes-abstract.txt
+ cache_artifact: references_cache/PMID_28440800.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Trichodesmium_Alteromonas_Marine_Consortium
+ node: Putative Alteromonas Helper Functions in Trichodesmium Colonies
+ evidence_index: 0
+ reference: PMID:28440800
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/tricho_genomes-abstract.txt
+ cache_artifact: references_cache/PMID_28440800.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Trichodesmium_Alteromonas_Marine_Consortium
+ node: Putative Alteromonas Helper Functions in Trichodesmium Colonies
+ evidence_index: 1
+ reference: PMID:28440800
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/tricho_genomes-abstract.txt
+ cache_artifact: references_cache/PMID_28440800.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Trichodesmium_Alteromonas_Marine_Consortium
+ node: Field Host-Microbiome Diel Coexpression
+ evidence_index: 0
+ reference: PMID:29382945
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/tricho_diel-abstract.txt
+ cache_artifact: references_cache/PMID_29382945.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Trichodesmium_Alteromonas_Marine_Consortium
+ node: Field Host-Microbiome Diel Coexpression
+ evidence_index: 1
+ reference: PMID:29382945
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/tricho_diel-abstract.txt
+ cache_artifact: references_cache/PMID_29382945.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+discussion_snippet_checks:
+- record: Thalassiosira_Marinobacter_Marine_Snow_Coculture
+ node: hp15-aggregation-mediation-and-conditions
+ evidence_index: 0
+ reference: PMID:25375640
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/future_ocean-primary.txt
+ cache_artifact: references_cache/PMID_25375640.md
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Thalassiosira_Ruegeria_Phycosphere_Coculture
+ node: ruegeria-recognition-mediation-and-b12-extension
+ evidence_index: 0
+ reference: PMID:28631440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/diatom_recognition-abstract.txt
+ cache_artifact: references_cache/PMID_28631440.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+- record: Trichodesmium_Alteromonas_Marine_Consortium
+ node: trichodesmium-helper-flux-and-field-identity
+ evidence_index: 0
+ reference: PMID:29382945
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch113/tricho_diel-abstract.txt
+ cache_artifact: references_cache/PMID_29382945.txt
+ scope: Normalized contiguous match, not entailment proof. Fresh primary text.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - target: CommunityMech:000162
+ artifact: /private/tmp/communitymech-batch113/edison-dry-run/Thalassiosira_Ruegeria_Phycosphere_Coculture-edison-literature-causal-meta.yaml
+ sha256: 4e371d688d522e5288bf5f0ed47abf41785e62199d53466e58d450627fdd90b1
+ query_sha256: 1b2797a8920505adf873e50a02f8827e5aa23ac5e5aa8387603ef7310bb42e67
+ authorized_invocations: 1
+ invocation_exit_code: 1
+ blocked_stage: load_api_key before client creation
+ task_id: null
+ blocker: Configured Edison key unavailable; no other credential locations inspected.
+ issue: 1883
+ repair_scope: Existing-node evidence/scope corrections and removal of four unsupported arrows; no added nodes
+ or directions.
+limitations:
+- Fresh pre-source baseline across both roots:460 records,923 caches,56 warnings,zero structural defects. All10
+ existing nodes/6directions reviewed;10nodes/2directions retained,4unsupported arrows removed. No new topology.
+- Three whole canonical records and existing snippet evidence read. Fresh primary metadata/abstracts and Crossref
+ identities for nine sources; MEPS has no retrieved abstract. Full fresh extracted main bodies:2014future-ocean1-167,HP15genome1-89,2020partitioning1-163.
+ Table1 of the 2020 paper also parsed as structured XML to confirm the Ruegeria column.
+- Full PDF extracted text read:2011aggregation pages1-10 from existing user PDF,2017recognition pages1-14 from WHOI,2017Trichodesmium
+ pages1-12 from author research site. Visual review:aggregation pages5/6/8(Figs1/2/3/5),recognition pages2/3/8(Figs1/2/4),Trichodesmium
+ pages7/9(text and Fig3). Other figure pixels, separate supplements and raw data not reviewed.
+- 2018diel existing curator TXT read lines1-810, including abstract,complete main body and beginning references;
+ reference-list tail not read. Fresh primary abstract independently retrieved. FullTextXML attempts failed for
+ aggregation,chemotaxis,Trichodesmium2017 and diel2018. Chemotaxis graph is abstract-bounded; MEPS public PDF returned401
+ twice, no bypass or full-paper claim. Existing caption retained PARTIAL and not treated as proof of all TEP chemistry.
+- No PDFs or publication bodies added to the repository;923 existing caches untouched. Graph/discussion quote matches
+ are independently checked against fresh primary texts except one existing MEPS caption-only quote. Cache matching
+ is not entailment or Linux reference-loader certification. Some long cache bodies were not read in full; the independent
+ primary bodies and existing target snippets were reviewed.
+- HP15 preserves positive2011and null2014assay effects; no universal attachment/TEP/aggregation/sinking chain, no
+ measured ocean sequestration. Inactivation has possible surface/exudate confounding. Mutant attachment and abiotic
+ biofilm phenotypes are not selective aggregation mediation.
+- Ruegeria preserves supported organic-carbon feeding and transcript responses. DMSP/GlcNAc expression and proline/guanosine
+ net drawdown have distinct evidence grades; net depletion is not a traced transfer flux.2017B12-limited growth
+ rescue is distinct from laterL1assay. Missing reciprocal B12topology remains needs_research in1883.
+- Trichodesmium association,genomic complementation and field coexpression are distinct evidence levels. Preserve
+ potential helper mechanisms andROScompound/process#297; vitamin provision is proposed host-to-epibiont and2017facultativeuse
+ must not become obligatory dependence. Field node does not assert exactIMS101orA.macleodii membership; only canonical
+ microbiome guild is credited there. Non-graph identity issues remain1886.
+- Issue-title/body dedup covered all1124existing issues initially and a fresh pre-creation sweep; nine matching
+ issue bodies read. Ignored/hidden-inclusive local path index covers128files,excluding.git/docs/site/references_cache/.env,not
+ all historical file bodies. Historical PR comments were not exhaustively searched.
+- Edison one-community dry run completed. Scope-specific credit-spending invocation authorized by execution approval,
+ then stopped in load_api_key before client creation:configured key unavailable. No task submitted,report received
+ or provider credit spent. User asked to configure key securely. Previous denied and unanswered scopes not retried.
+ No absence claim about credentials elsewhere.
+- Non-graph blocks,457otherrecords,923caches and prior histories preserved. No runtime/schema/validator changes.
+ Required validation and measured census are recorded separately; self-review is not independent approval. Issues
+ remain open until protected-main merge or separately verified followup. RootCI blocker1836 forbids invented CI
+ or premature merge/branch cleanup.
+records:
+- path: kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml
+ id: CommunityMech:000259
+ original_sha256: b86ee85b9c0415276d87f5606da4f9fef01e56b87e8d3fc17a7980c09dd5215b
+ record_sha256: 8b79efb0b04a43548b3c73ac280ac987b83c4e97f2531b55da5c940f29485eae
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; source-bounded graph repair, not whole-record certification.
+ summary: Preserve the positive 2011 aggregation phenotype and the 2014 null effect without universal dependence
+ or colonization typing.; Replace TEP cross-feeding with an assay-bounded polymer outcome and qualify the existing
+ aggregation direction.; Preserve mutant attachment evidence but distinguish bacterial attachment from diatom
+ benefit and downstream mediation.; Keep the existing sinking/export interpretation, remove niche-partitioning
+ typing and separate measurements from extrapolation.
+ node_decisions:
+ - node: Condition-Dependent Diatom Aggregation
+ rationale: Preserve the positive 2011 aggregation phenotype and the 2014 null effect without universal dependence
+ or colonization typing.
+ - node: Condition-Dependent TEP Formation
+ rationale: Replace TEP cross-feeding with an assay-bounded polymer outcome and qualify the existing aggregation
+ direction.
+ - node: Chemotaxis-Mediated Attachment
+ rationale: Preserve mutant attachment evidence but distinguish bacterial attachment from diatom benefit and
+ downstream mediation.
+ - node: Aggregate Sinking and Carbon Export Interpretation
+ rationale: Keep the existing sinking/export interpretation, remove niche-partitioning typing and separate measurements
+ from extrapolation.
