- Niche partitioning
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -678,9 +673,8 @@
Ecological Interactions
Low-pH Mixed-Ion Rhodanobacter Tolerance
- NICHE_PARTITIONING
-
Low pH plus U(VI), Mn(II), Al(III), Cd(II), Zn(II), Co(II), and Ni(II) form a mixed-ion stress regime that Rhodanobacter isolates from contaminated Oak Ridge FRC wells tolerate better than most non-Rhodanobacter isolates from the site.
+
R2A dose-response and mixture assays support differential tolerance to low pH and seven metal ions: uranyl, manganese, aluminium, cadmium, zinc, cobalt and nickel. Eight Rhodanobacter isolates from contaminated wells grew under the pH-4 mixture, whereas 186 tested isolates from uncontaminated wells did not. This is an isolate-panel result, not a whole-groundwater-community perturbation or universal genus trait; strain provenance is confounded with genus, and some Pseudomonas isolates tolerate neutral-pH mixtures.
"low pH and high UO_{2}^{2+}, Mn^{2+}, Al^{3+}, Cd^{2+}, Zn^{2+}, Co^{2+}, and Ni^{2+} are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well"
+
"few isolates aside from Rhodanobacter can tolerate these eight ions."
@@ -776,7 +765,7 @@
Evidence
- SUPPORT (IN_VITRO)
-
"few isolates aside from Rhodanobacter can tolerate these eight ions."
+
"selectively inhibitory of non-Rhodanobacter isolates from uncontaminated wells"
@@ -787,12 +776,9 @@
Evidence
Contaminant-Selected Rhodanobacter Dominance
- NICHE_PARTITIONING
-
Low pH and high concentrations of uranium and other ions select for Rhodanobacter enrichment in the most contaminated Oak Ridge FRC groundwater wells, while inhibiting many other isolates.
-
+
PARTIAL - Rhodanobacter genus enrichment in the most contaminated groundwater wells is consistent with the experimentally supported acid/mixed-metal tolerance mechanism. The field association and isolate perturbations support selective filtering, not demonstrated niche partitioning, species-resolved denitrification flux or universal Rhodanobacter resistance. Nitrate is a correlated co-contaminant and possible electron acceptor, not a selectively toxic driver in the tested strain comparison.
-
Source Taxon: Rhodanobacter denitrificans and related Rhodanobacter spp.
"We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions."
+
"In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus."
@@ -863,9 +838,8 @@
Evidence
Mixed Metal and Nitrate Reduction Potential
- CROSS_FEEDING
-
The contaminated well FW113-47 selected for bacteria associated with uranium, nitrate, and iron reduction, indicating bioremediation-relevant redox capacity in the natural groundwater community.
+
PARTIAL - The four-well 16S clone-library study associates taxa in FW113-47 with previously recognized uranium-, nitrate- and iron-reducing capabilities and identifies bioremediation potential across the wells. The accessible abstract does not quantify community reduction rates or metabolite exchange. This redox-capacity inference is distinct from the later mixed-ion isolate-tolerance experiment; it does not demonstrate cross-feeding or prove that tolerant Rhodanobacter drive uranium immobilization.
PMID:22988623
- - SUPPORT (IN_VIVO)
+ - PARTIAL (IN_VIVO)
"Metal-reducing bacteria were present in all four wells, which may suggest that there is potential for successful bioremediation of the groundwater at the Oak Ridge FRC."
@@ -927,7 +893,7 @@
Evidence
PMID:22988623
- - SUPPORT (IN_VIVO)
+ - PARTIAL (IN_VIVO)
"The high concentrations of contaminants present in well FW113-47 stimulated the growth of organisms capable of reducing uranium (Shewanella and Pseudomonas), nitrate (Pseudomonas, Rhodanobacter and Xanthomonas) and iron (Stenotrophomonas), and which were unique to this well."
@@ -943,6 +909,45 @@
Evidence
+
+
Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How do isolate-specific metal tolerance and groundwater chemistry alter actual redox fluxes in the same wells?
+
+
The full tolerance paper supports a likely selective mechanism, but not the removed tolerance-to-redox-guild arrow. Field clone-library evidence remains abstract bounded after normal publisher access returned403. Quantify exact-well activity and distinguish nitrate respiration from selective nitrate toxicity. Canonical membership is preserved, not recertified at species level.
+
+
Attaches to: ecological_interactions#Low-pH Mixed-Ion Rhodanobacter Tolerance, ecological_interactions#Contaminant-Selected Rhodanobacter Dominance, ecological_interactions#Mixed Metal and Nitrate Reduction Potential
Metal-reducing bacteria were present in all four wells, which may suggest that there is potential for successful bioremediation of the groundwater at the Oak Ridge FRC.
+
Supports taxon-associated redox potential in the field survey, not measured reduction flux, chemical speciation or interspecies transfer.
+
+
+
+
+
+
+
+
@@ -1149,11 +1154,11 @@
Environmental Factors
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
- metabolites.push("uranium(VI)");
+ metabolites.push("uranyl ion");
metabolites.push("manganese(2+)");
@@ -1193,21 +1198,17 @@
Environmental Factors
(function() {
var intId = "interaction:1";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
- metabolites.push("uranium(VI)");
+ metabolites.push("uranyl ion");
metabolites.push("nitrate");
var processes = [];
-
- processes.push("denitrification");
-
-
var evidenceCount = 2;
nodes.push({
@@ -1221,27 +1222,18 @@
Environmental Factors
});
- var srcKey = "Rhodanobacter denitrificans and related Rhodanobacter spp.";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
-
})();
(function() {
var intId = "interaction:2";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
- metabolites.push("uranium(VI)");
-
metabolites.push("nitrate");
- metabolites.push("iron(3+)");
-
var processes = [];
diff --git a/docs/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.html b/docs/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.html
index 4612cfe7a..623005fb7 100644
--- a/docs/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.html
+++ b/docs/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.html
@@ -596,6 +596,11 @@
The FY34 met10Δ and FY31 str3Δ O. polymorpha auxotrophs were co-cultured as a sulfur-assimilation cross-feeding pair whose deleted metabolic nodes complemented one another in Delft minimal medium.
+
The met10Delta-str3Delta O. polymorpha pair showed reproducible growth complementation in Delft minimal medium on glucose and methanol. The reported glucose maximum OD600 range 27.3-28.5 spans this pair and str3Delta-leu2Delta, with no significant advantage over FY00 (26.8); methanol growth remained below FY00. FY34 met10Delta-mCherry and FY31 str3Delta-EGFP were the labeled derivatives used for population tracking, not identities established for every screening assay. Cooperative rescue is observed; specific sulfur exchange remains inferred.
@@ -664,7 +669,7 @@
Evidence
Asymmetric Homocysteine Dependency
CROSS_FEEDING
-
Supplementation assays indicated that the met10Δ mutant could recover growth with L-cysteine, cystathionine, or homocysteine, whereas str3Δ only showed substantial recovery with homocysteine.
+
HYPOTHESIZED - The model proposes homocysteine supply from met10Delta to str3Delta and multiple organic sulfur intermediates in the reverse direction. Single-strain supplementation at 20 mg/L restored met10Delta growth with L-cysteine, cystathionine or homocysteine, but not sodium sulfide; str3Delta recovered substantially only with homocysteine among the tested compounds. These are demonstrated nutrient-rescue profiles, not measured interstrain transfer, secretion, exchange rates or an exhaustive nutrient requirement. The paper calls for isotope labeling or targeted metabolomics to identify coculture exchange.
PMID:42318495
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"met10Δ can utilize multiple sulfur-containing intermediates, whereas str3Δ relies exclusively on homocysteine."
@@ -717,9 +722,8 @@
Evidence
Initial Ratio-Dependent Met10 Enrichment
- MUTUALISM
-
The inoculated met10Δ:str3Δ ratio controlled community establishment and final biomass, while surviving cocultures shifted toward a met10Δ-biased composition.
+
Controlled initial met10Delta:str3Delta ratios at total OD600 0.4 changed growth and composition on glucose. Ratios 1:10, 1:5 and 1:1 achieved higher final biomass, with met10Delta fractions increasing; 5:1 and 10:1 maintained met10Delta dominance but grew weakly. Endpoint composition was generally met10Delta-biased at 168 h, not evidence that every culture increased its met10Delta fraction, grew robustly or converged to one identical ratio. Longer-term continuous and product-producing stability was not established.
@@ -752,7 +756,7 @@
Evidence
- SUPPORT (IN_VITRO)
-
"the initial inoculation ratio critically determines community establishment and final biomass"
+
"Communities with initially higher frequencies of str3Δ (1:10, 1:5, and 1:1 groups) achieved higher final OD600 values."
@@ -765,7 +769,7 @@
Evidence
- SUPPORT (IN_VITRO)
-
"all co-cultures converging toward met10Δ enrichment over time"
+
"In contrast, groups initially dominated by met10Δ (5:1 and 10:1) showed weak growth throughout."
@@ -778,6 +782,45 @@
Evidence
+
+
Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which metabolites are actually exchanged, and how do they mediate the tested initial-ratio effect on growth?
+
+
The full paper explicitly infers directional exchange from single-strain supplement profiles and proposes tracers/metabolomics. Figure schematics are not transfer measurements. Growth restoration and ratio effects remain supported; distinct input/outcome and proposed exchange-to-rescue topology remain a research task. Prior dangling phenotype arrows remain absent. One-record Edison dry run is not an inspected provider report or paid authorization.
The isotopic labeling or targeted metabolomics would help to directly identify the specific metabolites exchanged in co-culture
+
Explicitly identifies the unresolved exchange measurement.
+
+
+
+
+
+
+
+
@@ -1309,7 +1352,7 @@
Evidence
(function() {
var intId = "interaction:2";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
diff --git a/docs/communities/Okeke_Lu_Cellulolytic_Consortium.html b/docs/communities/Okeke_Lu_Cellulolytic_Consortium.html
index a53c4f24f..40c93d295 100644
--- a/docs/communities/Okeke_Lu_Cellulolytic_Consortium.html
+++ b/docs/communities/Okeke_Lu_Cellulolytic_Consortium.html
@@ -685,7 +685,7 @@
Ecological Interactions
@@ -693,8 +693,8 @@
Ecological Interactions
Syntrophy
+ aria-hidden="true" data-symbol="symbolTriangle2"
+ data-color="#929caa"> Other
@@ -702,10 +702,9 @@
Ecological Interactions
-
Cellulose Degradation
- SYNTROPHY
+
Cellulose-Hydrolyzing Isolate Enzyme Activities
-
The defined consortium expressed filter-paper cellulase and beta-glucosidase activities, led by DB1 and DB2 filter-paper cellulases and DB1 beta-glucosidase, to support cellulose hydrolysis.
+
Selected members of the five-isolate consortium had measured cellulolytic activity in individual isolate cultures: DB1 and DB2 filter-paper cellulase activities were 27.83 and 31.22 U per mg, and DB1 beta-glucosidase was 18.07 U per mg. These positive isolate results support the consortium design, not a directly measured combined-culture rate or obligate syntrophy in the accessible abstract.
@@ -743,8 +742,8 @@
Cellulose Degradation
Downstream Effects:
- → Synergistic Lignocellulose Degradation
-
Cellulase and beta-glucosidase activities provide the cellulose-hydrolysis branch of the combined cellulolytic-xylanolytic consortium.
HYPOTHESIZED - Measured isolate hydrolases provide the cellulose-hydrolysis branch proposed to complement the other enzyme activities in the assembled consortium. The causal contribution is biochemical potential inferred from isolate assays and consortium construction, not a measured increase in combined-culture degradation or demonstrated synergistic flux.
@@ -763,7 +762,7 @@
Evidence
- SUPPORT (IN_VITRO)
-
"Use of microbial consortium in bioprocessing of lignocelluloses could reduce problems such as incomplete synergistic enzymes, end-product inhibition, adsorption, and requirement for high amounts of enzymes in direct use of enzymes."
+
"Isolates DB1 and DB2 displayed the highest filter paper cellulase: 27.83 and 31.22 U mg⁻¹, respectively."
@@ -773,10 +772,9 @@
Evidence
-
Hemicellulose Degradation
- SYNTROPHY
+
Xylan-Hydrolyzing Isolate Enzyme Activities
-
The defined consortium expressed xylanase and beta-xylosidase activities, with DB2 producing the strongest xylanase activity and DB13 producing the strongest beta-xylosidase activity, to support hemicellulose hydrolysis.
+
Isolate DB2 produced the highest xylanase activity, 103.05 U per mg, and DB13 the highest beta-xylosidase activity, 7.72 U per mg, in the tested isolate panel. These observed activities support a hemicellulose-hydrolysis contribution to the defined five-isolate design; the accessible abstract does not supply a combined-culture activity or demonstrate obligate metabolic exchange.
@@ -814,8 +812,8 @@
Hemicellulose Degradation
Downstream Effects:
- → Synergistic Lignocellulose Degradation
-
Xylanase and beta-xylosidase activities provide the hemicellulose-hydrolysis branch of the combined cellulolytic-xylanolytic consortium.
HYPOTHESIZED - Measured isolate hydrolases provide the hemicellulose-hydrolysis branch proposed to complement the other enzyme activities in the assembled consortium. The causal contribution is biochemical potential inferred from isolate assays and consortium construction, not a measured increase in combined-culture degradation or demonstrated synergistic flux.
@@ -844,10 +842,9 @@
Evidence
-
Synergistic Lignocellulose Degradation
- SYNTROPHY
+
Proposed Complementary Lignocellulose Hydrolysis
-
The five-isolate consortium combines cellulolytic and xylanolytic enzymes to process cellulose and hemicellulose together, reducing the incomplete-enzyme limitation of enzyme-only lignocellulose bioprocessing.
+
HYPOTHESIZED - Five selected isolates were assembled into a defined consortium with cellulolytic and xylanolytic capabilities. Their complementary enzyme activities could broaden cellulose/hemicellulose processing and reduce incomplete-enzyme limitations. The accessible primary abstract proposes this benefit; it does not quantify synergy above additive monoculture activities, relief of product inhibition, lower enzyme demand or lignin breakdown. Full-text experiments remain uninspected behind subscription access, not demonstrated absent.
@@ -907,7 +904,7 @@
Evidence
PMID:20859703
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"Use of microbial consortium in bioprocessing of lignocelluloses could reduce problems such as incomplete synergistic enzymes, end-product inhibition, adsorption, and requirement for high amounts of enzymes in direct use of enzymes."
@@ -923,6 +920,45 @@
Evidence
+
+
Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Does the assembled five-isolate consortium outperform its component hydrolases or relieve end-product inhibition?
+
+
The accessible primary abstract and existing cache establish isolate activities and consortium construction. Normal publisher access is a subscription preview, so the combined-culture controls and any quantitative synergy remain uninspected. Both proposed hydrolytic-contribution arrows are retained explicitly as hypotheses; obtain authorized full text before strengthening them or adding topology.
Use of microbial consortium in bioprocessing of lignocelluloses could reduce problems such as incomplete synergistic enzymes, end-product inhibition, adsorption, and requirement for high amounts of enzymes in direct use of enzymes.
+
The authors propose potential processing benefits; this is not a quantitative combined-consortium superiority result.
+
+
+
+
+
+
+
+
@@ -1364,7 +1400,7 @@
Evidence
(function() {
var intId = "interaction:0";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1383,7 +1419,7 @@
The five-strain Group 41 formulation of SynCom 3 produced the highest 48 h neutral-detergent-fiber degradation in the Box-Behnken in vitro screen and exceeded the sterile-water control by 20.56%.
+
The five-strain Group 41 formulation selected from 41 combinations achieved 66.84% neutral-detergent-fiber degradation at 48 h, reported as 20.56% above the sterile-water control. Dry-matter degradation and gas production were not different in this optimized comparison. This is the five-member derivative, not the initial seven-member SynCom3 whose gas-production result differs. Reported strain concentrations describe the added suspension, not a justified final 61-mL bottle concentration. Results are in vitro with filtration-sterilized rumen fluid, not cattle colonization or proven pairwise synergy.
Whole-genome sequencing of the five SynCom 3 strains supported a broad carbohydrate-degradation enzyme repertoire, including glycoside hydrolases, carbohydrate-binding modules, carbohydrate esterases, and KEGG enzymes linked to cellulose, hemicellulose, pectin, glucose, and volatile-fatty-acid metabolism.
+
Whole-genome sequencing and COG, CAZy and KEGG annotation identify a broad predicted carbohydrate-active enzyme complement across the five strains, including GH, CBM and CE families and pathways for cellulose, hemicellulose, pectin, glucose and VFA metabolism. The reported 47 GH and 19 CBM families absent from three reference fibrolytic bacteria support genomic breadth, not measured expression, enzyme synergy, donor-recipient exchange or causally resolved community flux.
@@ -852,7 +852,7 @@
Evidence
In situ cattle rumen fermentation shift
-
Supplementing fistulated Huaxi cattle with the five-strain optimized SynCom altered rumen fermentation and trended toward higher DM, NDF, and ADF degradation at 72 h, with significant VFA and NH3-N shifts.
+
Dosing six fistulated Huaxi cattle in two groups of three with the optimized SynCom or sterile water altered rumen fermentation. At 72 h, DM/NDF/ADF degradation increases of 2.61%/7.81%/11.47% were not statistically significant. Total VFA was lower at 12 h, higher at 24/48 h, and nonsignificantly higher at 72 h; acetate rose at 24/48/72 h, propionate did not differ, and NH3-N fell at 48/72 h. Three nylon bags per animal are subsamples, not nine independent cattle per treatment. These outcomes do not prove durable engraftment or genomic-pathway mediation.