+ removed_node_decisions: []
+ renamed_nodes:
+ Bacteria-Dependent Diatom Aggregation: Condition-Dependent Diatom Aggregation
+ Transparent Exopolymer Particle Enhancement: Condition-Dependent TEP Formation
+ Marine Snow Carbon Flux Model: Aggregate Sinking and Carbon Export Interpretation
+ edges_before:
+ - &id001
+ source: Transparent Exopolymer Particle Enhancement
+ target: Bacteria-Dependent Diatom Aggregation
+ description: 'HP15-associated transparent exopolymer particle formation provides the exopolymeric matrix that
+ supports diatom aggregation and marine-snow particle formation.
+
+ '
+ - &id003
+ source: Chemotaxis-Mediated Attachment
+ target: Bacteria-Dependent Diatom Aggregation
+ description: 'M. adhaerens chemotaxis and surface attachment support physical association with diatom cells
+ and TEP aggregates before aggregate formation.
+
+ '
+ edges_after:
+ - &id002
+ source: Condition-Dependent TEP Formation
+ target: Condition-Dependent Diatom Aggregation
+ description: 'PARTIAL: TEP can provide an adhesive matrix enabling diatom aggregation, but the amount-aggregation
+ relationship is condition dependent. The 2011 association is not a selective mediation test; the 2014 higher-TEP/lower-aggregation
+ result rules out a universal monotonic effect, and polymer stickiness was not directly resolved.'
+ - &id004
+ source: Chemotaxis-Mediated Attachment
+ target: Condition-Dependent Diatom Aggregation
+ description: 'HYPOTHESIZED: chemotaxis-dependent attachment may enable the close association underlying the
+ earlier HP15 aggregation phenotype. The reviewed chemotaxis abstract demonstrates reduced attachment, not
+ selective mediation of the aggregation endpoint; aggregation effects cannot be assumed in every environmental
+ treatment.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: 'PARTIAL: TEP can provide an adhesive matrix enabling diatom aggregation, but the amount-aggregation
+ relationship is condition dependent. The 2011 association is not a selective mediation test; the 2014 higher-TEP/lower-aggregation
+ result rules out a universal monotonic effect, and polymer stickiness was not directly resolved.'
+ - before: *id003
+ after: *id004
+ rationale: 'HYPOTHESIZED: chemotaxis-dependent attachment may enable the close association underlying the earlier
+ HP15 aggregation phenotype. The reviewed chemotaxis abstract demonstrates reduced attachment, not selective
+ mediation of the aggregation endpoint; aggregation effects cannot be assumed in every environmental treatment.'
+ removed_edge_decisions: []
+ references:
+ - PMID:20827289
+ - PMID:22820333
+ - PMID:25375640
+ - doi:10.3354/meps09894
+ - doi:10.4056/sigs.922139
+ issues:
+ - 1880
+ - 1884
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Thalassiosira_Marinobacter_Marine_Snow_Coculture/2026-10-08T083138Z-codex-825172.yaml
+- path: kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml
+ id: CommunityMech:000162
+ original_sha256: e494809cc294a96f346c77422073e5e5b3c1826fcf693c7251b23d22c837813f
+ record_sha256: f1e51614a8c4a7856a2669afe12574d1c982f12dcebf9f53f49c65d470f747d6
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; source-bounded graph repair, not whole-record certification.
+ summary: Retain a putative recognition response without colonization typing or a restatement arrow to other transcript
+ changes.; Preserve supported organic-carbon feeding, grade metabolite evidence and remove the shared-substrate-to-transcript
+ arrow.; Retain the chitin/lipid response as transcription, not reverse cross-feeding; preserve the separate
+ B12 growth-benefit boundary.
+ node_decisions:
+ - node: Putative Diatom Recognition Response to Ruegeria
+ rationale: Retain a putative recognition response without colonization typing or a restatement arrow to other
+ transcript changes.
+ - node: Phytoplankton Metabolite Transfer to Ruegeria
+ rationale: Preserve supported organic-carbon feeding, grade metabolite evidence and remove the shared-substrate-to-transcript
+ arrow.
+ - node: Diatom Chitin and Lipid Response During Coculture
+ rationale: Retain the chitin/lipid response as transcription, not reverse cross-feeding; preserve the separate
+ B12 growth-benefit boundary.
+ removed_node_decisions: []
+ renamed_nodes:
+ Diatom Recognition of Ruegeria: Putative Diatom Recognition Response to Ruegeria
+ edges_before:
+ - &id005
+ source: Diatom Recognition of Ruegeria
+ target: Diatom Chitin and Lipid Response During Coculture
+ description: 'Ruegeria-triggered diatom recognition is reflected in the downstream T. pseudonana transcriptional
+ response affecting chitin metabolism and lipid biosynthesis during coculture.
+
+ '
+ - &id006
+ source: Phytoplankton Metabolite Transfer to Ruegeria
+ target: Diatom Chitin and Lipid Response During Coculture
+ description: 'Diatom-derived substrates consumed by Ruegeria include chitin-related sugar derivatives, linking
+ the transfer node to the chitin-metabolism component of the diatom transcriptional response.
+
+ '
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - before: *id005
+ rationale: Co-occurring transcription or shared substrate terminology does not demonstrate this source-to-target
+ causal mediation.
+ - before: *id006
+ rationale: Co-occurring transcription or shared substrate terminology does not demonstrate this source-to-target
+ causal mediation.
+ references:
+ - PMID:28631440
+ - PMID:33097854
+ issues:
+ - 1881
+ - 1885
+ - 1883
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Thalassiosira_Ruegeria_Phycosphere_Coculture/2026-10-08T083139Z-codex-dd87e7.yaml
+- path: kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml
+ id: CommunityMech:000147
+ original_sha256: e7f148febf34a85e71939396d324dee6ebe45a5b0c4e404d185847d36dbaa81f
+ record_sha256: 0d2e03b468366edc434574c18f28c80e5f3ce5ebf4a69d31169fa647f6edcdd0
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; source-bounded graph repair, not whole-record certification.
+ summary: Represent colony association without commensal neutrality or a habitat-setting arrow; distinguish laboratory
+ and field identities.; Bound helper functions to hypotheses, preserve ROS compound/process grounding and correct
+ the B12 direction and facultative-use distinction.; Retain field coexpression without cross-feeding typing or
+ exact IMS101 attribution; narrow connectivity to the supported guild.
+ node_decisions:
+ - node: Colony Substrate Colonization by Heterotrophs
+ rationale: Represent colony association without commensal neutrality or a habitat-setting arrow; distinguish
+ laboratory and field identities.
+ - node: Putative Alteromonas Helper Functions in Trichodesmium Colonies
+ rationale: Bound helper functions to hypotheses, preserve ROS compound/process grounding and correct the B12
+ direction and facultative-use distinction.
+ - node: Field Host-Microbiome Diel Coexpression
+ rationale: Retain field coexpression without cross-feeding typing or exact IMS101 attribution; narrow connectivity
+ to the supported guild.
+ removed_node_decisions: []
+ renamed_nodes:
+ Alteromonas Helper Functions in Trichodesmium Colonies: Putative Alteromonas Helper Functions in Trichodesmium
+ Colonies
+ Diel Coordinated Resource Cycling: Field Host-Microbiome Diel Coexpression
+ edges_before:
+ - &id007
+ source: Colony Substrate Colonization by Heterotrophs
+ target: Diel Coordinated Resource Cycling
+ description: Trichodesmium colony colonization provides the host-microbiome setting in which diel nitrogen,
+ carbon, iron, and B12 expression patterns were observed.
+ - &id008
+ source: Alteromonas Helper Functions in Trichodesmium Colonies
+ target: Diel Coordinated Resource Cycling
+ description: Alteromonas Fe, P, B12, carbon-catabolism, and ROS-detoxification gene complements are candidate
+ mechanisms for resource-linked diel coordination in Trichodesmium colonies.
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - before: *id007
+ rationale: Habitat context or a cross-study genomic candidate explanation is not demonstrated causation of field
+ coexpression.
+ - before: *id008
+ rationale: Habitat context or a cross-study genomic candidate explanation is not demonstrated causation of field
+ coexpression.
+ references:
+ - PMID:28440800
+ - PMID:29382945
+ issues:
+ - 1882
+ - 1886
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Trichodesmium_Alteromonas_Marine_Consortium/2026-10-08T083139Z-codex-a37037.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index f4989d1a9..3b9424b15 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -418,8 +418,8 @@ kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml CommunityMech:
kb/communities/THOR_Rhizosphere_Model_Community.yaml CommunityMech:000079 ec95272c2b0ded1ac096cd9e9a53509ae052e7316d4c88b9ef51ceefb58b9f71 4 2 100.0 pending
kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml CommunityMech:000072 01cbb6970852dad836fce77b480e680a086b088a5ad488aeedfd4788e96f64dc 4 4 100.0 pending
kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml CommunityMech:000100 1c99ca183a340680a90fcfa14327288bb8dac56f57733c219bc19902dbb5abac 6 2 100.0 pending
-kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml CommunityMech:000259 b86ee85b9c0415276d87f5606da4f9fef01e56b87e8d3fc17a7980c09dd5215b 4 2 100.0 pending
-kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml CommunityMech:000162 e494809cc294a96f346c77422073e5e5b3c1826fcf693c7251b23d22c837813f 3 2 100.0 pending
+kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml CommunityMech:000259 8b79efb0b04a43548b3c73ac280ac987b83c4e97f2531b55da5c940f29485eae 4 2 90.0 reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml reviewed
+kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml CommunityMech:000162 f1e51614a8c4a7856a2669afe12574d1c982f12dcebf9f53f49c65d470f747d6 3 0 68.3 reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml needs_research
kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml CommunityMech:000182 e06917ad89ca7d9c8b51c924bd8cf0ef18aed4feb86d4795f3b000bad0398639 3 2 100.0 pending
kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml CommunityMech:000454 ab97378f5f2ca6160bdceebee4eb24276dbc2ffddc1b49051355ba4609dfae35 2 0 70.0 pending
kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml CommunityMech:000416 07c4856308831b4b7bdf1fc50d2442584f1a4c2e5c8431a334e81557eec66727 2 0 70.0 pending
@@ -435,7 +435,7 @@ kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.y
kb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml CommunityMech:000205 4ea126e913b09702e406501449cb83080bdfd4af1623651299737147b08b2e9a 3 2 100.0 pending
kb/communities/Trichoderma_Lactate_Platform.yaml CommunityMech:000075 e12191dd7b1c95d88b85136f635d1c33bcd7af642f105574fed48883dd2b1585 3 2 100.0 pending
kb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml CommunityMech:000270 d1652308f8e0e4f2fcebf880a03b8d0e311063a176bcaed2094983b038f59cea 3 2 100.0 pending
-kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml CommunityMech:000147 e7f148febf34a85e71939396d324dee6ebe45a5b0c4e404d185847d36dbaa81f 3 2 100.0 pending
+kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml CommunityMech:000147 0d2e03b468366edc434574c18f28c80e5f3ce5ebf4a69d31169fa647f6edcdd0 3 0 65.0 reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml reviewed
kb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml CommunityMech:000337 d85b790e5a06d3ac843b09fd66fa53917986a736d4f153bd37793f238d9e0aa6 4 2 100.0 pending
kb/communities/Urine_Nitrification_SynCom.yaml CommunityMech:000117 4bbd0c7a64269175c74f01c84e8d04eecb2907e16b890b7a33246733769fe9df 3 2 100.0 pending
kb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml CommunityMech:000213 bb21defe22c0f2ff7c483d725b1a4584223f1b0e164b09a0eccb3ab79ba445f0 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index ee3c377d6..5a24bf12d 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -3,13 +3,13 @@
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
"nodes": 1380,
- "edges": 543,
+ "edges": 539,
"records_without_nodes": 10,
- "records_without_edges": 185,
+ "records_without_edges": 187,
"review_status_counts": {
- "needs_research": 53,
- "pending": 45,
- "reviewed": 362
+ "needs_research": 54,
+ "pending": 42,
+ "reviewed": 364
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch113.json b/reports/causal_graph_review/validation-20261008-batch113.json
new file mode 100644
index 000000000..bcc89ad98
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch113.json
@@ -0,0 +1,1024 @@
+{
+ "base_commit": "7a920570e99167cd0e97083f1dbc32cc20c317b9",
+ "scope": [
+ "kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml",
+ "kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml",
+ "kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch113.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/focused.log",
+ "log_sha256": "af78259842a7603f343814db9d16841e38aade19d99e25626a0d4d904275cb66",
+ "output_tail": ".......... [100%]\n10 passed in 1.97s\n"
+ },
+ {
+ "check": "Thalassiosira_Marinobacter_Marine_Snow_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Marinobacter_Marine_Snow_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thalassiosira_Marinobacter_Marine_Snow_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch113/Thalassiosira_Marinobacter_Marine_Snow_Coculture-strict.tsv",
+ "kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Marinobacter_Marine_Snow_Coculture-strict.log",
+ "log_sha256": "a79fc43d1d0e5299fbacf35b9e5f2b9ddabe8d9e8728a44b83dfad4a414e2639",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch113/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-batch113/Thalassiosira_Marinobacter_Marine_Snow_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Thalassiosira_Marinobacter_Marine_Snow_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Marinobacter_Marine_Snow_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Thalassiosira_Marinobacter_Marine_Snow_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Marinobacter_Marine_Snow_Coculture-references.log",
+ "log_sha256": "eb6a90596eeaeeb6d25cf7b0bd73e0c24dddea8517bcf59956fc7953faf19718",
+ "output_tail": "Validating kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Thalassiosira_Marinobacter_Marine_Snow_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Marinobacter_Marine_Snow_Coculture-snippets.log",
+ "log_sha256": "2ffa6e242265b4c1c2eb555bd8bd14abb6cc63ed4d5a8a818da9b515db44daff",
+ "output_tail": "# 24 evidence snippets scanned across 1 files\n MATCH 24\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": "Thalassiosira_Marinobacter_Marine_Snow_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Marinobacter_Marine_Snow_Coculture-rank.log",
+ "log_sha256": "ea063803b9d68aad5ddbc37ec51e5293a6dcf666f7ee865dc4509800304a2f79",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000259\",\n \"name\": \"Thalassiosira-Marinobacter Marine Snow Coculture\",\n \"score\": 90.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 12,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Thalassiosira_Marinobacter_Marine_Snow_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Thalassiosira_Marinobacter_Marine_Snow_Coculture/2026-10-08T083138Z-codex-825172.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Marinobacter_Marine_Snow_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thalassiosira_Ruegeria_Phycosphere_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Ruegeria_Phycosphere_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thalassiosira_Ruegeria_Phycosphere_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch113/Thalassiosira_Ruegeria_Phycosphere_Coculture-strict.tsv",
+ "kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Ruegeria_Phycosphere_Coculture-strict.log",
+ "log_sha256": "2e50bc23aea0547835a2af7742566ff05306edaf3ee87ba185c2c45a617f549a",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch113/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-batch113/Thalassiosira_Ruegeria_Phycosphere_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Thalassiosira_Ruegeria_Phycosphere_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Ruegeria_Phycosphere_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Thalassiosira_Ruegeria_Phycosphere_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Ruegeria_Phycosphere_Coculture-references.log",
+ "log_sha256": "2eafead55f584bd751455b3044e2433b4e8c9a6df6107d524aaae59df9fb0c64",
+ "output_tail": "Validating kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Thalassiosira_Ruegeria_Phycosphere_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Ruegeria_Phycosphere_Coculture-snippets.log",
+ "log_sha256": "2ffa6e242265b4c1c2eb555bd8bd14abb6cc63ed4d5a8a818da9b515db44daff",
+ "output_tail": "# 24 evidence snippets scanned across 1 files\n MATCH 24\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": "Thalassiosira_Ruegeria_Phycosphere_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Ruegeria_Phycosphere_Coculture-rank.log",
+ "log_sha256": "b5c5ce67b542cbf9174d054d1e85f039cddbf5b8e9ed22021d5bfcb2056c54a8",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000162\",\n \"name\": \"Thalassiosira-Ruegeria Phycosphere Coculture\",\n \"score\": 68.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Thalassiosira_Ruegeria_Phycosphere_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Thalassiosira_Ruegeria_Phycosphere_Coculture/2026-10-08T083139Z-codex-dd87e7.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Thalassiosira_Ruegeria_Phycosphere_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Trichodesmium_Alteromonas_Marine_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Trichodesmium_Alteromonas_Marine_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Trichodesmium_Alteromonas_Marine_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch113/Trichodesmium_Alteromonas_Marine_Consortium-strict.tsv",