@@ -961,7 +961,7 @@
OPEN
Which transcript-level pathways and metabolite exchanges connect the five optimized SynCom 3 strains during rumen fiber degradation?
-
The paper annotated complementary carbohydrate-active enzyme potential from isolate genomes, but it names transcriptomics and metabolic cross-feeding as future work. This record therefore does not assert directional pairwise cross-feeding edges among the five strains.
+
The paper annotated complementary carbohydrate-active enzyme potential from isolate genomes, but it names transcriptomics and metabolic cross-feeding as future work. This record therefore does not assert directional pairwise cross-feeding edges among the five strains. The full main text was inspected: the genomic complement is computational evidence, and no new genotype-to-phenotype or laboratory-to-cattle arrow is justified. The initial seven-strain and optimized five-strain gas results differ. Six cattle provide three animals per group; bags are nested subsamples, and gene-family breadth does not establish expression or exchange.
Attaches to: ecological_interactions#Genome-annotated carbohydrate-active enzyme complement
diff --git a/history/records/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community/2026-10-07T050635Z-codex-ddf580.yaml b/history/records/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community/2026-10-07T050635Z-codex-ddf580.yaml
new file mode 100644
index 000000000..de0ebe00b
--- /dev/null
+++ b/history/records/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community/2026-10-07T050635Z-codex-ddf580.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml
+ slug: Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community
+session:
+ id: 2026-10-07T050635Z-codex-ddf580
+ timestamp: '2026-10-07T05:06:35Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1652
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain controlled isolate tolerance, correct uranyl grounding and keep bounded
+ selection arrow; remove unsupported redox coupling.; Retain genus-level field enrichment
+ without species/denitrification or nitrate-selective-toxicity overclaims.; Keep abstract-bounded
+ redox potential without cross-feeding, measured flux or unmeasured ionic speciation.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
diff --git a/history/records/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture/2026-10-07T050635Z-codex-aab572.yaml b/history/records/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture/2026-10-07T050635Z-codex-aab572.yaml
new file mode 100644
index 000000000..dd69a25be
--- /dev/null
+++ b/history/records/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture/2026-10-07T050635Z-codex-aab572.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml
+ slug: Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture
+session:
+ id: 2026-10-07T050635Z-codex-aab572
+ timestamp: '2026-10-07T05:06:35Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1653
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve observed complementation with two-pair OD range, carbon-source and labeled-strain
+ limits.; Retain directed sulfur-exchange model as hypothesized while preserving measured
+ supplement rescue.; Preserve controlled ratio effects without universal growth, increasing-fraction
+ or identical-endpoint claims.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
diff --git a/history/records/Okeke_Lu_Cellulolytic_Consortium/2026-10-07T050635Z-codex-3eb057.yaml b/history/records/Okeke_Lu_Cellulolytic_Consortium/2026-10-07T050635Z-codex-3eb057.yaml
new file mode 100644
index 000000000..494f90c7e
--- /dev/null
+++ b/history/records/Okeke_Lu_Cellulolytic_Consortium/2026-10-07T050635Z-codex-3eb057.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml
+ slug: Okeke_Lu_Cellulolytic_Consortium
+session:
+ id: 2026-10-07T050635Z-codex-3eb057
+ timestamp: '2026-10-07T05:06:35Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1654
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve quantified DB1/DB2 cellulase and DB1 beta-glucosidase activities at isolate-assay
+ scope.; Preserve positive DB2/DB13 xylan-hydrolase results and qualify their proposed
+ contribution.; Retain assembled-consortium potential and both hypothesis arrows without
+ promoting prospective benefits to measured synergy.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
diff --git a/history/records/Optimized_Rumen_Fiber_Degrading_SynCom3/2026-10-07T050635Z-codex-4f5a19.yaml b/history/records/Optimized_Rumen_Fiber_Degrading_SynCom3/2026-10-07T050635Z-codex-4f5a19.yaml
new file mode 100644
index 000000000..1a05c9e40
--- /dev/null
+++ b/history/records/Optimized_Rumen_Fiber_Degrading_SynCom3/2026-10-07T050635Z-codex-4f5a19.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml
+ slug: Optimized_Rumen_Fiber_Degrading_SynCom3
+session:
+ id: 2026-10-07T050635Z-codex-4f5a19
+ timestamp: '2026-10-07T05:06:35Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1655
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve significant optimized laboratory NDFD with null endpoints, formulation
+ and inoculum-concentration limits.; Preserve predicted enzyme complement and Fig7 evidence
+ without promoting annotation to demonstrated expression or synergy.; Preserve time-dependent
+ cattle fermentation outcomes and nonsignificant fiber trends with animal-level replication
+ limits.
+ details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
diff --git a/kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml b/kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml
index f36e92ae6..42719cb54 100644
--- a/kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml
+++ b/kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml
@@ -129,16 +129,17 @@ taxonomy:
well.
ecological_interactions:
- name: Low-pH Mixed-Ion Rhodanobacter Tolerance
- description: Low pH plus U(VI), Mn(II), Al(III), Cd(II), Zn(II), Co(II), and Ni(II)
- form a mixed-ion stress regime that Rhodanobacter isolates from contaminated Oak Ridge
- FRC wells tolerate better than most non-Rhodanobacter isolates from the site.
- interaction_type: NICHE_PARTITIONING
+ description: 'R2A dose-response and mixture assays support differential tolerance to low pH and seven metal ions:
+ uranyl, manganese, aluminium, cadmium, zinc, cobalt and nickel. Eight Rhodanobacter isolates from contaminated
+ wells grew under the pH-4 mixture, whereas 186 tested isolates from uncontaminated wells did not. This is an
+ isolate-panel result, not a whole-groundwater-community perturbation or universal genus trait; strain provenance
+ is confounded with genus, and some Pseudomonas isolates tolerate neutral-pH mixtures.'
scope: COMMUNITY_LEVEL
metabolites:
- - preferred_term: uranium(VI)
+ - preferred_term: uranyl ion
term:
- id: CHEBI:32992
- label: uranium(6+)
+ id: CHEBI:43515
+ label: dioxouranium(2+)
- preferred_term: manganese(2+)
term:
id: CHEBI:29035
@@ -170,82 +171,63 @@ ecological_interactions:
label: response to metal ion
downstream:
- target: Contaminant-Selected Rhodanobacter Dominance
- description: Rhodanobacter tolerance to the low-pH U(VI)-Mn(II)-Al(III)-Cd(II)-
- Zn(II)-Co(II)-Ni(II) ion mixture identifies a selective mechanism for the
- Rhodanobacter enrichment observed in the most contaminated FRC wells.
- - target: Mixed Metal and Nitrate Reduction Potential
- description: Mixed metal tolerance defines the contaminated groundwater guilds
- that retain uranium, nitrate, and iron reduction potential under the high-stress
- conditions of well FW113-47.
+ description: PARTIAL - Differential survival under low-pH mixed-metal stress supplies an experimentally supported
+ selection mechanism for field Rhodanobacter enrichment when relevant ions reach inhibitory concentrations.
+ This combines isolate perturbations with field abundance/geochemistry, not an in situ manipulation or proof
+ that nitrate toxicity selects Rhodanobacter. Organic matter, speciation and strain provenance limit transfer
+ of thresholds to groundwater.
evidence:
- reference: PMID:30523276
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: low pH and high UO_{2}^{2+}, Mn^{2+}, Al^{3+}, Cd^{2+}, Zn^{2+}, Co^{2+},
- and Ni^{2+} are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated
- well vs. a Rhodanobacter isolate from a contaminated well
- explanation: Supports low pH and mixed metal ions as selective pressures favoring
- Rhodanobacter over less tolerant Oak Ridge groundwater isolates.
+ snippet: few isolates aside from Rhodanobacter can tolerate these eight ions.
+ explanation: Preserves the observed mixture-tolerance result; the eight selective ions include protons, not
+ eight metals.
- reference: PMID:30523276
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: few isolates aside from Rhodanobacter can tolerate these eight ions.
- explanation: Supports the site-wide rarity of mixed-ion tolerance outside
- Rhodanobacter isolates.
+ snippet: selectively inhibitory of non-Rhodanobacter isolates from uncontaminated wells
+ explanation: Supports differential isolate susceptibility, not a universal property of all Pseudomonas or field
+ populations.
- name: Contaminant-Selected Rhodanobacter Dominance
- description: Low pH and high concentrations of uranium and other ions select for Rhodanobacter enrichment
- in the most contaminated Oak Ridge FRC groundwater wells, while inhibiting many other isolates.
- interaction_type: NICHE_PARTITIONING
+ description: PARTIAL - Rhodanobacter genus enrichment in the most contaminated groundwater wells is consistent
+ with the experimentally supported acid/mixed-metal tolerance mechanism. The field association and isolate perturbations
+ support selective filtering, not demonstrated niche partitioning, species-resolved denitrification flux or universal
+ Rhodanobacter resistance. Nitrate is a correlated co-contaminant and possible electron acceptor, not a selectively
+ toxic driver in the tested strain comparison.
scope: COMMUNITY_LEVEL
- source_taxon:
- preferred_term: Rhodanobacter denitrificans and related Rhodanobacter spp.
- term:
- id: NCBITaxon:666685
- label: Rhodanobacter denitrificans
metabolites:
- - preferred_term: uranium(VI)
+ - preferred_term: uranyl ion
term:
- id: CHEBI:32992
- label: uranium(6+)
+ id: CHEBI:43515
+ label: dioxouranium(2+)
- preferred_term: nitrate
term:
id: CHEBI:17632
label: nitrate
- biological_processes:
- - preferred_term: denitrification
- term:
- id: GO:0019333
- label: denitrification pathway
evidence:
- reference: PMID:30523276
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients
- of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions.
- explanation: Establishes the geochemical gradients that structure the community.
+ snippet: In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus.
+ explanation: Directly supports genus-level field enrichment, not a resolved species assignment.
- reference: PMID:30523276
supports: SUPPORT
evidence_source: IN_VITRO
snippet: few isolates aside from Rhodanobacter can tolerate these eight ions.
- explanation: Supports contaminant tolerance as a mechanism favoring Rhodanobacter under mixed ion stress.
+ explanation: Supplies the isolate-selection mechanism with strain/condition limits.
- name: Mixed Metal and Nitrate Reduction Potential
- description: The contaminated well FW113-47 selected for bacteria associated with uranium, nitrate, and
- iron reduction, indicating bioremediation-relevant redox capacity in the natural groundwater community.
- interaction_type: CROSS_FEEDING
+ description: PARTIAL - The four-well 16S clone-library study associates taxa in FW113-47 with previously recognized
+ uranium-, nitrate- and iron-reducing capabilities and identifies bioremediation potential across the wells.
+ The accessible abstract does not quantify community reduction rates or metabolite exchange. This redox-capacity
+ inference is distinct from the later mixed-ion isolate-tolerance experiment; it does not demonstrate cross-feeding
+ or prove that tolerant Rhodanobacter drive uranium immobilization.
scope: COMMUNITY_LEVEL
metabolites:
- - preferred_term: uranium(VI)
- term:
- id: CHEBI:32992
- label: uranium(6+)
- preferred_term: nitrate
term:
id: CHEBI:17632
label: nitrate
- - preferred_term: iron(3+)
- term:
- id: CHEBI:29034
- label: iron(3+)
biological_processes:
- preferred_term: denitrification
term:
@@ -253,18 +235,20 @@ ecological_interactions:
label: denitrification pathway
evidence:
- reference: PMID:22988623
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: Metal-reducing bacteria were present in all four wells, which may suggest that there is
- potential for successful bioremediation of the groundwater at the Oak Ridge FRC.
- explanation: Supports bioremediation relevance of metal-reducing members.
+ snippet: Metal-reducing bacteria were present in all four wells, which may suggest that there is potential for
+ successful bioremediation of the groundwater at the Oak Ridge FRC.
+ explanation: Supports taxon-associated redox potential in the field survey, not measured reduction flux, chemical
+ speciation or interspecies transfer.
- reference: PMID:22988623
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: The high concentrations of contaminants present in well FW113-47 stimulated the growth
- of organisms capable of reducing uranium (Shewanella and Pseudomonas), nitrate (Pseudomonas,
- Rhodanobacter and Xanthomonas) and iron (Stenotrophomonas), and which were unique to this well.
- explanation: Links community members to uranium, nitrate, and iron redox processes.
+ snippet: The high concentrations of contaminants present in well FW113-47 stimulated the growth of organisms
+ capable of reducing uranium (Shewanella and Pseudomonas), nitrate (Pseudomonas, Rhodanobacter and Xanthomonas)
+ and iron (Stenotrophomonas), and which were unique to this well.
+ explanation: Supports taxon-associated redox potential in the field survey, not measured reduction flux, chemical
+ speciation or interspecies transfer.
environmental_factors:
- name: Groundwater pH, nitrate, uranium, and metals
value: pH 3 to 7; nitrate 44 to 23,400 mg/L; uranium 0.73 to 60.36 mg/L
@@ -359,3 +343,35 @@ metals_present:
metal_relevance: PRIMARY
metal_notes: Uranium and iron are directly tied to reported reduction potential; nickel, cobalt, and zinc
are included as selective metal contaminants reported in Oak Ridge FRC ion-mixture studies.
+discussions:
+- discussion_id: field-selection-versus-redox-flux
+ prompt: How do isolate-specific metal tolerance and groundwater chemistry alter actual redox fluxes in the same
+ wells?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Low-pH Mixed-Ion Rhodanobacter Tolerance
+ - ecological_interactions#Contaminant-Selected Rhodanobacter Dominance
+ - ecological_interactions#Mixed Metal and Nitrate Reduction Potential
+ rationale: The full tolerance paper supports a likely selective mechanism, but not the removed tolerance-to-redox-guild
+ arrow. Field clone-library evidence remains abstract bounded after normal publisher access returned403. Quantify
+ exact-well activity and distinguish nitrate respiration from selective nitrate toxicity. Canonical membership
+ is preserved, not recertified at species level.
+ evidence:
+ - reference: PMID:22988623
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: Metal-reducing bacteria were present in all four wells, which may suggest that there is potential for
+ successful bioremediation of the groundwater at the Oak Ridge FRC.
+ explanation: Supports taxon-associated redox potential in the field survey, not measured reduction flux, chemical
+ speciation or interspecies transfer.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-07T05:06:33Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain controlled isolate tolerance, correct uranyl grounding and keep bounded selection arrow; remove
+ unsupported redox coupling.; Retain genus-level field enrichment without species/denitrification or nitrate-selective-toxicity
+ overclaims.; Keep abstract-bounded redox potential without cross-feeding, measured flux or unmeasured ionic
+ speciation. Issue #1652; reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml b/kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml
index 3349eeba1..beed728f8 100644
--- a/kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml
+++ b/kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml
@@ -99,8 +99,11 @@ taxonomy:
explanation: Supports the engineered deletion and fluorescent-marker status of the tracked auxotrophic member.
ecological_interactions:
- name: MET10-STR3 Sulfur Auxotrophy Cross-Feeding
- description: The FY34 met10Δ and FY31 str3Δ O. polymorpha auxotrophs were co-cultured as a sulfur-assimilation cross-feeding
- pair whose deleted metabolic nodes complemented one another in Delft minimal medium.
+ description: The met10Delta-str3Delta O. polymorpha pair showed reproducible growth complementation in Delft minimal
+ medium on glucose and methanol. The reported glucose maximum OD600 range 27.3-28.5 spans this pair and str3Delta-leu2Delta,
+ with no significant advantage over FY00 (26.8); methanol growth remained below FY00. FY34 met10Delta-mCherry
+ and FY31 str3Delta-EGFP were the labeled derivatives used for population tracking, not identities established
+ for every screening assay. Cooperative rescue is observed; specific sulfur exchange remains inferred.
interaction_type: MUTUALISM
scope: COMMUNITY_LEVEL
participating_taxa:
@@ -116,16 +119,22 @@ ecological_interactions:
- reference: PMID:42318495
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The met10Δ and str3Δ mutants harbor deletions in the sulfur assimilation pathway at MET10 and STR3, respectively.
+ snippet: The met10Δ and str3Δ mutants harbor deletions in the sulfur assimilation pathway at MET10 and STR3,
+ respectively.
explanation: Places the two deletions in the sulfur-assimilation pathway.
- reference: PMID:42318495
supports: SUPPORT
evidence_source: IN_VITRO
snippet: The strongly complementary pairs (met10Δ-str3Δ and str3Δ-leu2Δ) reached maximum OD600 values of 27.3–28.5
- explanation: Quantifies robust complementation for the curated met10Δ-str3Δ pair.
+ explanation: Reports the range across two complementary pairs, not an exact value or significant superiority
+ for this pair alone.
- name: Asymmetric Homocysteine Dependency
- description: Supplementation assays indicated that the met10Δ mutant could recover growth with L-cysteine, cystathionine,
- or homocysteine, whereas str3Δ only showed substantial recovery with homocysteine.