+ "kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Trichodesmium_Alteromonas_Marine_Consortium-strict.log",
+ "log_sha256": "a12497ca0d9e386b54a7ef6f7e87f929bc6a417e2ff763c77ad664f4f443bd90",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch113/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-batch113/Trichodesmium_Alteromonas_Marine_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Trichodesmium_Alteromonas_Marine_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Trichodesmium_Alteromonas_Marine_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Trichodesmium_Alteromonas_Marine_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Trichodesmium_Alteromonas_Marine_Consortium-references.log",
+ "log_sha256": "b45d72556a58a9ae3aa8d60e9ac21a2d63d74747effe9c8cb834b5d051360f39",
+ "output_tail": "Validating kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Trichodesmium_Alteromonas_Marine_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Trichodesmium_Alteromonas_Marine_Consortium-snippets.log",
+ "log_sha256": "8084678f5cf248d78dd90bd74538a6320ef0dcc9940ae3e5b5f759e13588ade6",
+ "output_tail": "# 19 evidence snippets scanned across 1 files\n MATCH 19\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Trichodesmium_Alteromonas_Marine_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Trichodesmium_Alteromonas_Marine_Consortium-rank.log",
+ "log_sha256": "2a0357c662893690ade3bb40106a52f6b90b646328e1ee136fd5d32c4b53a671",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000147\",\n \"name\": \"Trichodesmium-Alteromonas Marine Consortium\",\n \"score\": 65.0,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Trichodesmium_Alteromonas_Marine_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Trichodesmium_Alteromonas_Marine_Consortium/2026-10-08T083139Z-codex-a37037.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/Trichodesmium_Alteromonas_Marine_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "inventory",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "reports/causal_graph_review/build_inventory.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/inventory.log",
+ "log_sha256": "bf935b322150eac84ef82e5b8853d2d69a22c6ebf069c26260c9bcb9a5eedb59",
+ "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\": 1380,\n \"edges\": 539,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 187,\n \"review_status_counts\": {\n \"needs_research\": 54,\n \"pending\": 42,\n \"reviewed\": 364\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-batch113/verification/network.log",
+ "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+ "output_tail": " \"total_genomes\": 17191,\n \"is_reclassified\": false,\n \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n },\n \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"mexZ\"\n },\n \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n \"evidence\": [\n {\n \"reference\": \"PMID:42153623\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/just-network-json.log",
+ "log_sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/rank-all.log",
+ "log_sha256": "d749a76e6f0ef826166673cf1e4f31cb7562d44f970826fd691c5dc3296b4961",
+ "output_tail": "Model Community\t3\t3\t0\t4\t2\t8\tinteraction_type\t0\t0\n402\t97.5\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t8\tinteraction_type\t0\t0\n403\t97.5\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\t8\tinteraction_type\t0\t0\n404\t97.9\tkb/communities/Maize_Drought_Response_SynCom.yaml\tCommunityMech:000103\tMaize Drought Response SynCom\t1\t1\t0\t7\t7\t8\tmetabolites_or_biological_processes\t0\t0\n405\t98.3\tkb/communities/Populus_Salt_Tolerant_SynComs.yaml\tCommunityMech:000090\tPopulus Salt-Tolerant Rhizosphere SynComs\t1\t1\t0\t3\t2\t3\tmetabolites_or_biological_processes\t0\t0\n406\t98.3\tkb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml\tCommunityMech:000404\tWollastonite Ramichloridium-Talaromyces Fungal Consortium\t2\t2\t0\t3\t2\t5\tmetabolites_or_biological_processes\t0\t0\n407\t98.8\tdata/isolates/Chromobacterium_Gold_Biocyanidation.yaml\tCommunityMech:000273\tChromobacterium Gold Biocyanidation Platform\t1\t1\t0\t4\t2\t7\tmetabolites_or_biological_processes\t0\t0\n408\t100.0\tdata/isolates/Aspergillus_Indium_LED_Recovery.yaml\tCommunityMech:000320\tAspergillus Indium LCD Recovery Platform\t1\t1\t0\t5\t4\t6\t\t0\t0\n409\t100.0\tdata/isolates/Methylobacterium_REE_Ewaste_Platform.yaml\tCommunityMech:000322\tMethylobacterium REE E-waste Platform\t1\t1\t0\t4\t2\t6\t\t0\t0\n410\t100.0\tkb/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.yaml\tCommunityMech:000276\tANME/SRB Anaerobic Methanotrophic Syntrophic Consortia\t6\t6\t0\t3\t2\t7\t\t0\t0\n411\t100.0\tkb/communities/Anabaena_MGS1_Anaerobic_Digestion_Methanogen_Consortium.yaml\tCommunityMech:000307\tAnabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium\t1\t1\t0\t5\t2\t7\t\t0\t0\n412\t100.0\tkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml\tCommunityMech:000245\tAvena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds\t1\t1\t0\t5\t2\t7\t\t0\t0\n413\t100.0\tkb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml\tCommunityMech:000142\tBacteroides-Methanobrevibacter Gnotobiotic Mouse Mutualism\t2\t2\t0\t3\t2\t3\t\t0\t0\n414\t100.0\tkb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml\tCommunityMech:000012\tBioModels MODEL2405300001 Infant Gut HMO SynCom\t13\t13\t0\t3\t2\t6\t\t0\t0\n415\t100.0\tkb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml\tCommunityMech:000215\tCalifornia Grassland Precipitation Legacy Soil Community\t1\t1\t0\t3\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml\tCommunityMech:000089\tCellulose-to-Methane Quad-Culture SynCom\t4\t4\t0\t6\t5\t9\t\t0\t0\n417\t100.0\tkb/communities/DVM_Triculture.yaml\tCommunityMech:000021\tDVM Tri-culture\t3\t3\t0\t4\t2\t7\t\t0\t0\n418\t100.0\tkb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml\tCommunityMech:000301\tDehalococcoides mccartyi CWV2 Dechlorinating Consortium\t1\t1\t0\t5\t2\t6\t\t0\t0\n419\t100.0\tkb/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.yaml\tCommunityMech:000296\tEscherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.yaml\tCommunityMech:000350\tHigh-Ammonia Biogas 0B Butyrate-Oxidizing Enrichment\t4\t4\t0\t3\t2\t6\t\t0\t0\n421\t100.0\tkb/communities/Honeybee_Core20_Defined_Microbiota.yaml\tCommunityMech:000124\tHoneybee Core-20 Defined Microbiota\t1\t1\t0\t3\t2\t3\t\t0\t0\n422\t100.0\tkb/communities/Microbacterium_Terrabacter_Sulfadiazine_CrossFeeding_Coculture.yaml\tCommunityMech:000462\tMicrobacterium-Terrabacter Sulfadiazine Cross-Feeding Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.yaml\tCommunityMech:000157\tMicrocoleus-Massilia Cyanosphere Urea Mutualism\t2\t2\t0\t3\t2\t5\t\t0\t0\n424\t100.0\tkb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml\tCommunityMech:000119\tMultiomics Corn Straw Degradation SynCom\t1\t1\t0\t4\t3\t9\t\t0\t0\n425\t100.0\tkb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml\tCommunityMech:000156\tNeocallimastix-Methanobrevibacter Xylanolytic Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n426\t100.0\tkb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml\tCommunityMech:000190\tPelotomaculum-Methanocella Propionate RNA-Seq Coculture\t2\t2\t0\t4\t2\t9\t\t0\t0\n427\t100.0\tkb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\tCommunityMech:000052\tPelotomaculum-Methanothermobacter Syntrophic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n428\t100.0\tkb/communities/Phenol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n429\t100.0\tkb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml\tCommunityMech:000290\tPhosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture\t2\t2\t0\t3\t2\t4\t\t0\t0\n430\t100.0\tkb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml\tCommunityMech:000289\tPseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n431\t100.0\tkb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml\tCommunityMech:000092\tRhodopseudomonas-E. coli Cross-Feeding Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n432\t100.0\tkb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml\tCommunityMech:000109\tRice Acid Soil Bioinoculant SynCom\t1\t1\t0\t4\t4\t4\t\t0\t0\n433\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t4\t2\t4\t\t0\t0\n434\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n435\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n436\t100.0\tkb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\tCommunityMech:000100\tTeosinte-Derived Maize Biofertilizer SynCom7\t4\t4\t0\t6\t2\t12\t\t0\t0\n437\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n438\t100.0\tkb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\tCommunityMech:000282\tThermophilic Lignocellulose-degrading Composting SynCom\t5\t5\t0\t3\t2\t3\t\t0\t0\n439\t100.0\tkb/communities/Thermophilic_Pyrite_QS_Consortium.yaml\tCommunityMech:000073\tThermophilic Pyrite Quorum Sensing Consortium\t3\t3\t0\t6\t2\t14\t\t0\t0\n440\t100.0\tkb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\tCommunityMech:000186\tThermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\t2\t2\t0\t3\t2\t8\t\t0\t0\n441\t100.0\tkb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml\tCommunityMech:000239\tThiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community\t3\t3\t0\t3\t2\t3\t\t0\t0\n442\t100.0\tkb/communities/Tinto_River_Iron_Cycling_Community.yaml\tCommunityMech:000074\tTinto River Iron Cycling Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n443\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n444\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n445\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n448\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/render.log",
+ "log_sha256": "a6504ed754052aab2e60d23de6072c2ecf048fe2c077a455bebe2dbb7450ee19",
+ "output_tail": "unitymech-causal-batch113/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch113/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch113/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch113/docs/index.html\n"
+ },
+ {
+ "check": "render-repeat",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/render-repeat.log",
+ "log_sha256": "a6504ed754052aab2e60d23de6072c2ecf048fe2c077a455bebe2dbb7450ee19",
+ "output_tail": "unitymech-causal-batch113/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch113/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch113/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch113/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch113/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']()))"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/connectivity-survey.log",
+ "log_sha256": "6ced8e07d41f815c4aba1ab0dc77c4d7dfc5a271e0d36842bb2cfbb8da94e02d",
+ "output_tail": "{\"records\": 460, \"with_community_level\": 412, \"mixed\": 136, \"community_level_only\": 276, \"taxa\": 1563, \"credited_solely_by_the_rule\": 1273}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_batch107.py",
+ "tests/test_causal_review_batch108.py",
+ "tests/test_causal_review_batch109.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch110.py",
+ "tests/test_causal_review_batch111.py",
+ "tests/test_causal_review_batch112.py",
+ "tests/test_causal_review_batch113.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-batch113/verification/regressions.log",
+ "log_sha256": "4527e0a3f81c7da9e88756f76e89a8d9d5d95da1b4b9c0ef6e7c0914bc6bad1c",
+ "output_tail": "........................................................................ [ 7%]\n........................................................................ [ 14%]\n........................................................................ [ 21%]\n........................................................................ [ 28%]\n........................................................................ [ 35%]\n........................................................................ [ 42%]\n........................................................................ [ 49%]\n........................................................................ [ 56%]\n........................................................................ [ 63%]\n........................................................................ [ 70%]\n........................................................................ [ 77%]\n........................................................................ [ 84%]\n........................................................................ [ 91%]\n........................................................................ [ 98%]\n................ [100%]\n1024 passed in 306.57s (0:05:06)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/just-lint.log",
+ "log_sha256": "35f88d8bfb625d1f4196da0175f92edd5c4500ce42238965d5301be4fce9d3ee",
+ "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n366 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n"
+ },
+ {
+ "check": "mypy-explicit-runtime",
+ "command": [
+ "/private/tmp/communitymech-batch100/lint-env/bin/mypy",
+ "--no-incremental",
+ "--python-executable",
+ "/private/tmp/communitymech-batch100/lint-env/bin/python",
+ "src/"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/mypy-explicit-runtime.log",
+ "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875",
+ "output_tail": "Success: no issues found in 49 source files\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/audit-snippets-all.log",
+ "log_sha256": "d388cb9c44ba828e5129cfd8f3f8599108b629187388b3afb3afd8f887f09991",
+ "output_tail": "# 9017 evidence snippets scanned across 460 files\n MATCH 8872\n RENDERING 28\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch113/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Fresh pre-source baseline across both roots:460 records,923 caches,56 warnings,zero structural defects. All10 existing nodes/6directions reviewed;10nodes/2directions retained,4unsupported arrows removed. No new topology.",
+ "Three whole canonical records and existing snippet evidence read. Fresh primary metadata/abstracts and Crossref identities for nine sources; MEPS has no retrieved abstract. Full fresh extracted main bodies:2014future-ocean1-167,HP15genome1-89,2020partitioning1-163. Table1 of the 2020 paper also parsed as structured XML to confirm the Ruegeria column.",
+ "Full PDF extracted text read:2011aggregation pages1-10 from existing user PDF,2017recognition pages1-14 from WHOI,2017Trichodesmium pages1-12 from author research site. Visual review:aggregation pages5/6/8(Figs1/2/3/5),recognition pages2/3/8(Figs1/2/4),Trichodesmium pages7/9(text and Fig3). Other figure pixels, separate supplements and raw data not reviewed.",
+ "2018diel existing curator TXT read lines1-810, including abstract,complete main body and beginning references; reference-list tail not read. Fresh primary abstract independently retrieved. FullTextXML attempts failed for aggregation,chemotaxis,Trichodesmium2017 and diel2018. Chemotaxis graph is abstract-bounded; MEPS public PDF returned401 twice, no bypass or full-paper claim. Existing caption retained PARTIAL and not treated as proof of all TEP chemistry.",
+ "No PDFs or publication bodies added to the repository;923 existing caches untouched. Graph/discussion quote matches are independently checked against fresh primary texts except one existing MEPS caption-only quote. Cache matching is not entailment or Linux reference-loader certification. Some long cache bodies were not read in full; the independent primary bodies and existing target snippets were reviewed.",
+ "HP15 preserves positive2011and null2014assay effects; no universal attachment/TEP/aggregation/sinking chain, no measured ocean sequestration. Inactivation has possible surface/exudate confounding. Mutant attachment and abiotic biofilm phenotypes are not selective aggregation mediation.",
+ "Ruegeria preserves supported organic-carbon feeding and transcript responses. DMSP/GlcNAc expression and proline/guanosine net drawdown have distinct evidence grades; net depletion is not a traced transfer flux.2017B12-limited growth rescue is distinct from laterL1assay. Missing reciprocal B12topology remains needs_research in1883.",
+ "Trichodesmium association,genomic complementation and field coexpression are distinct evidence levels. Preserve potential helper mechanisms andROScompound/process#297; vitamin provision is proposed host-to-epibiont and2017facultativeuse must not become obligatory dependence. Field node does not assert exactIMS101orA.macleodii membership; only canonical microbiome guild is credited there. Non-graph identity issues remain1886.",
+ "Issue-title/body dedup covered all1124existing issues initially and a fresh pre-creation sweep; nine matching issue bodies read. Ignored/hidden-inclusive local path index covers128files,excluding.git/docs/site/references_cache/.env,not all historical file bodies. Historical PR comments were not exhaustively searched.",
+ "Edison one-community dry run completed. Scope-specific credit-spending invocation authorized by execution approval, then stopped in load_api_key before client creation:configured key unavailable. No task submitted,report received or provider credit spent. User asked to configure key securely. Previous denied and unanswered scopes not retried. No absence claim about credentials elsewhere.",
+ "Non-graph blocks,457otherrecords,923caches and prior histories preserved. No runtime/schema/validator changes. Required validation and measured census are recorded separately; self-review is not independent approval. Issues remain open until protected-main merge or separately verified followup. RootCI blocker1836 forbids invented CI or premature merge/branch cleanup."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml": {
+ "MATCH": 24,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml": {
+ "MATCH": 24,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml": {
+ "MATCH": 19,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 457,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 46,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": true,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [
+ {
+ "target": "CommunityMech:000162",
+ "artifact": "/private/tmp/communitymech-batch113/edison-dry-run/Thalassiosira_Ruegeria_Phycosphere_Coculture-edison-literature-causal-meta.yaml",
+ "sha256": "4e371d688d522e5288bf5f0ed47abf41785e62199d53466e58d450627fdd90b1",
+ "query_sha256": "1b2797a8920505adf873e50a02f8827e5aa23ac5e5aa8387603ef7310bb42e67"
+ }
+ ],
+ "authorized_invocations": 1,
+ "invocation_exit_code": 1,
+ "blocked_stage": "load_api_key before client creation",
+ "task_id": null,
+ "blocker": "Configured Edison key unavailable; no other credential locations inspected.",
+ "issue": 1883,
+ "repair_scope": "Existing-node evidence/scope corrections and removal of four unsupported arrows; no added nodes or directions."