+ description: HYPOTHESIZED - The model proposes homocysteine supply from met10Delta to str3Delta and multiple organic
+ sulfur intermediates in the reverse direction. Single-strain supplementation at 20 mg/L restored met10Delta
+ growth with L-cysteine, cystathionine or homocysteine, but not sodium sulfide; str3Delta recovered substantially
+ only with homocysteine among the tested compounds. These are demonstrated nutrient-rescue profiles, not measured
+ interstrain transfer, secretion, exchange rates or an exhaustive nutrient requirement. The paper calls for isotope
+ labeling or targeted metabolomics to identify coculture exchange.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -140,20 +149,23 @@ ecological_interactions:
label: Ogataea polymorpha
evidence:
- reference: PMID:42318495
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: met10Δ can utilize multiple sulfur-containing intermediates, whereas str3Δ relies exclusively on homocysteine.
- explanation: Supports the asymmetric sulfur-intermediate dependency.
+ explanation: Abstract summarizes asymmetric use of the tested supplements; this only partially supports the
+ directed exchange model.
- reference: PMID:42318495
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: met10Δ recovered growth in the presence of L-Cys, Cysta, or Hcy, but not with Na2S. str3Δ, by contrast, showed
- substantial growth recovery only with Hcy.
- explanation: Reports the single-mutant supplementation result used to infer the homocysteine-centered cross-feeding model.
+ snippet: met10Δ recovered growth in the presence of L-Cys, Cysta, or Hcy, but not with Na2S. str3Δ, by contrast,
+ showed substantial growth recovery only with Hcy.
+ explanation: Directly supports single-strain supplementation outcomes, not donor-to-recipient transfer.
- name: Initial Ratio-Dependent Met10 Enrichment
- description: The inoculated met10Δ:str3Δ ratio controlled community establishment and final biomass, while surviving cocultures
- shifted toward a met10Δ-biased composition.
- interaction_type: MUTUALISM
+ description: Controlled initial met10Delta:str3Delta ratios at total OD600 0.4 changed growth and composition
+ on glucose. Ratios 1:10, 1:5 and 1:1 achieved higher final biomass, with met10Delta fractions increasing; 5:1
+ and 10:1 maintained met10Delta dominance but grew weakly. Endpoint composition was generally met10Delta-biased
+ at 168 h, not evidence that every culture increased its met10Delta fraction, grew robustly or converged to one
+ identical ratio. Longer-term continuous and product-producing stability was not established.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Ogataea polymorpha FY34 met10Δ-mCherry
@@ -168,13 +180,14 @@ ecological_interactions:
- reference: PMID:42318495
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: the initial inoculation ratio critically determines community establishment and final biomass
- explanation: Supports the ratio-dependence of community assembly.
+ snippet: Communities with initially higher frequencies of str3Δ (1:10, 1:5, and 1:1 groups) achieved higher
+ final OD600 values.
+ explanation: Supports the positive ratio-dependent biomass response.
- reference: PMID:42318495
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: all co-cultures converging toward met10Δ enrichment over time
- explanation: Supports the met10Δ-biased population trajectory.
+ snippet: In contrast, groups initially dominated by met10Δ (5:1 and 10:1) showed weak growth throughout.
+ explanation: Distinguishes maintained compositional bias from successful high-biomass establishment.
growth_media:
- name: Delft minimal glucose medium
temperature: '37'
@@ -333,15 +346,15 @@ curation_history:
- timestamp: '2026-09-27T13:08:02Z'
curator: codex
action: CREATE_OGATAEA_SULFUR_CROSSFEEDING_COCULTURE
- changes: Created CommunityMech:000450 from PMID:42318495 and DOI 10.1016/j.synbio.2026.05.008 with evidence-backed O. polymorpha
- FY34 met10Δ-mCherry and FY31 str3Δ-EGFP membership, auxotrophy-based sulfur cross-feeding, asymmetric homocysteine dependency,
- inoculation-ratio tracking, and Delft glucose/methanol batch cultivation conditions.
+ changes: Created CommunityMech:000450 from PMID:42318495 and DOI 10.1016/j.synbio.2026.05.008 with evidence-backed
+ O. polymorpha FY34 met10Δ-mCherry and FY31 str3Δ-EGFP membership, auxotrophy-based sulfur cross-feeding, asymmetric
+ homocysteine dependency, inoculation-ratio tracking, and Delft glucose/methanol batch cultivation conditions.
llm_assisted: true
- timestamp: '2026-09-27T13:16:09Z'
curator: codex
action: ADD_OD600_GROWTH_MEDIA_EVIDENCE
- changes: 'Added exact Methods evidence snippets for glucose screening, FY31/FY34 population tracking, and methanol initial
- OD600 values after adversarial review issue #1149.'
+ changes: 'Added exact Methods evidence snippets for glucose screening, FY31/FY34 population tracking, and methanol
+ initial OD600 values after adversarial review issue #1149.'
llm_assisted: true
- timestamp: '2026-09-27T13:21:06Z'
curator: codex
@@ -349,3 +362,33 @@ curation_history:
changes: 'Removed two Ogataea downstream outcome labels that the network audit correctly treated as dangling interaction-edge
targets for issue #1150.'
llm_assisted: true
+- timestamp: '2026-10-07T05:06:34Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve observed complementation with two-pair OD range, carbon-source and labeled-strain limits.;
+ Retain directed sulfur-exchange model as hypothesized while preserving measured supplement rescue.; Preserve
+ controlled ratio effects without universal growth, increasing-fraction or identical-endpoint claims. Issue #1653;
+ reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml'
+ llm_assisted: true
+discussions:
+- discussion_id: sulfur-exchange-and-ratio-mediation
+ prompt: Which metabolites are actually exchanged, and how do they mediate the tested initial-ratio effect on growth?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#MET10-STR3 Sulfur Auxotrophy Cross-Feeding
+ - ecological_interactions#Asymmetric Homocysteine Dependency
+ - ecological_interactions#Initial Ratio-Dependent Met10 Enrichment
+ rationale: The full paper explicitly infers directional exchange from single-strain supplement profiles and proposes
+ tracers/metabolomics. Figure schematics are not transfer measurements. Growth restoration and ratio effects
+ remain supported; distinct input/outcome and proposed exchange-to-rescue topology remain a research task. Prior
+ dangling phenotype arrows remain absent. One-record Edison dry run is not an inspected provider report or paid
+ authorization.
+ evidence:
+ - reference: PMID:42318495
+ supports: SUPPORT
+ evidence_source: OTHER
+ snippet: The isotopic labeling or targeted metabolomics would help to directly identify the specific metabolites
+ exchanged in co-culture
+ explanation: Explicitly identifies the unresolved exchange measurement.
+ posed_by: codex
diff --git a/kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml b/kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml
index eb4cb8213..4079dfae6 100644
--- a/kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml
+++ b/kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml
@@ -97,11 +97,11 @@ taxonomy:
similar to Pseudoxanthomonas byssovorax (99%), Microbacterium oxydans (99%), Bacillus sp. (99%),
Ochrobactrum anthropi (98%), and Klebsiella trevisanii (99%)
ecological_interactions:
-- name: Cellulose Degradation
- description: The defined consortium expressed filter-paper cellulase and beta-glucosidase
- activities, led by DB1 and DB2 filter-paper cellulases and DB1 beta-glucosidase,
- to support cellulose hydrolysis.
- interaction_type: SYNTROPHY
+- name: Cellulose-Hydrolyzing Isolate Enzyme Activities
+ description: 'Selected members of the five-isolate consortium had measured cellulolytic activity in individual
+ isolate cultures: DB1 and DB2 filter-paper cellulase activities were 27.83 and 31.22 U per mg, and DB1 beta-glucosidase
+ was 18.07 U per mg. These positive isolate results support the consortium design, not a directly measured combined-culture
+ rate or obligate syntrophy in the accessible abstract.'
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: cellulose
@@ -118,21 +118,23 @@ ecological_interactions:
id: GO:0030245
label: cellulose catabolic process
downstream:
- - target: Synergistic Lignocellulose Degradation
- description: Cellulase and beta-glucosidase activities provide the cellulose-hydrolysis
- branch of the combined cellulolytic-xylanolytic consortium.
+ - target: Proposed Complementary Lignocellulose Hydrolysis
+ description: HYPOTHESIZED - Measured isolate hydrolases provide the cellulose-hydrolysis branch proposed to
+ complement the other enzyme activities in the assembled consortium. The causal contribution is biochemical
+ potential inferred from isolate assays and consortium construction, not a measured increase in combined-culture
+ degradation or demonstrated synergistic flux.
evidence:
- reference: PMID:20859703
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Use of microbial consortium in bioprocessing of lignocelluloses could reduce problems such
- as incomplete synergistic enzymes, end-product inhibition, adsorption, and requirement for high
- amounts of enzymes in direct use of enzymes.
-- name: Hemicellulose Degradation
- description: The defined consortium expressed xylanase and beta-xylosidase activities,
- with DB2 producing the strongest xylanase activity and DB13 producing the strongest
- beta-xylosidase activity, to support hemicellulose hydrolysis.
- interaction_type: SYNTROPHY
+ snippet: 'Isolates DB1 and DB2 displayed the highest filter paper cellulase: 27.83 and 31.22 U mg⁻¹, respectively.'
+ explanation: Directly supports individual DB1/DB2 cellulase activities rather than a proposed future processing
+ benefit.
+- name: Xylan-Hydrolyzing Isolate Enzyme Activities
+ description: Isolate DB2 produced the highest xylanase activity, 103.05 U per mg, and DB13 the highest beta-xylosidase
+ activity, 7.72 U per mg, in the tested isolate panel. These observed activities support a hemicellulose-hydrolysis
+ contribution to the defined five-isolate design; the accessible abstract does not supply a combined-culture
+ activity or demonstrate obligate metabolic exchange.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: xylan
@@ -149,20 +151,24 @@ ecological_interactions:
id: GO:0045493
label: xylan catabolic process
downstream:
- - target: Synergistic Lignocellulose Degradation
- description: Xylanase and beta-xylosidase activities provide the hemicellulose-hydrolysis
- branch of the combined cellulolytic-xylanolytic consortium.
+ - target: Proposed Complementary Lignocellulose Hydrolysis
+ description: HYPOTHESIZED - Measured isolate hydrolases provide the hemicellulose-hydrolysis branch proposed
+ to complement the other enzyme activities in the assembled consortium. The causal contribution is biochemical
+ potential inferred from isolate assays and consortium construction, not a measured increase in combined-culture
+ degradation or demonstrated synergistic flux.
evidence:
- reference: PMID:20859703
supports: SUPPORT
evidence_source: IN_VITRO
snippet: Isolate DB2 produced the highest xylanase activity (103.05 U mg⁻¹), while the highest β-xylosidase
activity (7.72 U mg⁻¹) was observed with DB13
-- name: Synergistic Lignocellulose Degradation
- description: The five-isolate consortium combines cellulolytic and xylanolytic enzymes
- to process cellulose and hemicellulose together, reducing the incomplete-enzyme
- limitation of enzyme-only lignocellulose bioprocessing.
- interaction_type: SYNTROPHY
+ explanation: Directly reports DB2/DB13 isolate enzyme activities, not the activity of the assembled community.
+- name: Proposed Complementary Lignocellulose Hydrolysis
+ description: HYPOTHESIZED - Five selected isolates were assembled into a defined consortium with cellulolytic
+ and xylanolytic capabilities. Their complementary enzyme activities could broaden cellulose/hemicellulose processing
+ and reduce incomplete-enzyme limitations. The accessible primary abstract proposes this benefit; it does not
+ quantify synergy above additive monoculture activities, relief of product inhibition, lower enzyme demand or
+ lignin breakdown. Full-text experiments remain uninspected behind subscription access, not demonstrated absent.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: lignocellulose
@@ -182,16 +188,17 @@ ecological_interactions:
- reference: PMID:20859703
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Five selected isolates (DB1, DB2, DB7, DB8, and DB13) were used to compose a defined
- consortium and characterized by 16S ribosomal RNA gene sequence analysis.
- explanation: Supports the five-isolate defined consortium assembled from the
- cellulolytic-xylanolytic enrichment.
+ snippet: Five selected isolates (DB1, DB2, DB7, DB8, and DB13) were used to compose a defined consortium and
+ characterized by 16S ribosomal RNA gene sequence analysis.
+ explanation: Supports the five-isolate defined consortium assembled from the cellulolytic-xylanolytic enrichment.
- reference: PMID:20859703
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: Use of microbial consortium in bioprocessing of lignocelluloses could reduce problems such
- as incomplete synergistic enzymes, end-product inhibition, adsorption, and requirement for high
- amounts of enzymes in direct use of enzymes.
+ snippet: Use of microbial consortium in bioprocessing of lignocelluloses could reduce problems such as incomplete
+ synergistic enzymes, end-product inhibition, adsorption, and requirement for high amounts of enzymes in direct
+ use of enzymes.
+ explanation: The authors propose potential processing benefits; this is not a quantitative combined-consortium
+ superiority result.
environmental_factors:
- name: Source environment
value: Alabama soil
@@ -385,3 +392,36 @@ metals_present:
- IRON
metal_relevance: INCIDENTAL
metal_notes: Metal/REE detected via environmental factor measurements
+discussions:
+- discussion_id: combined-consortium-versus-isolate-assays
+ prompt: Does the assembled five-isolate consortium outperform its component hydrolases or relieve end-product
+ inhibition?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Cellulose-Hydrolyzing Isolate Enzyme Activities
+ - ecological_interactions#Xylan-Hydrolyzing Isolate Enzyme Activities
+ - ecological_interactions#Proposed Complementary Lignocellulose Hydrolysis
+ rationale: The accessible primary abstract and existing cache establish isolate activities and consortium construction.
+ Normal publisher access is a subscription preview, so the combined-culture controls and any quantitative synergy
+ remain uninspected. Both proposed hydrolytic-contribution arrows are retained explicitly as hypotheses; obtain
+ authorized full text before strengthening them or adding topology.
+ evidence:
+ - reference: PMID:20859703
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: Use of microbial consortium in bioprocessing of lignocelluloses could reduce problems such as incomplete
+ synergistic enzymes, end-product inhibition, adsorption, and requirement for high amounts of enzymes in direct
+ use of enzymes.
+ explanation: The authors propose potential processing benefits; this is not a quantitative combined-consortium
+ superiority result.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-07T05:06:34Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve quantified DB1/DB2 cellulase and DB1 beta-glucosidase activities at isolate-assay scope.; Preserve
+ positive DB2/DB13 xylan-hydrolase results and qualify their proposed contribution.; Retain assembled-consortium
+ potential and both hypothesis arrows without promoting prospective benefits to measured synergy. Issue #1654;
+ reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml b/kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml
index f938fd7ce..9f6beeaa1 100644
--- a/kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml
+++ b/kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml
@@ -163,8 +163,12 @@ taxonomy:
explanation: Names P. mucosa 6360 as a member of the efficient five-strain SynCom.
ecological_interactions:
- name: Box-Behnken optimized in vitro fiber degradation
- description: The five-strain Group 41 formulation of SynCom 3 produced the highest 48 h neutral-detergent-fiber degradation
- in the Box-Behnken in vitro screen and exceeded the sterile-water control by 20.56%.
+ description: The five-strain Group 41 formulation selected from 41 combinations achieved 66.84% neutral-detergent-fiber
+ degradation at 48 h, reported as 20.56% above the sterile-water control. Dry-matter degradation and gas production
+ were not different in this optimized comparison. This is the five-member derivative, not the initial seven-member
+ SynCom3 whose gas-production result differs. Reported strain concentrations describe the added suspension, not
+ a justified final 61-mL bottle concentration. Results are in vitro with filtration-sterilized rumen fluid, not
+ cattle colonization or proven pairwise synergy.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: cellulose catabolic process
@@ -179,16 +183,19 @@ ecological_interactions:
- reference: doi:10.1186/s40168-025-02331-3
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Group 41, consisting of 1 × 108 CFU/mL of S. equinus 5640 and E. lactis 6088, 1 × 106 CFU/mL of P. mucosa 6360,
- and 1 × 105 CFU/mL of L. delbrueckii 5812 and P. acetatigenes 6076, achieved the highest 48 h NDFD (66.84%), significantly
- higher than the control group by 20.56%, but had no difference in 48 h DMD and gas production (P < 0.05, Fig. 6 C).
- The results demonstrated that favorable concentrations and ratios of strains in SynComs are more effective in promoting
- fermentation performance and facilitating industrial application.
- explanation: Supports the optimized five-strain Group 41 formulation and its 48 h in vitro NDFD improvement.
+ snippet: Group 41, consisting of 1 × 108 CFU/mL of S. equinus 5640 and E. lactis 6088, 1 × 106 CFU/mL of P.
+ mucosa 6360, and 1 × 105 CFU/mL of L. delbrueckii 5812 and P. acetatigenes 6076, achieved the highest 48 h
+ NDFD (66.84%), significantly higher than the control group by 20.56%, but had no difference in 48 h DMD and
+ gas production (P < 0.05, Fig. 6 C). The results demonstrated that favorable concentrations and ratios of
+ strains in SynComs are more effective in promoting fermentation performance and facilitating industrial application.
+ explanation: Preserves significant optimized Group41 NDFD and the reported absence of DMD/gas differences; do
+ not generalize the paragraph-end P-value to those null endpoints.
- name: Genome-annotated carbohydrate-active enzyme complement
- description: Whole-genome sequencing of the five SynCom 3 strains supported a broad carbohydrate-degradation enzyme repertoire,
- including glycoside hydrolases, carbohydrate-binding modules, carbohydrate esterases, and KEGG enzymes linked to cellulose,
- hemicellulose, pectin, glucose, and volatile-fatty-acid metabolism.
+ description: Whole-genome sequencing and COG, CAZy and KEGG annotation identify a broad predicted carbohydrate-active
+ enzyme complement across the five strains, including GH, CBM and CE families and pathways for cellulose, hemicellulose,
+ pectin, glucose and VFA metabolism. The reported 47 GH and 19 CBM families absent from three reference fibrolytic
+ bacteria support genomic breadth, not measured expression, enzyme synergy, donor-recipient exchange or causally
+ resolved community flux.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: cellulose catabolic process
@@ -203,28 +210,32 @@ ecological_interactions:
- reference: doi:10.1186/s40168-025-02331-3
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: The fiber degrading strains S. equinus 5640, L. delbrueckii 5812, P. acetatigenes 6076, E. lactis 6088, and P.
- mucosa 6360 had whole genome sequencing at Biozeron.
+ snippet: The fiber degrading strains S. equinus 5640, L. delbrueckii 5812, P. acetatigenes 6076, E. lactis 6088,
+ and P. mucosa 6360 had whole genome sequencing at Biozeron.
explanation: Identifies the five SynCom strains sequenced for whole-genome functional annotation.
- reference: doi:10.1186/s40168-025-02331-3
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: Genome sequence analysis revealed the synergistic and complementary actions of these five bacterial strains in
- carbohydrate degradation processes.
+ snippet: Genome sequence analysis revealed the synergistic and complementary actions of these five bacterial
+ strains in carbohydrate degradation processes.
explanation: Supports the genome-annotation inference of complementary carbohydrate-degradation processes.
- reference: doi:10.1186/s40168-025-02331-3
supports: SUPPORT
evidence_source: COMPUTATIONAL
- snippet: Fig. 7 Fiber degradation pathways of the five strains in SynComm 3. A Number of COG genes in carbohydrate transport
- and metabolism. B–D Venn diagram of genes in glycoside hydrolases (GHs), carbohydrate-binding modules (CBMs),
- and carbohydrate esterases (CEs) from CAZy database. E Relative abundance of KEGG pathway on level 3. F, G Number
- of genes involved in fiber degradation, glucose degradation, and VFA synthesis. H Metabolic profiles of fibrous
- substrates, glucose, and VFA
+ snippet: Fig. 7 Fiber degradation pathways of the five strains in SynComm 3. A Number of COG genes in carbohydrate
+ transport and metabolism. B–D Venn diagram of genes in glycoside hydrolases (GHs), carbohydrate-binding modules
+ (CBMs), and carbohydrate esterases (CEs) from CAZy database. E Relative abundance of KEGG pathway on level
+ 3. F, G Number of genes involved in fiber degradation, glucose degradation, and VFA synthesis. H Metabolic
+ profiles of fibrous substrates, glucose, and VFA
explanation: Directly supports the CAZy GH/CBM/CE and KEGG enzyme annotations behind the inferred carbohydrate-active
enzyme complement.
- name: In situ cattle rumen fermentation shift
- description: Supplementing fistulated Huaxi cattle with the five-strain optimized SynCom altered rumen fermentation and
- trended toward higher DM, NDF, and ADF degradation at 72 h, with significant VFA and NH3-N shifts.
+ description: Dosing six fistulated Huaxi cattle in two groups of three with the optimized SynCom or sterile water
+ altered rumen fermentation. At 72 h, DM/NDF/ADF degradation increases of 2.61%/7.81%/11.47% were not statistically
+ significant. Total VFA was lower at 12 h, higher at 24/48 h, and nonsignificantly higher at 72 h; acetate rose
+ at 24/48/72 h, propionate did not differ, and NH3-N fell at 48/72 h. Three nylon bags per animal are subsamples,
+ not nine independent cattle per treatment. These outcomes do not prove durable engraftment or genomic-pathway
+ mediation.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: carbohydrate metabolic process
@@ -235,22 +246,24 @@ ecological_interactions:
- reference: doi:10.1186/s40168-025-02331-3
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: The in situ feeding trial demonstrated that the supplementation of the SynCom significantly altered the rumen
- fermentation profile and enhanced feed fiber degradation in Huaxi cattle. The ruminal degradation rates of DM, NDF,
- and ADF exhibited a positive trend in the TRE group, with increases of 2.61%, 7.81%, and 11.47%, respectively, at 72 h
- compared to the CON group, although these differences were not statistically significant (Fig. 8 A–C, P > 0.05). SynCom
- supplementation profoundly influenced ruminal VFA production. While the total VFA concentration in the TRE group was
- significantly lower than in the CON group at 12 h (Fig. 8 F, P = 0.0011), it increased progressively over time, becoming
- significantly higher in the TRE group at 24 h (P = 0.0196) and 48 h (P = 0.0001), and remaining 10.80% higher at 72 h
- (P > 0.05). This shift was driven by a significantly elevated acetate concentration in the TRE group at 24, 48, and
- 72 h (Fig. 8 G, P < 0.05), with no significant difference observed in propionate levels. Consequently, the A:P ratio
- was significantly elevated in the treatment group at 48 h and 72 h (Fig. 8 M, P < 0.05). The concentrations of butyrate,
- isobutyrate, and isovalerate in the TRE group were also significantly higher than in the CON group at 24 and 48 h (Fig.
- 8 I, J, and L, P < 0.05). In contrast, valerate concentration in the TRE group was significantly lower than in the CON
- group at 48 h (Fig. 8 K, P = 0.0013) and 72 h (Fig. 8 K, P < 0.0001). Concomitantly, the NH3-N concentration was significantly
- lower in the TRE group at 48 h and 72 h (Fig. 8 E, P< 0.0001 and P = 0.0034, respectively), implying improved nitrogen
- utilization by the rumen microbiota.
- explanation: Supports the in situ rumen response to the optimized SynCom.
+ snippet: The in situ feeding trial demonstrated that the supplementation of the SynCom significantly altered
+ the rumen fermentation profile and enhanced feed fiber degradation in Huaxi cattle. The ruminal degradation
+ rates of DM, NDF, and ADF exhibited a positive trend in the TRE group, with increases of 2.61%, 7.81%, and
+ 11.47%, respectively, at 72 h compared to the CON group, although these differences were not statistically
+ significant (Fig. 8 A–C, P > 0.05). SynCom supplementation profoundly influenced ruminal VFA production.
+ While the total VFA concentration in the TRE group was significantly lower than in the CON group at 12 h (Fig.
+ 8 F, P = 0.0011), it increased progressively over time, becoming significantly higher in the TRE group at
+ 24 h (P = 0.0196) and 48 h (P = 0.0001), and remaining 10.80% higher at 72 h (P > 0.05). This shift was driven
+ by a significantly elevated acetate concentration in the TRE group at 24, 48, and 72 h (Fig. 8 G, P < 0.05),
+ with no significant difference observed in propionate levels. Consequently, the A:P ratio was significantly
+ elevated in the treatment group at 48 h and 72 h (Fig. 8 M, P < 0.05). The concentrations of butyrate, isobutyrate,
+ and isovalerate in the TRE group were also significantly higher than in the CON group at 24 and 48 h (Fig.
+ 8 I, J, and L, P < 0.05). In contrast, valerate concentration in the TRE group was significantly lower than
+ in the CON group at 48 h (Fig. 8 K, P = 0.0013) and 72 h (Fig. 8 K, P < 0.0001). Concomitantly, the NH3-N
+ concentration was significantly lower in the TRE group at 48 h and 72 h (Fig. 8 E, P< 0.0001 and P = 0.0034,
+ respectively), implying improved nitrogen utilization by the rumen microbiota.
+ explanation: Preserves positive time-specific fermentation responses while distinguishing nonsignificant fiber
+ trends, propionate and late total-VFA results.
growth_media:
- name: Total-mixed-ration rumen-fluid in vitro fermentation medium
temperature: 39
@@ -346,40 +359,50 @@ associated_datasets:
explanation: Names BioProject PRJNA1297957 for the whole-genome sequencing datasets.
discussions:
- discussion_id: cross-feeding-mechanism-unresolved
- prompt: Which transcript-level pathways and metabolite exchanges connect the five optimized SynCom 3 strains during rumen
- fiber degradation?
+ prompt: Which transcript-level pathways and metabolite exchanges connect the five optimized SynCom 3 strains during
+ rumen fiber degradation?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- ecological_interactions#Genome-annotated carbohydrate-active enzyme complement
- rationale: The paper annotated complementary carbohydrate-active enzyme potential from isolate genomes, but it names transcriptomics
- and metabolic cross-feeding as future work. This record therefore does not assert directional pairwise cross-feeding edges
- among the five strains.
+ rationale: 'The paper annotated complementary carbohydrate-active enzyme potential from isolate genomes, but it
+ names transcriptomics and metabolic cross-feeding as future work. This record therefore does not assert directional
+ pairwise cross-feeding edges among the five strains. The full main text was inspected: the genomic complement
+ is computational evidence, and no new genotype-to-phenotype or laboratory-to-cattle arrow is justified. The
+ initial seven-strain and optimized five-strain gas results differ. Six cattle provide three animals per group;
+ bags are nested subsamples, and gene-family breadth does not establish expression or exchange.'
evidence:
- reference: doi:10.1186/s40168-025-02331-3
supports: SUPPORT
evidence_source: full_text
- snippet: Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms of
- fiber-degrading strains in the rumen.
+ snippet: Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms
+ of fiber-degrading strains in the rumen.
explanation: The authors explicitly leave transcriptomics and cross-feeding mechanisms to future research.
posed_by: claude
curation_history:
- timestamp: '2026-09-20T21:12:42Z'
curator: claude
action: CREATE_COMMUNITY_RECORD
- changes: Created DOI-backed optimized rumen SynCom 3 community with five strains, in vitro and in situ interactions, cultivation
- conditions, BioProject datasets, and an unresolved cross-feeding discussion.
+ changes: Created DOI-backed optimized rumen SynCom 3 community with five strains, in vitro and in situ interactions,
+ cultivation conditions, BioProject datasets, and an unresolved cross-feeding discussion.
llm_assisted: true
- timestamp: '2026-09-20T21:34:16Z'
curator: codex
action: ADDRESS_ADVERSARIAL_REVIEW
- changes: Added more local evidence for CAZy and KEGG genome annotations and for mixed SynCom inoculation into the in vitro
- bottle fermentation setup.
+ changes: Added more local evidence for CAZy and KEGG genome annotations and for mixed SynCom inoculation into
+ the in vitro bottle fermentation setup.
llm_assisted: true
- timestamp: '2026-10-02T06:00:47Z'
curator: codex
action: REPAIR_CAUSAL_GRAPH
- changes: Removed the workflow edge that carried the Box-Behnken in vitro Group
- 41 formulation into the later fistulated-cattle dosing assay instead of
- linking two source-backed biological states.
+ changes: Removed the workflow edge that carried the Box-Behnken in vitro Group 41 formulation into the later fistulated-cattle
+ dosing assay instead of linking two source-backed biological states.
+ llm_assisted: true
+- timestamp: '2026-10-07T05:06:34Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Preserve significant optimized laboratory NDFD with null endpoints, formulation and inoculum-concentration
+ limits.; Preserve predicted enzyme complement and Fig7 evidence without promoting annotation to demonstrated
+ expression or synergy.; Preserve time-dependent cattle fermentation outcomes and nonsignificant fiber trends
+ with animal-level replication limits. Issue #1655; reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml'
llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index e09d30ac4..88ec56350 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,33 @@ 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`.
+## Batch79: Field Selection, Nutrient Rescue And Hydrolysis
+
+[Decisions](decisions/20261007-four-records-batch79.yaml),
+[validation](validation-20261007-batch79.json) and
+[self-adversarial review](adversarial-review-20261007-batch79.yaml) account for
+12 existing nodes and four arrows across four records. Three bounded arrows
+remain: experimentally supported field selection and two proposed hydrolase
+contributions. The cross-study tolerance-to-redox arrow is removed.
+
+Positive isolate tolerance, yeast complementation and ratio effects, individual
+hydrolase activities, optimized rumen NDFD and cattle fermentation responses
+remain. Transfer measurements, quantitative consortium synergy and genomic
+mediation are distinguished from the measured outcomes. Uranyl grounding is
+corrected without changing canonical membership or non-graph metadata.
+
+All 21 graph quotations match fresh primary text and existing caches. Three
+complete main bodies were read; three further references remain abstract
+bounded. Subscription/access restrictions were respected. Separate supplements,
+raw datasets and original figure pixels were not audited. All 920 caches and
+456 other records are unchanged; four append-only histories are included.
+
+Research #1656/#1657 remains open for yeast topology and authorized Okeke
+full-text review. One Ogataea Edison dry run spent no credits; scoped paid
+authorization remains unanswered. Repairs #1652-#1655 stay open until protected
+main merge, and metadata #1658 remains open afterward. This is self-review,
+not independent approval or completion of the corpus.
+
## Batch78: Redox, Engraftment And Model Evidence
[Decisions](decisions/20261007-four-records-batch78.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261007-batch79.yaml b/reports/causal_graph_review/adversarial-review-20261007-batch79.yaml
new file mode 100644
index 000000000..73f528e09
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261007-batch79.yaml
@@ -0,0 +1,244 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: d9da91dd8003dc1958f1d13a30cd3b957e3bf5a4
+scope:
+- kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml
+- kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml
+- kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml
+- kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
+validation_report: reports/causal_graph_review/validation-20261007-batch79.json
+findings:
+- issue: 1652
+ severity: P2
+ status: addressed_in_this_change
+ finding: Oak Ridge species/chemistry and cross-study redox overclaims.
+ disposition: Close only after protected-main merge.
+- issue: 1653
+ severity: P2
+ status: addressed_in_this_change
+ finding: Ogataea nutrient rescue versus inferred exchange and endpoint bias.
+ disposition: Close only after protected-main merge.
+- issue: 1654
+ severity: P2
+ status: addressed_in_this_change
+ finding: Okeke isolate hydrolases versus proposed consortium synergy.
+ disposition: Close only after protected-main merge.
+- issue: 1655
+ severity: P2
+ status: addressed_in_this_change
+ finding: Rumen formulation, genome inference and animal-level assay boundaries.
+ disposition: Close only after protected-main merge.
+- issue: 1656
+ severity: P2
+ status: unresolved_research
+ finding: Missing Ogataea input-to-outcome and proposed exchange topology.
+ disposition: Keep OPEN after repair merge; source access and scoped causal-research workflow remain incomplete.
+- issue: 1657
+ severity: P2
+ status: unresolved_research
+ finding: Okeke authorized full-text comparison and mechanism detail.
+ disposition: Keep OPEN after repair merge; source access and scoped causal-research workflow remain incomplete.
+- issue: 1658
+ severity: P2
+ status: unresolved_non_graph
+ finding: Identity, origin, medium and provenance metadata.
+ disposition: Keep OPEN after graph-repair merge.
+adversarial_checks:
+- Fresh baseline across kb/communities and data/isolates preceded papers. Whole records and every12existing node/4arrow
+ were read. One cross-study arrow removed and three bounded arrows retained. Sparse graphs remain in scope; topology
+ is not invented to satisfy density.
+- Oak Ridge has real isolate perturbation evidence for field selection, not merely a correlation. Preserve eight
+ resistant contaminated-well Rhodanobacter isolates and186uncontaminated-well comparator isolates, recognizing
+ provenance confounding. Neutral-pH resistance of some Pseudomonas strains prevents a universal genus-susceptibility
+ claim.
+- Low pH plus seven metal ions is eight selective ions including protons. Nitrate is correlated/toxic but not selectively
+ inhibitory in the assayed pair; it may be an electron acceptor. Organic carbon and speciation alter thresholds,
+ and no direct in situ perturbation was done. Preserve the selection arrow with these limits.
+- Correct uranyl to official ChEBI43515, not free uranium6+. Remove the unproved species-specific source annotation
+ from genus enrichment while preserving canonical taxonomy. Field clone-library redox potential is not flux or
+ cross-feeding; remove tolerance-to-redox-guild coupling between different studies. Do not transfer isolate R2A
+ culture conditions to the field community.
+- Ogataea growth complementation is a positive result on glucose and methanol. The27.3-28.5range covers two pairs
+ and does not establish significant superiority over FY00; methanol remains below FY00. Distinguish fluorescent
+ tracking derivatives FY31/FY34 from all screening strains, preserving canonical labels and OD600medium evidence.
+- Retain the directed sulfur-exchange model as hypothesized. Single-strain supplement rescue proves differential
+ use of the tested compounds, not secretion or transfer. No rescue by sodium sulfide is not proof of a particular
+ toxicity mechanism. Figure1/5schematics do not override the explicit isotope/metabolomics research gap.
+- 'Controlled initial ratios affect growth: low initial met10fraction gives higher biomass, high met10ratios grow
+ weakly while remaining biased. Endpoint met10bias is not necessarily increasing fraction in every culture, identical
+ final ratio, equal establishment or long-term stability. Keep ratio biology without an unisolated mutualism annotation.'
+- Okeke isolate filter-paper cellulase, beta-glucosidase, xylanase and beta-xylosidase are positive measured results,
+ and five-isolate consortium construction is retained. Accessible abstract proposes broad processing benefit rather
+ than quantifying synergy. Keep both contribution arrows as hypotheses; no obligate syntrophy, lignin degradation
+ or demonstrated product-inhibition relief inferred.