+ },
+ "primary_artifacts": {
+ "/Users/marcin/Documents/VIMSS/ontology/KG-Hub/KG-Microbe/Mechs/CommunityMech/references_cache/files/PMID_20827289.pdf": "c40b3aae947563128b03f872f642c6536a02e7ee45c4b683eb4378c38dc566de",
+ "/private/tmp/communitymech-batch113/aggregation-abstract.txt": "6602a281735718e8d20d977d6b57a3a44c1b62945737647b86ba339130610273",
+ "/private/tmp/communitymech-batch113/aggregation-crossref.json": "7d98024e3648863fbd53a23c894c640f8b49da36a5cd7e26cb0c742808ce9366",
+ "/private/tmp/communitymech-batch113/aggregation-metadata.json": "042e636f0aa5a0adaee6122d75475f8699d5c77d2bccd0eadbd5e54f41bb418f",
+ "/private/tmp/communitymech-batch113/baseline.json": "e4e0d15e305843d5a7dc342cd390e15fed00e3d022b87656cd9c17c074e5dd9b",
+ "/private/tmp/communitymech-batch113/chemotaxis-abstract.txt": "52802fe41fbc850bf7e3d66dcbd8d25b1b9851c4056cb710a0d0138ddf0baca6",
+ "/private/tmp/communitymech-batch113/chemotaxis-crossref.json": "b8837a95cc8c934ec3f30a92481715d1bf1ae54530f11e91899aa4f536bb5dce",
+ "/private/tmp/communitymech-batch113/chemotaxis-metadata.json": "edd759fb7ae40d70e9250490c0bcd8777e12c0fdb52c9f174968af8b1ad2fa1b",
+ "/private/tmp/communitymech-batch113/chitin_fibres-crossref.json": "b4e2a85dc4026196d90842079c53fd97c4412c6d688d0798fc83b5a4324c97f9",
+ "/private/tmp/communitymech-batch113/chitin_fibres-metadata.json": "46c175c7c1bedf3d5063f4085a81414bf839cc88a7837d5f1e2e3195797962df",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-abstract.txt": "d3f04faaac74cdabf7e42e93a97804f4efae39c8ae31cc5f5031c046399759f5",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-crossref.json": "8fbe1add7e0d17867c975e94ab91e6a35c3dd1e83924c0adcf7eac616ed42e50",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-metadata.json": "ff0c87dcffb15d9a6e073330db0b59ef3e0b7590987b7c97a8ad8765d75e2b81",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-primary.txt": "f06ba6d9c770005c9271e24bd5f89c87eedd34672b874ea147116e43275d125b",
+ "/private/tmp/communitymech-batch113/diatom_partitioning-primary.xml": "1aa91708805c535b3b9363e3510400d97fb1b40c78f93864a93a6f71d47ab502",
+ "/private/tmp/communitymech-batch113/diatom_recognition-abstract.txt": "03ec4e345f442b5d3af2d277174d529850174cc13ebf7f6af18ecabe9ab4d36d",
+ "/private/tmp/communitymech-batch113/diatom_recognition-crossref.json": "e59d76b0c2834c32d634bbe696498138f0b6b8061ebd36fddd1084adc91262e5",
+ "/private/tmp/communitymech-batch113/diatom_recognition-metadata.json": "b5b2825c12c9b91976b88c021b20952abf36464383303350484c43db92cfc79f",
+ "/private/tmp/communitymech-batch113/edison-dry-run/Thalassiosira_Ruegeria_Phycosphere_Coculture-edison-literature-causal-meta.yaml": "4e371d688d522e5288bf5f0ed47abf41785e62199d53466e58d450627fdd90b1",
+ "/private/tmp/communitymech-batch113/future_ocean-abstract.txt": "e9c5914658fcdc16f5b7fa8f590bfabb8c823db78c34d6d4f9222cc308ebd3c2",
+ "/private/tmp/communitymech-batch113/future_ocean-crossref.json": "ca69baa7ea820aad173c3d7367e99167e3167ea10ab09df079ed5610986eb2ae",
+ "/private/tmp/communitymech-batch113/future_ocean-metadata.json": "fdc42361e42c671d2693c8390d07ec17493fbc312eba91175bafba286ec40958",
+ "/private/tmp/communitymech-batch113/future_ocean-primary.txt": "643dcf6d94231c8e5ecb3657a5927876e74f6671e1ab08b79a97f65d36609658",
+ "/private/tmp/communitymech-batch113/future_ocean-primary.xml": "c7a2bd9e1d67cdcce76f95fc965b503964adbfd396c1322b7de99c9ce2db8ee0",
+ "/private/tmp/communitymech-batch113/hp15_genome-abstract.txt": "56b86a60698dc26e66213325e02057af921d875ae053bf2174d5d5da7fe695ae",
+ "/private/tmp/communitymech-batch113/hp15_genome-crossref.json": "49c7c5fa7d8757f1895f0fe25258191e5c0abdd6666636a0eee02e68528638e0",
+ "/private/tmp/communitymech-batch113/hp15_genome-metadata.json": "ffde0cc61de9fb5c78f24c2114510140c1c7afc6769d4b4132309b3fdab4ba53",
+ "/private/tmp/communitymech-batch113/hp15_genome-primary.txt": "927d5b049d31e29a3fe1a743cd900d813c1b0d8552ea792591d0e25ba8604cc8",
+ "/private/tmp/communitymech-batch113/hp15_genome-primary.xml": "0d6d31ae955dc9d1e27bcb5e49006689781a2b431a8fa53d87e0ed618b5f1e44",
+ "/private/tmp/communitymech-batch113/issue-dedup-current.json": "0052884b3bd38111520cbcd972261bce41d6ea21a2d814fd8a12e639a60e3613",
+ "/private/tmp/communitymech-batch113/local-matches.txt": "b002a9b7318d558c6fbba824a6b08e7521cc6b447fdb55ee2dc8e4a1bc125423",
+ "/private/tmp/communitymech-batch113/pdf-manifest.json": "ae11c81da4dec2e934c528b756c2a17ddffb11de6b13ae1ea2d71c5658780cbd",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-01.txt": "3ca0dd5312a023f6faa23e7fd34fbb8760b6b4e92b59f4744c478aa7584ff8ff",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-02.txt": "17502c1554503852058f015da583d68779bb51eb0a7e94c886774222a459401c",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-03.txt": "333425fd1c5fddaa54ee1120b44cca33100f0402d40c3759a800e75961a23a20",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-04.txt": "1592eaa05916cf3cbbd8b8e6d4f1df2d0361060d0b2a1c0f4042d7301b87cf2c",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-05.png": "db0766cda461e14083662eb40a1319d004be9689dd344d9bd005ea8c5e91af87",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-05.txt": "4e68b8ba881ca3cfb3130b477480a0b250b9d0333a8832c3131c627d6314978e",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-06.png": "8be896d575bb77ef4615f9fc3c85ec0859803617fc83e5f1736e04c3081e0115",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-06.txt": "95f842cab62873a04aa9fb666afa751da11ee1c3ac1cfb48306d41ffd98c1b01",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-07.txt": "2f06474d0c9f57ac021b64cb387c98039b501cca2854f3beeb13067b383b706e",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-08.png": "73b0a74b662f43f55efd26c78da9f0866dc3de53da4a030348c8eaf22b00fc50",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-08.txt": "23fd88022c3dae270f937ad15e538b5bb56113f7b1cd375e4aedd79d537c8a1f",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-09.txt": "dab70e059d5078aec9e2298148555596516cbb8e5be0c292ef672d46b5f4fdab",