+- Okeke normal publisher subscription preview and field publisher403 are respected. Inaccessible full text does
+ not prove experiments absent. Three full primary main bodies, captions and three further abstracts read; no separate
+ supplements, original figure pixels or raw datasets inspected. Whitespace-only primary/cache matching verifies21quotations
+ but does not replace entailment review.
+- Rumen Group41 preserves significant66.84%48hNDFD and20.56%reported relative improvement. Null DMD/gas in optimized
+ five-member group must not inherit initial seven-member gas improvement. Concentrations are added-suspension descriptors,
+ not final-bottle doses. Filtration-sterilized rumen fluid is not silently recast as a native living microbiota
+ inoculum.
+- Rumen CAZy/COG/KEGG annotations,47GH/19CBMfamily breadth and existing Fig7evidence survive. These predict function
+ without measuring expression, metabolic exchange or pathway mediation. The in vitro-to-cattle workflow arrow stays
+ removed.
+- Cattle DM/NDF/ADF72htrends are nonsignificant despite broader source conclusions. Preserve early negative and
+ later positive VFA effects, null propionate and lower NH3-N. Six cattle means three animals per treatment, not
+ nine independent animals from three bags each. No durable engraftment or gene-to-outcome causality asserted.
+- All456other records,920caches, canonical membership and raw non-graph blocks preserved; four new append-only histories.
+ Prior258/650/981/1149/1150/1151repairs maintained. Metadata1658 remains open, including documented provenance-vocabulary
+ inconsistency despite passing baseline gates; no nonexistent validation failure claimed.
+- Ogataea missing topology remains1656with one11815character Edison LITERATURE dry run, zero provider submissions/credits
+ and unanswered scoped approval. Okeke authorized full-text review remains1657. Repair1652-1655issues stay OPEN
+ until protected-main merge; research/metadata remain afterward. Self-review is COMMENT, not independent approval
+ or corpus completion.
+- All focused gates, both-root inventory/network/rank, related regressions and deterministic rendering have actual
+ logs/digests. Exact descriptions parsed across456pages are not browser screenshots. Postcommit docs-current and
+ remote exact-head COMMENT are separate publication gates; protected lifecycle must preserve dependent branches.
+verification:
+ combined_regressions: 706 passed in 206.85s (0:03:26)
+ new_regression_tests: 10
+ schema_strict_terms_history: Passed with actual outputs/digests
+ references: All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.
+ All21 graph quotations independently match fresh primary text and unchanged cache. Literal matching is not entailment.
+ Three main bodies and three further primary abstracts were read; no recertification of every cache or non-graph
+ field.
+ snippet_counts_by_record:
+ kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml:
+ MATCH: 18
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml:
+ MATCH: 28
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml:
+ MATCH: 16
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml:
+ MATCH: 19
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ primary_graph_snippet_proof:
+ primary_matched: 21
+ new_nodes_or_arrows: 0
+ complete_main_bodies_read: 3
+ other_primary_abstracts_read: 3
+ separate_supplements_raw_datasets_original_figure_pixels_audited: false
+ network:
+ existing_findings_preserved: 44
+ added_findings: {}
+ removed_findings: {}
+ interpretation: All44 baseline warnings preserved exactly. Community scope remains aggregate, not resolved member-specific
+ activity. No taxonomy or auditor-rule changes.
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml: 9dd19980fd51ff6885a8be6faf1aa5245931b8fb7b0adf4723fbdfa74ae3bb30
+ tests/test_causal_review_batch79.py: 6d0b452c6d10a5e31e0676a53a68bbcb070aa8a732e9c54d4ac037ca7e779bde
+ kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml: fd8891c4ada299a06c57062e47f8598fc7f5a1755fc2e1241255c44cff6211d4
+ kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml: 5feb6042f2cf7da47745ea846cab0dba57cd50b9fef9aa20a8ab60eb849e805e
+ kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml: 1992cf47e5fd154a6684b025a6117d7f10398c65beb8d8e5f65e8e2115ab8f42
+ kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml: ee1333388f5d7353daf7713abf744220accf40a855bdbe8b66389f9b7c5031c6
+ reports/causal_graph_review/README.md: faa44482b4add8042bc2009a0ad83e019900845dab2dcb48eb729d124336096a
+ unchanged_caches: 920
+ cache_changes: []
+ unchanged_records: 456
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - community_id: CommunityMech:000450
+ job: LITERATURE
+ query_chars: 11815
+ query_sha256: a1e91a88b4aaed8fe5fc8395f825150219e6441e7fc25119475e865b6ebe0cc7
+ meta_path: /private/tmp/communitymech-batch79/edison-ogataea/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous question unanswered; preselection is not approval.
+ post_commit_docs_current: Separate publication gate, not asserted before commit.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 393
+ mixed: 125
+ community_level_only: 268
+ taxa: 1511
+ credited_solely_by_the_rule: 1240
+ current:
+ records: 460
+ with_community_level: 393
+ mixed: 125
+ community_level_only: 268
+ taxa: 1511
+ credited_solely_by_the_rule: 1240
+ delta:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ interpretation: No scope-count change, taxonomy edit, or auditor-rule change. Aggregate outcomes do not establish
+ member-resolved activity.
+corpus:
+ records: 460
+ nodes: 1447
+ edges: 613
+ review_status_counts:
+ needs_research: 32
+ pending: 176
+ reviewed: 252
+limitations:
+- Fresh pre-paper baseline covers460 records and920 caches across both roots, including ignored/hidden files. Every12
+ existing node and4arrow was reviewed;12nodes3arrows remain. Four guarded repairs/history events;456 other records
+ and all920 caches unchanged.
+- 'Three complete primary main bodies read from fresh Europe PMC XML: metal-tolerance, Ogataea and rumen papers.
+ Captions read; no embedded main-text tables in these XML files. Field clone-library, Rhodanobacter taxonomy and
+ Okeke sources read at primary-abstract scope. No separate supplements, raw datasets or original figure pixels
+ audited.'
+- Normal Okeke publisher access confirms subscription preview; field publisher403 and Microbiology Society full-text
+ delivery failure respected. No access restriction bypass. Existing Okeke cache is abstract-only; inaccessible
+ full text does not establish absence of experiments.
+- All21 graph quotations independently match primary text and unchanged cache with whitespace-only comparison. Literal
+ matching is not entailment. Early oversized combined/cache reads were truncated; fresh main texts were read in
+ bounded chunks, and no absence finding relies on truncated output.
+- Oak Ridge retains experimentally supported selection, not mere unqualified correlation. Isolate provenance, pH,
+ mixture effects, organic matter and ion speciation bound transfer to field conditions. Nitrate toxicity was not
+ selective in the strain comparison; genus enrichment is not species identity or redox flux. Official ChEBI confirms
+ uranyl is43515, not free uranium6+.
+- Ogataea retains cooperative growth, actual nutrient rescue and controlled ratio effects. Directed metabolite exchange
+ is hypothesized, not measured. Two-pair OD range, methanol shortfall, distinct labeled tracking strains and weak-growth
+ high-met10 ratios are explicit; endpoint bias is not identical convergence or long-term stability.
+- Okeke positive isolate hydrolases and five-member construction remain. Both proposed hydrolytic-contribution arrows
+ are retained as hypotheses; accessible abstract does not quantify synergy, product-inhibition relief or lignin
+ degradation. Full-text acquisition remains needs_research, not a declaration of no experiments.
+- Rumen significant optimized in vitro NDFD, predicted gene complement and time-dependent cattle fermentation are
+ preserved. Initial seven-member gas effects differ from final five-member null gas result. Inoculum is not final
+ bottle concentration; bags are subsamples of three cattle per group. Nonsignificant72h fiber trends are not proven
+ improvement. No genome-to-outcome or workflow arrow added.
+- One Ogataea Edison LITERATURE dry run used zero provider submissions/credits. Scoped paid question unanswered.
+ Missing input/outcome and exchange-to-rescue structure stays1656; Okeke full-text follow-up1657 requires its own
+ workflow if new topology becomes justified. Earlier denied/pending scopes unchanged.
+- Dedup searched933 all-state issue titles/bodies and25 ignored/hidden-inclusive local matched files, excluding
+ git/docs/site/cache. Matching258/650/981/1149/1150/1151 read; no exhaustive PR-comment audit. Prior field-community,
+ medium, canonical-strain, Figure7 evidence and dangling/workflow-arrow fixes preserved.
+- 'Repair issues1652-1655 remain OPEN until protected-main merge; research1656/1657 and metadata1658 remain OPEN
+ afterward. Canonical membership and raw non-graph blocks are preserved, not certified. Rumen documented vocabulary
+ inconsistency is not a claimed gate failure: baseline schema and strict checks passed. Self-adversarial review
+ is not independent approval or corpus completion.'
diff --git a/reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml b/reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
new file mode 100644
index 000000000..a8328ec93
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
@@ -0,0 +1,563 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: d9da91dd8003dc1958f1d13a30cd3b957e3bf5a4
+baseline_commit: d9da91dd8003dc1958f1d13a30cd3b957e3bf5a4
+base_tree: 7b3e7d91a758f2249644d002bba89dff3d4a812e
+pre_source_baseline_sha256: 7586929f90340d7643aa5a1a97461cb2aeb355371584bc2199b57245ff6d7bb9
+issues:
+- 1652
+- 1653
+- 1654
+- 1655
+unresolved_non_graph_issues:
+- 1658
+unresolved_research_issues:
+- 1656
+- 1657
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 933
+ ignored_hidden_local_search: true
+ matching_local_files: 25
+ matching_issues:
+ - 258
+ - 650
+ - 981
+ - 1149
+ - 1150
+ - 1151
+primary_artifacts:
+ /private/tmp/communitymech-batch79/access-results.json: fe939480fa759a8f8feedaeecba55e4c07717550a0a2a1d2401db3f1c33b9198
+ /private/tmp/communitymech-batch79/baseline.json: 7586929f90340d7643aa5a1a97461cb2aeb355371584bc2199b57245ff6d7bb9
+ ? /private/tmp/communitymech-batch79/edison-ogataea/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-edison-literature-causal-meta.yaml
+ : 700dc8f86a306fd60032acd29a2c860525b4375cb27747d438b5852d72102ea1
+ /private/tmp/communitymech-batch79/frc_isolates-metadata.json: 7ed07dcf5d875ccdca1f5cf4dcf2cf33f91eee28a7109f84fdc57701280b0098
+ /private/tmp/communitymech-batch79/frc_isolates-primary.txt: 1a33ce5bad56bf220d95213eddde22b6932235d9fbeb423aec9aca2d41fb093b
+ /private/tmp/communitymech-batch79/frc_tolerance-metadata.json: ce987c60cdd82f2b6cf3b3b03a2fb25629f5cf82dfd6387b67964d7a9ae873a7
+ /private/tmp/communitymech-batch79/frc_tolerance-primary.txt: dcec0b3ad05d934d78754454c009a52f283d6076c6605917c1f9c9c799b1053a
+ /private/tmp/communitymech-batch79/frc_tolerance-primary.xml: 0ced6c91f494fd341adce7e4559e3af27a6e70983e5b33b54a9eb628dd566bf8
+ /private/tmp/communitymech-batch79/frc_tolerance-tables.txt: 01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b
+ /private/tmp/communitymech-batch79/frc_wells-metadata.json: 6062e88be83383c1fba31a5c4641fffe57aa71f8c1ac76755c5e8076b9e39e30
+ /private/tmp/communitymech-batch79/frc_wells-primary.txt: d77f8032aa5d23c3b68f6e4ac95e4affc166ddfced02bdb555f0bdbdbc6ae4a4
+ /private/tmp/communitymech-batch79/issue-matches.json: 06a1bdb5d05689edd6e5701ff22d057234d1d1a917f6f6c4ca0d8bf9b3291ba7
+ /private/tmp/communitymech-batch79/issues.json: e644d42955c048cb84b215a6a79759b5dc0e06f4a0cda0ebc841cb48792a12c1
+ /private/tmp/communitymech-batch79/local-matches.txt: 51e8e3ba10450433ed204263fdf33dcba169de7d8febd41c89f449ac4c379b1f
+ /private/tmp/communitymech-batch79/ogataea-metadata.json: 9d79fcd296d7478c13495bcbfde74327fcb8fbce533b2160764314dfc70cb5e2
+ /private/tmp/communitymech-batch79/ogataea-primary.txt: 2ea60a11fe9a86bf66183b3e8332363f1e631bcbcfd8eb3143aa1117d10b9a5a
+ /private/tmp/communitymech-batch79/ogataea-primary.xml: 0d0f08bce1cdf95f776608b9f6418d953c63585333e6ac64e8617f004aeb97b7
+ /private/tmp/communitymech-batch79/ogataea-tables.txt: 01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b
+ /private/tmp/communitymech-batch79/okeke-metadata.json: 11f99b3b01a530ad72714d7702dbb1829388ac4064a68aae873afac31d67f136
+ /private/tmp/communitymech-batch79/okeke-primary.txt: 41756012aa5ca7602ae608c6ae96e53e3e45c0badedc07d3f2759c7678f1a5b5
+ /private/tmp/communitymech-batch79/okeke-publisher.txt: fa4227054533b34184e796082df3adf7e2bbed3ba1c7ab4b3699a81c7a00aec0
+ /private/tmp/communitymech-batch79/primary-manifest.json: e824d33b2f6f07dcc1b4b5c1dbf281b2919fc98c5732d54d84b2399abe6460b2
+ /private/tmp/communitymech-batch79/rumen-baseline-strict.tsv: b184ed5450b968070bb6c75648407e388f41a1eaf7017890723cf560999fc3f7
+ /private/tmp/communitymech-batch79/rumen-metadata.json: 1cb5211de4bcf5b2f324c6642d884927ff6cc50d08bdefb9fbdcf91458b82082
+ /private/tmp/communitymech-batch79/rumen-primary.txt: 7f2e605efe3dca16f3ce1543b27ed7c79c2b3495722c7f2f298ad6555fce5868
+ /private/tmp/communitymech-batch79/rumen-primary.xml: 60e8fcb72928fb1fbd21a8e1b6547a77a27b6c9d53ecd511276a23116d8e5dbf
+ /private/tmp/communitymech-batch79/rumen-tables.txt: 01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b
+ /private/tmp/communitymech-batch79/uranyl-official.txt: 5231a1c0477342af6f36a3d95663c4cc9f067907df0fd8d65e5bbbd0517c6d59
+primary_urls:
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6461962/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A22988623+AND+SRC%3AMED&format=json&resultType=core
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A22140175+AND+SRC%3AMED&format=json&resultType=core
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13273856/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A20859703+AND+SRC%3AMED&format=json&resultType=core
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13037301/fullTextXML
+- https://link.springer.com/article/10.1007/s12010-010-9091-0
+- https://www.tandfonline.com/doi/full/10.1080/09593330.2011.641036
+- https://www.ebi.ac.uk/chebi/CHEBI:43515
+primary_graph_snippet_count: 21
+cache_matched_graph_snippet_count: 21
+snippet_checks:
+- record: Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community
+ node: Low-pH Mixed-Ion Rhodanobacter Tolerance
+ reference: PMID:30523276
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/frc_tolerance-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community
+ node: Low-pH Mixed-Ion Rhodanobacter Tolerance
+ reference: PMID:30523276
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/frc_tolerance-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community
+ node: Contaminant-Selected Rhodanobacter Dominance
+ reference: PMID:30523276
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/frc_tolerance-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community
+ node: Contaminant-Selected Rhodanobacter Dominance
+ reference: PMID:30523276
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/frc_tolerance-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community
+ node: Mixed Metal and Nitrate Reduction Potential
+ reference: PMID:22988623
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/frc_wells-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community
+ node: Mixed Metal and Nitrate Reduction Potential
+ reference: PMID:22988623
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/frc_wells-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture
+ node: MET10-STR3 Sulfur Auxotrophy Cross-Feeding
+ reference: PMID:42318495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/ogataea-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture
+ node: MET10-STR3 Sulfur Auxotrophy Cross-Feeding
+ reference: PMID:42318495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/ogataea-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture
+ node: Asymmetric Homocysteine Dependency
+ reference: PMID:42318495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/ogataea-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture
+ node: Asymmetric Homocysteine Dependency
+ reference: PMID:42318495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/ogataea-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture
+ node: Initial Ratio-Dependent Met10 Enrichment
+ reference: PMID:42318495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/ogataea-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture
+ node: Initial Ratio-Dependent Met10 Enrichment
+ reference: PMID:42318495
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/ogataea-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Okeke_Lu_Cellulolytic_Consortium
+ node: Cellulose-Hydrolyzing Isolate Enzyme Activities
+ reference: PMID:20859703
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/okeke-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Okeke_Lu_Cellulolytic_Consortium
+ node: Xylan-Hydrolyzing Isolate Enzyme Activities
+ reference: PMID:20859703
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/okeke-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Okeke_Lu_Cellulolytic_Consortium
+ node: Proposed Complementary Lignocellulose Hydrolysis
+ reference: PMID:20859703
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/okeke-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Okeke_Lu_Cellulolytic_Consortium
+ node: Proposed Complementary Lignocellulose Hydrolysis
+ reference: PMID:20859703
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/okeke-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Optimized_Rumen_Fiber_Degrading_SynCom3
+ node: Box-Behnken optimized in vitro fiber degradation
+ reference: doi:10.1186/s40168-025-02331-3
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/rumen-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Optimized_Rumen_Fiber_Degrading_SynCom3
+ node: Genome-annotated carbohydrate-active enzyme complement
+ reference: doi:10.1186/s40168-025-02331-3
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/rumen-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Optimized_Rumen_Fiber_Degrading_SynCom3
+ node: Genome-annotated carbohydrate-active enzyme complement
+ reference: doi:10.1186/s40168-025-02331-3
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/rumen-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Optimized_Rumen_Fiber_Degrading_SynCom3
+ node: Genome-annotated carbohydrate-active enzyme complement
+ reference: doi:10.1186/s40168-025-02331-3
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/rumen-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+- record: Optimized_Rumen_Fiber_Degrading_SynCom3
+ node: In situ cattle rumen fermentation shift
+ reference: doi:10.1186/s40168-025-02331-3
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch79/rumen-primary.txt
+ method: Whitespace-only comparison against fresh Europe PMC primary text or public abstract and the unchanged
+ cache.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: true
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs:
+ - community_id: CommunityMech:000450
+ job: LITERATURE
+ query_chars: 11815
+ query_sha256: a1e91a88b4aaed8fe5fc8395f825150219e6441e7fc25119475e865b6ebe0cc7
+ meta_path: /private/tmp/communitymech-batch79/edison-ogataea/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-edison-literature-causal-meta.yaml
+ authorization: Scoped asynchronous question unanswered; preselection is not approval.
+limitations:
+- Fresh pre-paper baseline covers460 records and920 caches across both roots, including ignored/hidden files. Every12
+ existing node and4arrow was reviewed;12nodes3arrows remain. Four guarded repairs/history events;456 other records
+ and all920 caches unchanged.
+- 'Three complete primary main bodies read from fresh Europe PMC XML: metal-tolerance, Ogataea and rumen papers.
+ Captions read; no embedded main-text tables in these XML files. Field clone-library, Rhodanobacter taxonomy and
+ Okeke sources read at primary-abstract scope. No separate supplements, raw datasets or original figure pixels
+ audited.'
+- Normal Okeke publisher access confirms subscription preview; field publisher403 and Microbiology Society full-text
+ delivery failure respected. No access restriction bypass. Existing Okeke cache is abstract-only; inaccessible
+ full text does not establish absence of experiments.
+- All21 graph quotations independently match primary text and unchanged cache with whitespace-only comparison. Literal
+ matching is not entailment. Early oversized combined/cache reads were truncated; fresh main texts were read in
+ bounded chunks, and no absence finding relies on truncated output.
+- Oak Ridge retains experimentally supported selection, not mere unqualified correlation. Isolate provenance, pH,
+ mixture effects, organic matter and ion speciation bound transfer to field conditions. Nitrate toxicity was not
+ selective in the strain comparison; genus enrichment is not species identity or redox flux. Official ChEBI confirms
+ uranyl is43515, not free uranium6+.
+- Ogataea retains cooperative growth, actual nutrient rescue and controlled ratio effects. Directed metabolite exchange
+ is hypothesized, not measured. Two-pair OD range, methanol shortfall, distinct labeled tracking strains and weak-growth
+ high-met10 ratios are explicit; endpoint bias is not identical convergence or long-term stability.
+- Okeke positive isolate hydrolases and five-member construction remain. Both proposed hydrolytic-contribution arrows
+ are retained as hypotheses; accessible abstract does not quantify synergy, product-inhibition relief or lignin
+ degradation. Full-text acquisition remains needs_research, not a declaration of no experiments.
+- Rumen significant optimized in vitro NDFD, predicted gene complement and time-dependent cattle fermentation are
+ preserved. Initial seven-member gas effects differ from final five-member null gas result. Inoculum is not final
+ bottle concentration; bags are subsamples of three cattle per group. Nonsignificant72h fiber trends are not proven
+ improvement. No genome-to-outcome or workflow arrow added.
+- One Ogataea Edison LITERATURE dry run used zero provider submissions/credits. Scoped paid question unanswered.
+ Missing input/outcome and exchange-to-rescue structure stays1656; Okeke full-text follow-up1657 requires its own
+ workflow if new topology becomes justified. Earlier denied/pending scopes unchanged.
+- Dedup searched933 all-state issue titles/bodies and25 ignored/hidden-inclusive local matched files, excluding
+ git/docs/site/cache. Matching258/650/981/1149/1150/1151 read; no exhaustive PR-comment audit. Prior field-community,
+ medium, canonical-strain, Figure7 evidence and dangling/workflow-arrow fixes preserved.
+- 'Repair issues1652-1655 remain OPEN until protected-main merge; research1656/1657 and metadata1658 remain OPEN
+ afterward. Canonical membership and raw non-graph blocks are preserved, not certified. Rumen documented vocabulary
+ inconsistency is not a claimed gate failure: baseline schema and strict checks passed. Self-adversarial review
+ is not independent approval or corpus completion.'
+records:
+- path: kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml
+ id: CommunityMech:000136
+ original_sha256: c151a2da760528280dbab8bc4c3225ce73841a58f7df24391cbb112af2b84c90
+ record_sha256: fd8891c4ada299a06c57062e47f8598fc7f5a1755fc2e1241255c44cff6211d4
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
+ scope: Whole record and every existing node/arrow, including sparse graphs and missing structures; not whole-record
+ certification.
+ summary: Retain controlled isolate tolerance, correct uranyl grounding and keep bounded selection arrow; remove
+ unsupported redox coupling.; Retain genus-level field enrichment without species/denitrification or nitrate-selective-toxicity
+ overclaims.; Keep abstract-bounded redox potential without cross-feeding, measured flux or unmeasured ionic
+ speciation.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Low-pH Mixed-Ion Rhodanobacter Tolerance
+ original_node: Low-pH Mixed-Ion Rhodanobacter Tolerance
+ rationale: Retain controlled isolate tolerance, correct uranyl grounding and keep bounded selection arrow; remove
+ unsupported redox coupling.
+ - node: Contaminant-Selected Rhodanobacter Dominance
+ original_node: Contaminant-Selected Rhodanobacter Dominance
+ rationale: Retain genus-level field enrichment without species/denitrification or nitrate-selective-toxicity
+ overclaims.
+ - node: Mixed Metal and Nitrate Reduction Potential
+ original_node: Mixed Metal and Nitrate Reduction Potential
+ rationale: Keep abstract-bounded redox potential without cross-feeding, measured flux or unmeasured ionic speciation.
+ removed_node_decisions: []
+ edges_before:
+ - source: Low-pH Mixed-Ion Rhodanobacter Tolerance
+ target: Contaminant-Selected Rhodanobacter Dominance
+ description: Rhodanobacter tolerance to the low-pH U(VI)-Mn(II)-Al(III)-Cd(II)- Zn(II)-Co(II)-Ni(II) ion mixture
+ identifies a selective mechanism for the Rhodanobacter enrichment observed in the most contaminated FRC wells.
+ - source: Low-pH Mixed-Ion Rhodanobacter Tolerance
+ target: Mixed Metal and Nitrate Reduction Potential
+ description: Mixed metal tolerance defines the contaminated groundwater guilds that retain uranium, nitrate,
+ and iron reduction potential under the high-stress conditions of well FW113-47.
+ edges_after:
+ - source: Low-pH Mixed-Ion Rhodanobacter Tolerance
+ target: Contaminant-Selected Rhodanobacter Dominance
+ description: PARTIAL - Differential survival under low-pH mixed-metal stress supplies an experimentally supported
+ selection mechanism for field Rhodanobacter enrichment when relevant ions reach inhibitory concentrations.
+ This combines isolate perturbations with field abundance/geochemistry, not an in situ manipulation or proof
+ that nitrate toxicity selects Rhodanobacter. Organic matter, speciation and strain provenance limit transfer
+ of thresholds to groundwater.
+ retained_edge_decisions:
+ - source: Low-pH Mixed-Ion Rhodanobacter Tolerance
+ target: Contaminant-Selected Rhodanobacter Dominance
+ description: PARTIAL - Differential survival under low-pH mixed-metal stress supplies an experimentally supported
+ selection mechanism for field Rhodanobacter enrichment when relevant ions reach inhibitory concentrations.
+ This combines isolate perturbations with field abundance/geochemistry, not an in situ manipulation or proof
+ that nitrate toxicity selects Rhodanobacter. Organic matter, speciation and strain provenance limit transfer
+ of thresholds to groundwater.
+ rationale: PARTIAL - Differential survival under low-pH mixed-metal stress supplies an experimentally supported
+ selection mechanism for field Rhodanobacter enrichment when relevant ions reach inhibitory concentrations.
+ This combines isolate perturbations with field abundance/geochemistry, not an in situ manipulation or proof
+ that nitrate toxicity selects Rhodanobacter. Organic matter, speciation and strain provenance limit transfer
+ of thresholds to groundwater.
+ removed_edge_decisions:
+ - source: Low-pH Mixed-Ion Rhodanobacter Tolerance
+ target: Mixed Metal and Nitrate Reduction Potential
+ description: Mixed metal tolerance defines the contaminated groundwater guilds that retain uranium, nitrate,
+ and iron reduction potential under the high-stress conditions of well FW113-47.
+ rationale: Mixed-ion isolate tolerance does not establish redox-guild selection or reduction flux in the different
+ four-well clone-library study.
+ references:
+ - PMID:22988623
+ - PMID:30523276
+ issues:
+ - 1652
+ - 1658
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community/2026-10-07T050635Z-codex-ddf580.yaml
+ source_review:
+ - source: frc_tolerance
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6461962/fullTextXML
+ scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+ data or original figure pixels.
+ - source: frc_wells
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A22988623+AND+SRC%3AMED&format=json&resultType=core
+ scope: Primary abstract only; full text not available through Europe PMC.
+ - source: frc_isolates
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A22140175+AND+SRC%3AMED&format=json&resultType=core
+ scope: Primary abstract only; full text not available through Europe PMC.
+- path: kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml
+ id: CommunityMech:000450
+ original_sha256: a6b1d3f9f3dd26c371733554918220ff570d308478415e5f8434828237d65f64
+ record_sha256: 5feb6042f2cf7da47745ea846cab0dba57cd50b9fef9aa20a8ab60eb849e805e
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
+ scope: Whole record and every existing node/arrow, including sparse graphs and missing structures; not whole-record
+ certification.
+ summary: Preserve observed complementation with two-pair OD range, carbon-source and labeled-strain limits.; Retain
+ directed sulfur-exchange model as hypothesized while preserving measured supplement rescue.; Preserve controlled
+ ratio effects without universal growth, increasing-fraction or identical-endpoint claims.
+ renamed_nodes: {}
+ node_decisions:
+ - node: MET10-STR3 Sulfur Auxotrophy Cross-Feeding
+ original_node: MET10-STR3 Sulfur Auxotrophy Cross-Feeding
+ rationale: Preserve observed complementation with two-pair OD range, carbon-source and labeled-strain limits.
+ - node: Asymmetric Homocysteine Dependency
+ original_node: Asymmetric Homocysteine Dependency
+ rationale: Retain directed sulfur-exchange model as hypothesized while preserving measured supplement rescue.
+ - node: Initial Ratio-Dependent Met10 Enrichment
+ original_node: Initial Ratio-Dependent Met10 Enrichment
+ rationale: Preserve controlled ratio effects without universal growth, increasing-fraction or identical-endpoint
+ claims.
+ removed_node_decisions: []
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42318495
+ issues:
+ - 1653
+ - 1656
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture/2026-10-07T050635Z-codex-aab572.yaml
+ source_review:
+ - source: ogataea
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13273856/fullTextXML
+ scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+ data or original figure pixels.
+- path: kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml
+ id: CommunityMech:000048
+ original_sha256: 31645319bff71e9bd1c8c4cc884c8fceb10b257457f6f18bc44b0a0c7cbe85ce
+ record_sha256: 1992cf47e5fd154a6684b025a6117d7f10398c65beb8d8e5f65e8e2115ab8f42
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
+ scope: Whole record and every existing node/arrow, including sparse graphs and missing structures; not whole-record
+ certification.
+ summary: Preserve quantified DB1/DB2 cellulase and DB1 beta-glucosidase activities at isolate-assay scope.; Preserve
+ positive DB2/DB13 xylan-hydrolase results and qualify their proposed contribution.; Retain assembled-consortium
+ potential and both hypothesis arrows without promoting prospective benefits to measured synergy.
+ renamed_nodes:
+ Cellulose Degradation: Cellulose-Hydrolyzing Isolate Enzyme Activities
+ Hemicellulose Degradation: Xylan-Hydrolyzing Isolate Enzyme Activities
+ Synergistic Lignocellulose Degradation: Proposed Complementary Lignocellulose Hydrolysis
+ node_decisions:
+ - node: Cellulose-Hydrolyzing Isolate Enzyme Activities
+ original_node: Cellulose Degradation
+ rationale: Preserve quantified DB1/DB2 cellulase and DB1 beta-glucosidase activities at isolate-assay scope.
+ - node: Xylan-Hydrolyzing Isolate Enzyme Activities
+ original_node: Hemicellulose Degradation
+ rationale: Preserve positive DB2/DB13 xylan-hydrolase results and qualify their proposed contribution.
+ - node: Proposed Complementary Lignocellulose Hydrolysis
+ original_node: Synergistic Lignocellulose Degradation
+ rationale: Retain assembled-consortium potential and both hypothesis arrows without promoting prospective benefits
+ to measured synergy.
+ removed_node_decisions: []
+ edges_before:
+ - source: Cellulose Degradation
+ target: Synergistic Lignocellulose Degradation
+ description: Cellulase and beta-glucosidase activities provide the cellulose-hydrolysis branch of the combined
+ cellulolytic-xylanolytic consortium.
+ - source: Hemicellulose Degradation
+ target: Synergistic Lignocellulose Degradation
+ description: Xylanase and beta-xylosidase activities provide the hemicellulose-hydrolysis branch of the combined
+ cellulolytic-xylanolytic consortium.
+ edges_after:
+ - source: Cellulose-Hydrolyzing Isolate Enzyme Activities
+ target: Proposed Complementary Lignocellulose Hydrolysis
+ description: HYPOTHESIZED - Measured isolate hydrolases provide the cellulose-hydrolysis branch proposed to
+ complement the other enzyme activities in the assembled consortium. The causal contribution is biochemical
+ potential inferred from isolate assays and consortium construction, not a measured increase in combined-culture
+ degradation or demonstrated synergistic flux.
+ - source: Xylan-Hydrolyzing Isolate Enzyme Activities
+ target: Proposed Complementary Lignocellulose Hydrolysis
+ description: HYPOTHESIZED - Measured isolate hydrolases provide the hemicellulose-hydrolysis branch proposed
+ to complement the other enzyme activities in the assembled consortium. The causal contribution is biochemical
+ potential inferred from isolate assays and consortium construction, not a measured increase in combined-culture
+ degradation or demonstrated synergistic flux.
+ retained_edge_decisions:
+ - source: Cellulose-Hydrolyzing Isolate Enzyme Activities
+ target: Proposed Complementary Lignocellulose Hydrolysis
+ description: HYPOTHESIZED - Measured isolate hydrolases provide the cellulose-hydrolysis branch proposed to
+ complement the other enzyme activities in the assembled consortium. The causal contribution is biochemical
+ potential inferred from isolate assays and consortium construction, not a measured increase in combined-culture
+ degradation or demonstrated synergistic flux.
+ rationale: HYPOTHESIZED - Measured isolate hydrolases provide the cellulose-hydrolysis branch proposed to complement
+ the other enzyme activities in the assembled consortium. The causal contribution is biochemical potential
+ inferred from isolate assays and consortium construction, not a measured increase in combined-culture degradation
+ or demonstrated synergistic flux.
+ - source: Xylan-Hydrolyzing Isolate Enzyme Activities
+ target: Proposed Complementary Lignocellulose Hydrolysis
+ description: HYPOTHESIZED - Measured isolate hydrolases provide the hemicellulose-hydrolysis branch proposed
+ to complement the other enzyme activities in the assembled consortium. The causal contribution is biochemical
+ potential inferred from isolate assays and consortium construction, not a measured increase in combined-culture
+ degradation or demonstrated synergistic flux.
+ rationale: HYPOTHESIZED - Measured isolate hydrolases provide the hemicellulose-hydrolysis branch proposed to
+ complement the other enzyme activities in the assembled consortium. The causal contribution is biochemical
+ potential inferred from isolate assays and consortium construction, not a measured increase in combined-culture
+ degradation or demonstrated synergistic flux.
+ removed_edge_decisions: []
+ references:
+ - PMID:20859703
+ issues:
+ - 1654
+ - 1657
+ - 1658
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Okeke_Lu_Cellulolytic_Consortium/2026-10-07T050635Z-codex-3eb057.yaml
+ source_review:
+ - source: okeke
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A20859703+AND+SRC%3AMED&format=json&resultType=core
+ scope: Primary abstract only; full text not available through Europe PMC.
+- path: kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml
+ id: CommunityMech:000398
+ original_sha256: 85de83d3b8aac334bbf269ce5e7480e8bd59bb40990f94bb0a59146565ac173e
+ record_sha256: ee1333388f5d7353daf7713abf744220accf40a855bdbe8b66389f9b7c5031c6
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml
+ scope: Whole record and every existing node/arrow, including sparse graphs and missing structures; not whole-record
+ certification.