+ "/private/tmp/communitymech-batch113/pdf-review/aggregation-page-10.txt": "b3d0dcd53c62215c225a10113863af68364f29a767e7b421c3ae835ed0cf643b",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-01.txt": "0c322412036dce7d93dd6dae1417e85b2b57a0f9b7fb98d42c9e3564b7dd0254",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-02.png": "4290234ee4fda993cc7973a862c55d4ad9b314ed08163230172e9914d68f1eca",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-02.txt": "736f8995b4e5468e6576acb30251e611bdcd8dcafa136f603f1374bdbaa986a9",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-03.png": "537e9af50077e8009213d2742ca5a9d9f989e74f5eca996deeddb2016f56fb12",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-03.txt": "13961998655e22b08b248dd72c2151a09d04379928eb0e3b14158effbd0b04fe",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-04.txt": "2607cc78a086788a0dab7647197749939fd0c021d52284f1a776dbbfb2e33044",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-05.txt": "30dc900193c467c48cd65cb9e5ac5ed84c9789fb1cd9f724aceae35af70f5ec5",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-06.txt": "99b89945ec9575f42377832689119926ae8bef63c5273a99cb2aac67cbd564e3",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-07.txt": "71fe8010e6b338fffed8a7d2488b76d57eb97762ac8b597489a1b91469c595b2",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-08.png": "4758d41e8d1230f3ddb8a49e9dbfd5da25693b9dd33dadfc20bb6e634812d543",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-08.txt": "385df38e55fdcd0419d68e38a575d7df3fa64bcedd5b1b6fb780eb35769ff8a7",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-09.txt": "7f66b550ad1699c3986f83c4e69a5fa35990918cbc79e7b01df9ee7988cd42c3",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-10.txt": "221790525e2cb7f41d9dfea2a312215ba7a4e95d3bf947e2540cbfb1b4c8fe2f",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-11.txt": "ddae72d484a907acd045f6ba35270b3376faaa3b5b6bbfcc7c98cc07d808ee77",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-12.txt": "b15f9c38c4aa6ae3e9c87c0a2b02bf5ea3e6f369cfc5b41f4417f3dcd1c7717e",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-13.txt": "a3f0e4bf51455bc042687d10069b3b26530a95f5c48b3c042cd927d8a6b19f62",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition-page-14.txt": "aeb41bc3ed63d5079300c1eac128e550afe878c95d70a516e52f594aabe5809f",
+ "/private/tmp/communitymech-batch113/pdf-review/diatom_recognition.pdf": "e37b48578e4a79183fb623596dc16fa3b9f3a4b476a537f4a7004f51cf0eedcc",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-01.txt": "ec50ca0d007c60e2150f15bd06150d6110e2dacc6aa6a739d80d8e10186beb40",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-02.txt": "26fe7f54a1936c2e06378014ed292b7e949eaa23e2eb03ae691ddfcdd5ffe10e",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-03.txt": "2986b3409b3dab656003a962431d6df2f97815edf9854bf461c1032b70ad83fe",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-04.txt": "1ceb990e8eb0a10830fc2b964019caa452531a0cb8e2601593be4a2dea0f807a",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-05.txt": "efaa89ffc5ae9f2f893f71ab67695a192cdde1520a32fcebfa12d21994ec3f5b",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-06.txt": "a1b9f112d4960b7e117b73df6a03fbf6ddb240cbe6782e3e51b369b6b04dd47e",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-07.png": "07d75b761276a419f616d8f38309dba1b2bb44d51c240a3f260b7f33a77f5160",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-07.txt": "e2caca889b886984f65492720e90c4c7144fb1a041367906c5a50c78fe384ac8",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-08.txt": "bb835fd938aa03cb04ff3765b650bee0c01fc7f14579c044a00045b8da086b69",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-09.png": "e99752f6f2bb5cc29aa9af074d1f189629f7c7a46caa71aefe21249c40cbb08f",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-09.txt": "51b694b8b6e620ce39ead86279b6dd97660956b1a937b50e0a6cbc8c750d5d1b",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-10.txt": "a18720a2e20dfe3fd30265523de3524a489654a42ff9e0fb0894910e6657f204",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-11.txt": "ce882142f780b31cc942954c34047a4e1259c92954c474d4f41e3f9b4e7fad51",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes-page-12.txt": "c04322725772e971985af10ae271489357e58a19b95e3ffc6e2722cd28191137",
+ "/private/tmp/communitymech-batch113/pdf-review/tricho_genomes.pdf": "3f6744880efd09ebfabe7c73682a5ce426575808c0b5c37b9f4dffc839f5da2c",
+ "/private/tmp/communitymech-batch113/primary-manifest.json": "54a487b8908feffa1feeed66fe7a60d59ee199d4755315503570e30299764f0b",
+ "/private/tmp/communitymech-batch113/rendered-figures.json": "7f9d1adf428f3c7ecc9b70cb3596ba4fbe80328036334d1e2adab66554921344",
+ "/private/tmp/communitymech-batch113/tricho_diel-abstract.txt": "991a5c5ccd82ebc4b1cb28a30182531c400708afd1f6c016def1f26764fed644",
+ "/private/tmp/communitymech-batch113/tricho_diel-crossref.json": "47a61b55e624a103901753ca83e8afd6367cbdabd0237ec852d15da8571ee4c1",
+ "/private/tmp/communitymech-batch113/tricho_diel-metadata.json": "cf30eb8d10292d1380ab625e26b77f1a7df7e4bcf3f49376a17b2aa226793136",
+ "/private/tmp/communitymech-batch113/tricho_genomes-abstract.txt": "17cbacbd2658c364b7e40e4a6e49d1107791b1729748f9fb21e147e79132f60a",
+ "/private/tmp/communitymech-batch113/tricho_genomes-crossref.json": "3a57b6801019907afe7a4dce0c16f384b6b76817b82ca70113854da655acc840",
+ "/private/tmp/communitymech-batch113/tricho_genomes-metadata.json": "20b87c1043e018e6f15da964a2419d6330ba35c11c1441bf1db44f8f9d153d7c",
+ "references_cache/PMID_20827289.md": "7886cc9bd5fb04794399faec79365aadb7045538a37bb29cf9cd72f1cf96f19e",
+ "references_cache/PMID_22820333.md": "b5e59d9bd1f234d9e34c96b3ec72f7af9a197633cd7f6abc0d6c5fcb4bad2451",
+ "references_cache/PMID_25375640.md": "b0acc6fc72bf7d22e01ccd22c51600e0ec337f30e91898732cee0875d42d8e16",
+ "references_cache/PMID_28440800.txt": "42d9afaeca8e20c30ceccab47e452631af33fd4c10d8d2e642e74e907598e7fa",
+ "references_cache/PMID_28631440.txt": "a64edc7b5bcf844fd640ad24b402260a7ed7a2f6389325dabe815123fce5f7b8",
+ "references_cache/PMID_29382945.txt": "822a4f5f9029897f4316affee3951d724ea2612862499c05ef30a7c832e27af6",
+ "references_cache/PMID_33097854.md": "a8e47a63b081b28ca3075345c1700e0abea0b46a18b64b4a4337df7781440d89",
+ "references_cache/doi_10.3354_meps09894.md": "b7de73cd4e0d3af39fabf09d998e038348d20305cb6e539f1b183e2d84d0df31",
+ "references_cache/doi_10.4056_sigs.922139.md": "139c13b694456bd96672197ec8d8f0de1b40fbfd561511c2ba850aa2d6a1c2b7"
+ },
+ "immutable_prior_history_and_decision_files": 858,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 21,
+ "discussion_quotations": 3,
+ "fresh_primary_literal_matches": 23,
+ "existing_caption_only": 1,
+ "all_cached_literal_matches": 24,
+ "retained_nodes": 10,
+ "removed_nodes": 0,
+ "renamed_nodes": 6,
+ "retained_arrows": 2,
+ "removed_arrows": 4,
+ "new_nodes_or_directions": 0
+ },
+ "network_delta": {
+ "existing_findings_preserved": 56,
+ "added_findings": {},
+ "removed_findings": {},
+ "structural_defects": 0
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1366,
+ "arrows": 531
+ },
+ "render_scope": "Deterministic rendering and exact HTML description parsing, not screenshots; postcommit docs-current still required.",
+ "participant_census": {
+ "current": {
+ "records": 460,
+ "with_community_level": 412,
+ "mixed": 136,
+ "community_level_only": 276,
+ "taxa": 1563,
+ "credited_solely_by_the_rule": 1273
+ },
+ "delta_from_batch112": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "explanation": "Two new explicit participant-list users; overall connectivity census unchanged. No connectivity rule or share-guard changes."