+ summary: Preserve significant optimized laboratory NDFD with null endpoints, formulation and inoculum-concentration
+ limits.; Preserve predicted enzyme complement and Fig7 evidence without promoting annotation to demonstrated
+ expression or synergy.; Preserve time-dependent cattle fermentation outcomes and nonsignificant fiber trends
+ with animal-level replication limits.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Box-Behnken optimized in vitro fiber degradation
+ original_node: Box-Behnken optimized in vitro fiber degradation
+ rationale: Preserve significant optimized laboratory NDFD with null endpoints, formulation and inoculum-concentration
+ limits.
+ - node: Genome-annotated carbohydrate-active enzyme complement
+ original_node: Genome-annotated carbohydrate-active enzyme complement
+ rationale: Preserve predicted enzyme complement and Fig7 evidence without promoting annotation to demonstrated
+ expression or synergy.
+ - node: In situ cattle rumen fermentation shift
+ original_node: In situ cattle rumen fermentation shift
+ rationale: Preserve time-dependent cattle fermentation outcomes and nonsignificant fiber trends with animal-level
+ replication limits.
+ removed_node_decisions: []
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - doi:10.1186/s40168-025-02331-3
+ issues:
+ - 1655
+ - 1658
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Optimized_Rumen_Fiber_Degrading_SynCom3/2026-10-07T050635Z-codex-4f5a19.yaml
+ source_review:
+ - source: rumen
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13037301/fullTextXML
+ scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+ data or original figure pixels.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 92faac241..9daf6f6d8 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -279,10 +279,10 @@ kb/communities/Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium.yaml Community
kb/communities/OMM12_Gnotobiotic_Mouse_Gut_Community.yaml CommunityMech:000133 850493028ce860f07a09dccf22edadd16a29743f9ba8c42363c36091ad0a5e38 3 1 90.0 reports/causal_graph_review/decisions/20261007-four-records-batch78.yaml reviewed
kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml CommunityMech:000176 151a414766ded2f1c8b094002819c6e620751b6344ef9753d1f3a988c1cf99dd 4 2 97.5 reports/causal_graph_review/decisions/20261007-four-records-batch78.yaml reviewed
kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml CommunityMech:000047 339ff13ebe407e9c101499ec4a8ec7618da7079c503e7457152577021ab71a04 5 3 92.0 reports/causal_graph_review/decisions/20261007-four-records-batch78.yaml needs_research
-kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml CommunityMech:000136 c151a2da760528280dbab8bc4c3225ce73841a58f7df24391cbb112af2b84c90 3 2 100.0 pending
-kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml CommunityMech:000450 a6b1d3f9f3dd26c371733554918220ff570d308478415e5f8434828237d65f64 3 0 70.0 pending
-kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml CommunityMech:000048 31645319bff71e9bd1c8c4cc884c8fceb10b257457f6f18bc44b0a0c7cbe85ce 3 2 100.0 pending
-kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml CommunityMech:000398 85de83d3b8aac334bbf269ce5e7480e8bd59bb40990f94bb0a59146565ac173e 3 0 65.0 pending
+kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml CommunityMech:000136 fd8891c4ada299a06c57062e47f8598fc7f5a1755fc2e1241255c44cff6211d4 3 1 80.0 reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml reviewed
+kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml CommunityMech:000450 5feb6042f2cf7da47745ea846cab0dba57cd50b9fef9aa20a8ab60eb849e805e 3 0 66.7 reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml needs_research
+kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml CommunityMech:000048 1992cf47e5fd154a6684b025a6117d7f10398c65beb8d8e5f65e8e2115ab8f42 3 2 90.0 reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml needs_research
+kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml CommunityMech:000398 ee1333388f5d7353daf7713abf744220accf40a855bdbe8b66389f9b7c5031c6 3 0 65.0 reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml reviewed
kb/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.yaml CommunityMech:000155 baa74026edc403e57902dcc1b3aadd94e8e25b7cc3ef6881728bc5004e99dfda 3 2 100.0 pending
kb/communities/PET_Artificial_FourSpecies_Degradation_Consortium.yaml CommunityMech:000163 aa7d95b77288e475304bc00b40d4ba95ebb66bd227071fbab6387e4bbea316f9 5 5 100.0 pending
kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml CommunityMech:000049 849547e3c5e5485f2ca58d5e699c40de1246352be383a5cb17b109c6a0c5b204 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 3d8f5c74c..734196e00 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": 1447,
- "edges": 614,
+ "edges": 613,
"records_without_nodes": 8,
"records_without_edges": 166,
"review_status_counts": {
- "needs_research": 30,
- "pending": 180,
- "reviewed": 250
+ "needs_research": 32,
+ "pending": 176,
+ "reviewed": 252
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261007-batch79.json b/reports/causal_graph_review/validation-20261007-batch79.json
new file mode 100644
index 000000000..1227680c7
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261007-batch79.json
@@ -0,0 +1,1025 @@
+{
+ "base_commit": "d9da91dd8003dc1958f1d13a30cd3b957e3bf5a4",
+ "scope": [
+ "kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml",
+ "kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml",
+ "kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml",
+ "kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch79/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-strict.tsv",
+ "kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-strict.log",
+ "log_sha256": "7b4fdd056d1f1418f2aeec3fad7988eee5408f15104ceb4a26e681c54384f5ad",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch79/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-batch79/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-strict.tsv\n"
+ },
+ {
+ "check": "Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-references.log",
+ "log_sha256": "a5708d8922f9b7ff1de1bb409c964c5a6c92a9e2583d96c9887c0cd5ea783fd6",
+ "output_tail": "Validating kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-snippets.log",
+ "log_sha256": "d6441c5dcfaf6a072d70e8708d5fe1bbd2c2a2d31da61b3014fb014108c34cef",
+ "output_tail": "# 18 evidence snippets scanned across 1 files\n MATCH 18\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": "Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-rank.log",
+ "log_sha256": "7af6196656617980ab711d1d261d1dfe26e141ec17017c5b34e522db125cc30c",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000136\",\n \"name\": \"Oak Ridge FRC Uranium-Nitrate Groundwater Community\",\n \"score\": 80.0,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community/2026-10-07T050635Z-codex-ddf580.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch79/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch79/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-strict.tsv",
+ "kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-strict.log",
+ "log_sha256": "7d59f6fa25a1d97c0020cf4c0742fe60ca4efc33239a38e2712c6c8a93631e43",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch79/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-batch79/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-references.log",
+ "log_sha256": "88a7a7caa08a92c64f675ed5cc93ad4d55afd554bd659526349fb170c5ebd3aa",
+ "output_tail": "Validating kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_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/Ogataea_Met10_Str3_Sulfur_CrossFeeding_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": "Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-snippets.log",
+ "log_sha256": "d353a2e438e49543043d94dbd2d275ccc825dad7bb23be8ad43bf853927d2fe3",
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+ },
+ {
+ "check": "Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch79/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-rank.log",
+ "log_sha256": "91d515c495b607f796fcd61de13fceb049d8344e60ae3031f2b62a08962a2fe2",
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+ "check": "Ogataea_Met10_Str3_Sulfur_CrossFeeding_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/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture/2026-10-07T050635Z-codex-aab572.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch79/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ {
+ "check": "Okeke_Lu_Cellulolytic_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch79/Okeke_Lu_Cellulolytic_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Okeke_Lu_Cellulolytic_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch79/Okeke_Lu_Cellulolytic_Consortium-strict.tsv",
+ "kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch79/Okeke_Lu_Cellulolytic_Consortium-strict.log",
+ "log_sha256": "baa63717c7c221be770b1b80be923c4cd8261a241488672556015fe1feb615f4",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch79/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-batch79/Okeke_Lu_Cellulolytic_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Okeke_Lu_Cellulolytic_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Okeke_Lu_Cellulolytic_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Okeke_Lu_Cellulolytic_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Okeke_Lu_Cellulolytic_Consortium-references.log",
+ "log_sha256": "522213a6907c477a5a009e7a5fec1d8e1a78e7e60e0c06437d67601f5f14a54e",
+ "output_tail": "Validating kb/communities/Okeke_Lu_Cellulolytic_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/Okeke_Lu_Cellulolytic_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": "Okeke_Lu_Cellulolytic_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Okeke_Lu_Cellulolytic_Consortium-snippets.log",
+ "log_sha256": "f77044cea09a90a006f3fc48666f62a208521829981c6819a3a36631506c4ec1",
+ "output_tail": "# 16 evidence snippets scanned across 1 files\n MATCH 16\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": "Okeke_Lu_Cellulolytic_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Okeke_Lu_Cellulolytic_Consortium-rank.log",
+ "log_sha256": "2db7bd837398d93cfb022a9d223130c294930f3b8445a7d4ddaba4bc651ff2ba",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000048\",\n \"name\": \"Okeke-Lu Cellulolytic-Xylanolytic Consortium\",\n \"score\": 90.0,\n \"taxonomy\": 5,\n \"connected_taxa\": 5,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Okeke_Lu_Cellulolytic_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/Okeke_Lu_Cellulolytic_Consortium/2026-10-07T050635Z-codex-3eb057.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Okeke_Lu_Cellulolytic_Consortium-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Optimized_Rumen_Fiber_Degrading_SynCom3-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Optimized_Rumen_Fiber_Degrading_SynCom3-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Optimized_Rumen_Fiber_Degrading_SynCom3-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch79/Optimized_Rumen_Fiber_Degrading_SynCom3-strict.tsv",
+ "kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Optimized_Rumen_Fiber_Degrading_SynCom3-strict.log",
+ "log_sha256": "a86b34d99a7e6e84a704917111f7967411cf1cfa1abf0801c423df5484433e3e",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch79/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-batch79/Optimized_Rumen_Fiber_Degrading_SynCom3-strict.tsv\n"
+ },
+ {
+ "check": "Optimized_Rumen_Fiber_Degrading_SynCom3-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Optimized_Rumen_Fiber_Degrading_SynCom3-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Optimized_Rumen_Fiber_Degrading_SynCom3-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Optimized_Rumen_Fiber_Degrading_SynCom3-references.log",
+ "log_sha256": "5bc1fa87dbe5f27b2814b628dd017523ebb715e4abaae48c5798099008b61823",
+ "output_tail": "Validating kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.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/Optimized_Rumen_Fiber_Degrading_SynCom3.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": "Optimized_Rumen_Fiber_Degrading_SynCom3-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Optimized_Rumen_Fiber_Degrading_SynCom3-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": "Optimized_Rumen_Fiber_Degrading_SynCom3-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Optimized_Rumen_Fiber_Degrading_SynCom3-rank.log",
+ "log_sha256": "63e0a2c78199e0a1bed884e799c69005ba0e4d215c575b8fea8279bd86636625",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000398\",\n \"name\": \"Optimized Rumen Fiber-Degrading SynCom 3\",\n \"score\": 65.0,\n \"taxonomy\": 5,\n \"connected_taxa\": 5,\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/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Optimized_Rumen_Fiber_Degrading_SynCom3-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Optimized_Rumen_Fiber_Degrading_SynCom3/2026-10-07T050635Z-codex-4f5a19.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/Optimized_Rumen_Fiber_Degrading_SynCom3-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-batch79/inventory.log",
+ "log_sha256": "d8deb3e3f3986570a6f10789021ea954f3643713353efce6c1e099b151c98587",
+ "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\": 1447,\n \"edges\": 613,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 166,\n \"review_status_counts\": {\n \"needs_research\": 32,\n \"pending\": 176,\n \"reviewed\": 252\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-batch79/network.log",
+ "log_sha256": "dcb33d46aa53f5e1dec55b1cd6463b83d3723e2ebf8c97999c93d0a5f4a2fed1",
+ "output_tail": "{\n \"preferred_term\": \"Legionella MAGs\",\n \"term\": {\n \"id\": \"NCBITaxon:445\",\n \"label\": \"Legionella\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n },\n \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n \"evidence\": [\n {\n \"reference\": \"PMID:41457319\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"COMPUTATIONAL\",\n \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n }\n ]\n },\n \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch79/rank-all.log",
+ "log_sha256": "1e98db369d872f6f98d3ff97314df4d789279436843d44c0bd7332873d76840d",
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Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 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Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch79/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch79/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch79/docs/index.html\n"
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/private/tmp/communitymech-causal-batch79/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch79/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch79/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch79/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch79/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch78')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/connectivity-survey.log",
+ "log_sha256": "52c3470443d3c017a6c5f5ffed2fbb43348feee7fe8afbea853d97b3c39e9ed4",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}, \"current\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/regressions.log",
+ "log_sha256": "0fa0603fcc3dc024850902cd8bf58d453ea00ecce2da677cb1c3b551362ed5f3",
+ "output_tail": "........................................................................ [ 10%]\n........................................................................ [ 20%]\n........................................................................ [ 30%]\n........................................................................ [ 40%]\n........................................................................ [ 50%]\n........................................................................ [ 61%]\n........................................................................ [ 71%]\n........................................................................ [ 81%]\n........................................................................ [ 91%]\n.......................................................... [100%]\n706 passed in 206.85s (0:03:26)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch79.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/black.log",
+ "log_sha256": "1a56c7cd8457fd05d978cfbd139d7bfd86e86acaa9b57668e718ef8bccc0cf48",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n1 file would be left unchanged.\n"
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch79.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ },
+ {
+ "check": "primary-graph-proof",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import hashlib,json,pathlib,yaml\nP=pathlib.Path\nledger=yaml.safe_load(P('reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml').read_text())\nfor p,h in ledger['primary_artifacts'].items():\n assert hashlib.sha256(P(p).read_bytes()).hexdigest()==h\nmanifest=json.loads(P('/private/tmp/communitymech-batch79/primary-manifest.json').read_text())\nsources={v['reference']:''.join(P(v['extracted_body']).read_text().split()) for v in manifest.values()}\ncount=0\nfor row in ledger['records']:\n doc=yaml.safe_load(P(row['path']).read_text())\n for n in doc['ecological_interactions']:\n for e in n['evidence']:\n assert ''.join(e['snippet'].split()) in sources[e['reference']]\n count+=1\nassert count==21\nassert sum(len(r['node_decisions']) for r in ledger['records'])==12\nassert sum(len(r['edges_before']) for r in ledger['records'])==4\nassert sum(len(r['edges_after']) for r in ledger['records'])==3\nassert sum(len(r['removed_edge_decisions']) for r in ledger['records'])==1\nassert sum(r['curation_events_added'] for r in ledger['records'])==4\nassert [r['status'] for r in ledger['records']]==['reviewed','needs_research','needs_research','reviewed']\nprint(json.dumps(dict(primary_matched=count,new_nodes_or_arrows=0,complete_main_bodies_read=3,other_primary_abstracts_read=3,separate_supplements_raw_datasets_original_figure_pixels_audited=False)))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/primary-graph-proof.log",
+ "log_sha256": "f6ec2860093d83fb9b3005ac95a6d5b1a93c10c12ea3844e404347b2d5886f17",
+ "output_tail": "{\"primary_matched\": 21, \"new_nodes_or_arrows\": 0, \"complete_main_bodies_read\": 3, \"other_primary_abstracts_read\": 3, \"separate_supplements_raw_datasets_original_figure_pixels_audited\": false}\n"
+ },
+ {
+ "check": "focused-final",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch79/focused-final.log",
+ "log_sha256": "3d3e06ec8977564d3b39b45adcb7d7ce2743c34fd78112158e7dbe74d008bbe6",
+ "output_tail": "................... [100%]\n19 passed in 16.68s\n"
+ }
+ ],
+ "limitations": [
+ "Fresh pre-paper baseline covers460 records and920 caches across both roots, including ignored/hidden files. Every12 existing node and4arrow was reviewed;12nodes3arrows remain. Four guarded repairs/history events;456 other records and all920 caches unchanged.",
+ "Three complete primary main bodies read from fresh Europe PMC XML: metal-tolerance, Ogataea and rumen papers. Captions read; no embedded main-text tables in these XML files. Field clone-library, Rhodanobacter taxonomy and Okeke sources read at primary-abstract scope. No separate supplements, raw datasets or original figure pixels audited.",
+ "Normal Okeke publisher access confirms subscription preview; field publisher403 and Microbiology Society full-text delivery failure respected. No access restriction bypass. Existing Okeke cache is abstract-only; inaccessible full text does not establish absence of experiments.",
+ "All21 graph quotations independently match primary text and unchanged cache with whitespace-only comparison. Literal matching is not entailment. Early oversized combined/cache reads were truncated; fresh main texts were read in bounded chunks, and no absence finding relies on truncated output.",
+ "Oak Ridge retains experimentally supported selection, not mere unqualified correlation. Isolate provenance, pH, mixture effects, organic matter and ion speciation bound transfer to field conditions. Nitrate toxicity was not selective in the strain comparison; genus enrichment is not species identity or redox flux. Official ChEBI confirms uranyl is43515, not free uranium6+.",
+ "Ogataea retains cooperative growth, actual nutrient rescue and controlled ratio effects. Directed metabolite exchange is hypothesized, not measured. Two-pair OD range, methanol shortfall, distinct labeled tracking strains and weak-growth high-met10 ratios are explicit; endpoint bias is not identical convergence or long-term stability.",
+ "Okeke positive isolate hydrolases and five-member construction remain. Both proposed hydrolytic-contribution arrows are retained as hypotheses; accessible abstract does not quantify synergy, product-inhibition relief or lignin degradation. Full-text acquisition remains needs_research, not a declaration of no experiments.",
+ "Rumen significant optimized in vitro NDFD, predicted gene complement and time-dependent cattle fermentation are preserved. Initial seven-member gas effects differ from final five-member null gas result. Inoculum is not final bottle concentration; bags are subsamples of three cattle per group. Nonsignificant72h fiber trends are not proven improvement. No genome-to-outcome or workflow arrow added.",
+ "One Ogataea Edison LITERATURE dry run used zero provider submissions/credits. Scoped paid question unanswered. Missing input/outcome and exchange-to-rescue structure stays1656; Okeke full-text follow-up1657 requires its own workflow if new topology becomes justified. Earlier denied/pending scopes unchanged.",
+ "Dedup searched933 all-state issue titles/bodies and25 ignored/hidden-inclusive local matched files, excluding git/docs/site/cache. Matching258/650/981/1149/1150/1151 read; no exhaustive PR-comment audit. Prior field-community, medium, canonical-strain, Figure7 evidence and dangling/workflow-arrow fixes preserved.",
+ "Repair issues1652-1655 remain OPEN until protected-main merge; research1656/1657 and metadata1658 remain OPEN afterward. Canonical membership and raw non-graph blocks are preserved, not certified. Rumen documented vocabulary inconsistency is not a claimed gate failure: baseline schema and strict checks passed. Self-adversarial review is not independent approval or corpus completion.",
+ "Exact HTML-description parser and repeat-render checks, not browser screenshots. Post-commit docs-current is separate."