+ },
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary established Python3.13 lint environment; project dependencies unchanged."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 9017,
+ "categories": {
+ "MATCH": 8872,
+ "RENDERING": 28,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 40,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Informational audit exit0 is not clean-corpus or entailment certification.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1380,
+ "edges": 539,
+ "records_without_nodes": 10,
+ "records_without_edges": 187,
+ "review_status_counts": {
+ "needs_research": 54,
+ "pending": 42,
+ "reviewed": 364
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml": "37a32697693f1a6298e472ddb74f6b9688b9d08b2902f4830c975c9f4f9b0f39",
+ "tests/test_causal_review_batch113.py": "84a0d66a0b217512ecca6a4988cd20009a0924f90a68eadce3da56c0aa7868d0",
+ "tests/test_participating_taxa.py": "a7daf71d4b29c7849293647ab82e6dbf828a42c88b26130eb0e39e9ffd3ee6ca",
+ "reports/causal_graph_review/cache-provenance-20261008-batch113.json": "6287cbceda5407c04d63c12b9739b6041e3824a6de5013ddde13f614796bfc09",
+ "kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml": "8b79efb0b04a43548b3c73ac280ac987b83c4e97f2531b55da5c940f29485eae",
+ "kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml": "f1e51614a8c4a7856a2669afe12574d1c982f12dcebf9f53f49c65d470f747d6",
+ "kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml": "0d2e03b468366edc434574c18f28c80e5f3ce5ebf4a69d31169fa647f6edcdd0"
+ },
+ "pre_research_baseline": {
+ "base_commit": "7a920570e99167cd0e97083f1dbc32cc20c317b9",
+ "base_tree": "9b2e9b908db769aa738f4a1358c20ec30433c1c3",
+ "research_worktree": "/private/tmp/communitymech-causal-batch113",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch113/baseline-rank.log",
+ "sha256": "9ee12c0f49c1240ac75a110e5186cb879515668008fd9b278658fbee139f4c2a"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch113/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-batch113/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-batch113/baseline-downstream.log",
+ "sha256": "39909032a9bbdb5fb0c5fb82b12d8c69aa9768492606977789f5f99525037c65"
+ }
+ ],
+ "baseline_sha256": "e4e0d15e305843d5a7dc342cd390e15fed00e3d022b87656cd9c17c074e5dd9b"
+ },
+ "reference_validator_caveat": "Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment. Total checks in the reference CLI counts issues, not examined snippets.",
+ "status": "verified_existing_graph_repairs_with_unfinished_ruegeria_extension",
+ "total_recorded_gate_outputs": 34
+}
diff --git a/tests/test_causal_review_batch113.py b/tests/test_causal_review_batch113.py
new file mode 100644
index 000000000..507a2ed8e
--- /dev/null
+++ b/tests/test_causal_review_batch113.py
@@ -0,0 +1,147 @@
+"""Preserve marine assay boundaries and distinguish correlation from causation."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-three-records-batch113.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_hp15_positive_and_null_aggregation_results_remain_distinct():
+ _, _, docs = records()
+ aggregation = docs[0]["ecological_interactions"][0]
+ assert aggregation["scope"] == "COMMUNITY_LEVEL"
+ assert "interaction_type" not in aggregation
+ assert "not a universal bacterial requirement" in aggregation["description"]
+ assert "much less, not uniformly zero" in aggregation["description"]
+ assert aggregation["evidence"][-1]["reference"] == "PMID:25375640"
+ assert "independent of the presence" in aggregation["evidence"][-1]["snippet"]
+
+
+def test_tep_is_not_directed_feeding_or_a_universal_aggregation_driver():
+ _, _, docs = records()
+ aggregation, tep, _, _ = docs[0]["ecological_interactions"]
+ assert tep["scope"] == "COMMUNITY_LEVEL" and "interaction_type" not in tep
+ assert "warmer treatments generated more TEP but less aggregation" in tep["description"]
+ assert tep["evidence"][2]["supports"] == "PARTIAL"
+ assert "not the identity of all TEP" in tep["description"]
+ assert tep["downstream"][0]["target"] == aggregation["name"]
+ assert tep["downstream"][0]["description"].startswith("PARTIAL:")
+
+
+def test_attachment_perturbation_does_not_demonstrate_aggregation_mediation():
+ _, _, docs = records()
+ attachment = docs[0]["ecological_interactions"][2]
+ assert "interaction_type" not in attachment
+ assert (
+ "fraction of bacteria attaching to the diatom decreased"
+ in attachment["evidence"][1]["snippet"]
+ )
+ assert "abiotic surfaces" in attachment["description"]
+ assert attachment["downstream"][0]["description"].startswith("HYPOTHESIZED:")
+ assert "not selective mediation" in attachment["downstream"][0]["description"]
+
+
+def test_export_interpretation_is_not_niche_partitioning_or_measured_field_flux():
+ _, _, docs = records()
+ export = docs[0]["ecological_interactions"][3]
+ assert "interaction_type" not in export and "downstream" not in export
+ assert "not a measured field flux" in export["description"]
+ assert all(e["supports"] == "PARTIAL" for e in export["evidence"])
+
+
+def test_ruegeria_recognition_and_chitin_response_are_not_exchange_or_mediation():
+ _, _, docs = records()
+ recognition, feeding, response = docs[1]["ecological_interactions"]
+ assert all("downstream" not in n for n in [recognition, feeding, response])
+ assert "interaction_type" not in recognition and "interaction_type" not in response
+ assert feeding["interaction_type"] == "CROSS_FEEDING"
+ assert "not selectively demonstrated" in recognition["description"]
+ assert "B12-replete axenic controls" in response["description"]
+ assert "does not negate the earlier B12-limited benefit" in response["description"]
+
+
+def test_metabolite_evidence_grades_are_specific_to_the_ruegeria_column():
+ _, _, docs = records()
+ feeding = docs[1]["ecological_interactions"][1]
+ assert feeding["evidence"][0]["supports"] == "PARTIAL"
+ assert "three separate bacterial pair cultures" in feeding["description"]
+ assert [m["notes"].split(" (")[0] for m in feeding["metabolites"]] == [
+ "Gene-expression inference",
+ "Gene-expression inference",
+ "Net metabolite drawdown",
+ "Net metabolite drawdown",
+ ]
+ assert all(
+ "not an individually traced transfer flux" in m["notes"] for m in feeding["metabolites"]
+ )
+
+
+def test_trichodesmium_helpers_remain_hypotheses_with_host_to_epibiont_b12():
+ _, _, docs = records()
+ colony, helper, diel = docs[2]["ecological_interactions"]
+ assert all(
+ "interaction_type" not in n and "downstream" not in n for n in [colony, helper, diel]
+ )
+ assert helper["description"].startswith("HYPOTHESIZED:")
+ assert "facultative B12 use" in helper["description"]
+ assert "Proposed Trichodesmium-to-Alteromonas provision" in helper["metabolites"][2]["notes"]
+ assert all(e["supports"] == "PARTIAL" for e in helper["evidence"])
+ assert helper["metabolites"][3]["term"]["id"] == "CHEBI:26523"
+ assert helper["biological_processes"][0]["term"]["id"] == "GO:0098869"
+
+
+def test_field_expression_does_not_credit_the_exact_laboratory_strain():
+ _, _, docs = records()
+ diel = docs[2]["ecological_interactions"][2]
+ assert "source_taxon" not in diel and "target_taxon" not in diel
+ assert [p["preferred_term"] for p in diel["participating_taxa"]] == [
+ "Trichodesmium-associated heterotrophic microbiome"
+ ]
+ assert "not demonstrated to be IMS101" in diel["description"]
+ assert "not directly demonstrated cross-feeding" in diel["description"]
+
+
+def test_dispositions_and_unfinished_extension_are_honest():
+ ledger, rows, _ = records()
+ counts = ledger["reviewed_counts"]
+ assert counts["original_nodes"] == counts["retained_nodes"] == 10
+ assert counts["original_arrows"] == 6 and counts["retained_arrows"] == 2
+ assert counts["removed_arrows"] == 4 and counts["renamed_nodes"] == 6
+ assert counts["graph_quotations"] == 21 and counts["discussion_quotations"] == 3
+ assert len(ledger["issues"]) == 3 and ledger["unresolved_research_issues"] == [1883]
+ assert [r["status"] for r in rows] == ["reviewed", "needs_research", "reviewed"]
+ assert ledger["edison"]["authorized_invocations"] == 1
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert ledger["edison"]["task_id"] is None
+ assert sum(not p["independent_primary_match"] for p in ledger["snippet_checks"]) == 1
+
+
+def test_hashes_history_and_canonical_participants_are_guarded():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert row["curation_events_added"] == len(row["history_files"]) == 1
+ assert (ROOT / row["history_files"][0]).exists()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ canonical = [
+ {k: t["taxon_term"][k] for k in ["preferred_term", "term"]} for t in doc["taxonomy"]
+ ]
+ for node in doc["ecological_interactions"]:
+ assert all(e["target"] in names for e in node.get("downstream", []))
+ assert all(
+ p in canonical and set(p) == {"preferred_term", "term"}
+ for p in node.get("participating_taxa", [])
+ )
+ for d in doc["discussions"]:
+ assert all(a.split("#", 1)[1] in names for a in d["attaches_to"])
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 402372079..405bb3afb 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -437,8 +437,10 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Syntrophus_Benzoate_Degrader.yaml",
"Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml",
"TCP_NonDehalogenimonas_Groundwater_Consortium.yaml",
+ "Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml",
"Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml",
"Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml",
+ "Trichodesmium_Alteromonas_Marine_Consortium.yaml",
"Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml",
"Urine_Nitrification_SynCom.yaml",
"Viili_Fungus_Bacterium_EPS_SynCom.yaml",