+ ],
+ "snippet_counts_by_record": {
+ "kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml": {
+ "MATCH": 18,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml": {
+ "MATCH": 28,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml": {
+ "MATCH": 16,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml": {
+ "MATCH": 19,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 58,
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 920,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": true,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [
+ {
+ "community_id": "CommunityMech:000450",
+ "job": "LITERATURE",
+ "query_chars": 11815,
+ "query_sha256": "a1e91a88b4aaed8fe5fc8395f825150219e6441e7fc25119475e865b6ebe0cc7",
+ "meta_path": "/private/tmp/communitymech-batch79/edison-ogataea/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-edison-literature-causal-meta.yaml",
+ "authorization": "Scoped asynchronous question unanswered; preselection is not approval."
+ }
+ ]
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch79/access-results.json": "fe939480fa759a8f8feedaeecba55e4c07717550a0a2a1d2401db3f1c33b9198",
+ "/private/tmp/communitymech-batch79/baseline.json": "7586929f90340d7643aa5a1a97461cb2aeb355371584bc2199b57245ff6d7bb9",
+ "/private/tmp/communitymech-batch79/edison-ogataea/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture-edison-literature-causal-meta.yaml": "700dc8f86a306fd60032acd29a2c860525b4375cb27747d438b5852d72102ea1",
+ "/private/tmp/communitymech-batch79/frc_isolates-metadata.json": "7ed07dcf5d875ccdca1f5cf4dcf2cf33f91eee28a7109f84fdc57701280b0098",
+ "/private/tmp/communitymech-batch79/frc_isolates-primary.txt": "1a33ce5bad56bf220d95213eddde22b6932235d9fbeb423aec9aca2d41fb093b",
+ "/private/tmp/communitymech-batch79/frc_tolerance-metadata.json": "ce987c60cdd82f2b6cf3b3b03a2fb25629f5cf82dfd6387b67964d7a9ae873a7",
+ "/private/tmp/communitymech-batch79/frc_tolerance-primary.txt": "dcec0b3ad05d934d78754454c009a52f283d6076c6605917c1f9c9c799b1053a",
+ "/private/tmp/communitymech-batch79/frc_tolerance-primary.xml": "0ced6c91f494fd341adce7e4559e3af27a6e70983e5b33b54a9eb628dd566bf8",
+ "/private/tmp/communitymech-batch79/frc_tolerance-tables.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b",
+ "/private/tmp/communitymech-batch79/frc_wells-metadata.json": "6062e88be83383c1fba31a5c4641fffe57aa71f8c1ac76755c5e8076b9e39e30",
+ "/private/tmp/communitymech-batch79/frc_wells-primary.txt": "d77f8032aa5d23c3b68f6e4ac95e4affc166ddfced02bdb555f0bdbdbc6ae4a4",
+ "/private/tmp/communitymech-batch79/issue-matches.json": "06a1bdb5d05689edd6e5701ff22d057234d1d1a917f6f6c4ca0d8bf9b3291ba7",
+ "/private/tmp/communitymech-batch79/issues.json": "e644d42955c048cb84b215a6a79759b5dc0e06f4a0cda0ebc841cb48792a12c1",
+ "/private/tmp/communitymech-batch79/local-matches.txt": "51e8e3ba10450433ed204263fdf33dcba169de7d8febd41c89f449ac4c379b1f",
+ "/private/tmp/communitymech-batch79/ogataea-metadata.json": "9d79fcd296d7478c13495bcbfde74327fcb8fbce533b2160764314dfc70cb5e2",
+ "/private/tmp/communitymech-batch79/ogataea-primary.txt": "2ea60a11fe9a86bf66183b3e8332363f1e631bcbcfd8eb3143aa1117d10b9a5a",
+ "/private/tmp/communitymech-batch79/ogataea-primary.xml": "0d0f08bce1cdf95f776608b9f6418d953c63585333e6ac64e8617f004aeb97b7",
+ "/private/tmp/communitymech-batch79/ogataea-tables.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b",
+ "/private/tmp/communitymech-batch79/okeke-metadata.json": "11f99b3b01a530ad72714d7702dbb1829388ac4064a68aae873afac31d67f136",
+ "/private/tmp/communitymech-batch79/okeke-primary.txt": "41756012aa5ca7602ae608c6ae96e53e3e45c0badedc07d3f2759c7678f1a5b5",
+ "/private/tmp/communitymech-batch79/okeke-publisher.txt": "fa4227054533b34184e796082df3adf7e2bbed3ba1c7ab4b3699a81c7a00aec0",
+ "/private/tmp/communitymech-batch79/primary-manifest.json": "e824d33b2f6f07dcc1b4b5c1dbf281b2919fc98c5732d54d84b2399abe6460b2",
+ "/private/tmp/communitymech-batch79/rumen-baseline-strict.tsv": "b184ed5450b968070bb6c75648407e388f41a1eaf7017890723cf560999fc3f7",
+ "/private/tmp/communitymech-batch79/rumen-metadata.json": "1cb5211de4bcf5b2f324c6642d884927ff6cc50d08bdefb9fbdcf91458b82082",
+ "/private/tmp/communitymech-batch79/rumen-primary.txt": "7f2e605efe3dca16f3ce1543b27ed7c79c2b3495722c7f2f298ad6555fce5868",
+ "/private/tmp/communitymech-batch79/rumen-primary.xml": "60e8fcb72928fb1fbd21a8e1b6547a77a27b6c9d53ecd511276a23116d8e5dbf",
+ "/private/tmp/communitymech-batch79/rumen-tables.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b",
+ "/private/tmp/communitymech-batch79/uranyl-official.txt": "5231a1c0477342af6f36a3d95663c4cc9f067907df0fd8d65e5bbbd0517c6d59"
+ },
+ "network_delta": {
+ "existing_findings_preserved": 44,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "All44 baseline warnings preserved exactly. Community scope remains aggregate, not resolved member-specific activity. No taxonomy or auditor-rule changes."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1433,
+ "arrows": 605
+ },
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 393,
+ "mixed": 125,
+ "community_level_only": 268,
+ "taxa": 1511,
+ "credited_solely_by_the_rule": 1240
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 393,
+ "mixed": 125,
+ "community_level_only": 268,
+ "taxa": 1511,
+ "credited_solely_by_the_rule": 1240
+ }
+ },
+ "delta": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "interpretation": "No scope-count change, taxonomy edit, or auditor-rule change. Aggregate outcomes do not establish member-resolved activity."
+ },
+ "network_warning_count": 44,
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1447,
+ "edges": 613,
+ "records_without_nodes": 8,
+ "records_without_edges": 166,
+ "review_status_counts": {
+ "needs_research": 32,
+ "pending": 176,
+ "reviewed": 252
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261007-four-records-batch79.yaml": "9dd19980fd51ff6885a8be6faf1aa5245931b8fb7b0adf4723fbdfa74ae3bb30",
+ "tests/test_causal_review_batch79.py": "6d0b452c6d10a5e31e0676a53a68bbcb070aa8a732e9c54d4ac037ca7e779bde",
+ "kb/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.yaml": "fd8891c4ada299a06c57062e47f8598fc7f5a1755fc2e1241255c44cff6211d4",
+ "kb/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.yaml": "5feb6042f2cf7da47745ea846cab0dba57cd50b9fef9aa20a8ab60eb849e805e",
+ "kb/communities/Okeke_Lu_Cellulolytic_Consortium.yaml": "1992cf47e5fd154a6684b025a6117d7f10398c65beb8d8e5f65e8e2115ab8f42",
+ "kb/communities/Optimized_Rumen_Fiber_Degrading_SynCom3.yaml": "ee1333388f5d7353daf7713abf744220accf40a855bdbe8b66389f9b7c5031c6",
+ "reports/causal_graph_review/README.md": "faa44482b4add8042bc2009a0ad83e019900845dab2dcb48eb729d124336096a"
+ },
+ "status": "verified_assay_boundary_graph_review",
+ "pre_research_baseline": {
+ "base_commit": "d9da91dd8003dc1958f1d13a30cd3b957e3bf5a4",
+ "base_tree": "7b3e7d91a758f2249644d002bba89dff3d4a812e",
+ "research_worktree": "/private/tmp/communitymech-causal-batch78",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch79/baseline-rank.log",
+ "sha256": "5d648ee7537de6316349e2d68913e86a3296c8b9353892e3c706ce96510f397b",
+ "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch79/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch79/baseline-network.log",
+ "sha256": "dcb33d46aa53f5e1dec55b1cd6463b83d3723e2ebf8c97999c93d0a5f4a2fed1",
+ "output_tail": " \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch79/baseline-downstream.log",
+ "sha256": "a575822bb99ac90f5e3313f3dbc640eefa8c08eb01a5c004e6bff7b374cd7396",
+ "output_tail": ".yaml:98: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:131: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:155: downstream:\nkb/communities/PMI_Variovorax_Thermotolerance_Collection.yaml:330: downstream:\nkb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml:125: downstream:\nkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:223: downstream:\nkb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml:342: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:295: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:339: downstream:\nkb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml:121: downstream:\nkb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml:149: downstream:\nkb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml:98: downstream:\nkb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml:155: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:199: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:267: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:281: downstream:\nkb/communities/Polaromonas_Vanadium_Reduction_Community.yaml:401: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:138: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:182: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:232: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:207: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:135: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:157: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:205: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "7586929f90340d7643aa5a1a97461cb2aeb355371584bc2199b57245ff6d7bb9"
+ },
+ "reference_validator_caveat": "All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All21 graph quotations independently match fresh primary text and unchanged cache. Literal matching is not entailment. Three main bodies and three further primary abstracts were read; no recertification of every cache or non-graph field."
+}
diff --git a/tests/test_causal_review_batch79.py b/tests/test_causal_review_batch79.py
new file mode 100644
index 000000000..903d0d435
--- /dev/null
+++ b/tests/test_causal_review_batch79.py
@@ -0,0 +1,172 @@
+"""Preserve positive outcomes without promoting assay/model scope to resolved flux."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261007-four-records-batch79.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_frc_controlled_tolerance_and_selection_survive():
+ _, _, docs = records()
+ tolerance, dominance, redox = docs[0]["ecological_interactions"]
+ assert "Eight Rhodanobacter" in tolerance["description"]
+ assert "186 tested isolates" in tolerance["description"]
+ assert "not a whole-groundwater-community perturbation" in tolerance["description"]
+ assert "some Pseudomonas isolates tolerate neutral-pH mixtures" in tolerance["description"]
+ assert [e["target"] for e in tolerance["downstream"]] == [dominance["name"]]
+ assert (
+ "experimentally supported selection mechanism" in tolerance["downstream"][0]["description"]
+ )
+ assert "downstream" not in redox
+
+
+def test_frc_uranyl_and_genus_scope_do_not_imply_nitrate_selection_or_exchange():
+ _, _, docs = records()
+ nodes = docs[0]["ecological_interactions"]
+ assert all(
+ n["metabolites"][0]["term"] == {"id": "CHEBI:43515", "label": "dioxouranium(2+)"}
+ for n in nodes[:2]
+ )
+ assert all("interaction_type" not in n for n in nodes)
+ assert "source_taxon" not in nodes[1]
+ assert "not a selectively toxic driver" in nodes[1]["description"]
+ assert nodes[1]["evidence"][0]["supports"] == "SUPPORT"
+ assert "accessible abstract does not quantify" in nodes[2]["description"]
+ assert all(e["supports"] == "PARTIAL" for e in nodes[2]["evidence"])
+ assert docs[0]["taxonomy"][0]["taxon_term"]["term"]["id"] == "NCBITaxon:666685"
+
+
+def test_ogataea_rescue_is_not_measured_directed_exchange():
+ _, _, docs = records()
+ rescue, sulfur, _ = docs[1]["ecological_interactions"]
+ assert rescue["interaction_type"] == "MUTUALISM"
+ assert "range 27.3-28.5 spans this pair" in rescue["description"]
+ assert "methanol growth remained below FY00" in rescue["description"]
+ assert "labeled derivatives used for population tracking" in rescue["description"]
+ assert sulfur["description"].startswith("HYPOTHESIZED -")
+ assert "not measured interstrain transfer" in sulfur["description"]
+ assert "not sodium sulfide" in sulfur["description"]
+ assert [e["supports"] for e in sulfur["evidence"]] == ["PARTIAL", "SUPPORT"]
+ assert sulfur["source_taxon"]["term"]["id"] == sulfur["target_taxon"]["term"]["id"]
+ assert sulfur["source_taxon"]["preferred_term"] != sulfur["target_taxon"]["preferred_term"]
+
+
+def test_ogataea_ratio_effect_retains_high_and_low_growth_arms():
+ _, rows, docs = records()
+ ratio = docs[1]["ecological_interactions"][2]
+ assert "1:10, 1:5 and 1:1 achieved higher final biomass" in ratio["description"]
+ assert "5:1 and 10:1 maintained met10Delta dominance but grew weakly" in ratio["description"]
+ assert "not evidence that every culture increased" in ratio["description"]
+ assert "interaction_type" not in ratio
+ assert rows[1]["status"] == "needs_research"
+ assert all("downstream" not in n for n in docs[1]["ecological_interactions"])
+ assert len(ratio["participating_taxa"]) == 2
+
+
+def test_okeke_positive_isolate_activities_and_proposed_contributions_remain():
+ _, _, docs = records()
+ cellulose, xylan, combined = docs[2]["ecological_interactions"]
+ assert "27.83 and 31.22" in cellulose["description"] and "18.07" in cellulose["description"]
+ assert "103.05" in xylan["description"] and "7.72" in xylan["description"]
+ for node in [cellulose, xylan]:
+ assert node["evidence"][0]["supports"] == "SUPPORT"
+ assert node["downstream"][0]["target"] == combined["name"]
+ assert node["downstream"][0]["description"].startswith("HYPOTHESIZED -")
+ assert all("interaction_type" not in n for n in [cellulose, xylan, combined])
+
+
+def test_okeke_access_limit_does_not_establish_absent_experiments():
+ _, rows, docs = records()
+ node = docs[2]["ecological_interactions"][2]
+ assert node["description"].startswith("HYPOTHESIZED -")
+ assert "not demonstrated absent" in node["description"]
+ assert "lignin breakdown" in node["description"]
+ assert [e["supports"] for e in node["evidence"]] == ["SUPPORT", "PARTIAL"]
+ assert rows[2]["status"] == "needs_research"
+ assert "authorized full text" in docs[2]["discussions"][0]["rationale"]
+
+
+def test_rumen_lab_result_and_genome_complement_remain_with_limits():
+ _, _, docs = records()
+ lab, genomes, _ = docs[3]["ecological_interactions"]
+ assert "66.84%" in lab["description"] and "20.56%" in lab["description"]
+ assert "Dry-matter degradation and gas production were not different" in lab["description"]
+ assert "not the initial seven-member" in lab["description"]
+ assert "not a justified final 61-mL bottle concentration" in lab["description"]
+ assert "47 GH and 19 CBM" in genomes["description"]
+ assert "not measured expression" in genomes["description"]
+ assert len(genomes["evidence"]) == 3
+ assert all(e["evidence_source"] == "COMPUTATIONAL" for e in genomes["evidence"])
+
+
+def test_rumen_cattle_trends_and_bags_are_not_significant_independent_replication():
+ _, _, docs = records()
+ node = docs[3]["ecological_interactions"][2]
+ assert "2.61%/7.81%/11.47% were not statistically significant" in node["description"]
+ assert "lower at 12 h, higher at 24/48 h" in node["description"]
+ assert "not nine independent cattle" in node["description"]
+ assert "propionate did not differ" in node["description"]
+ assert node["evidence"][0]["supports"] == "SUPPORT"
+ assert all("downstream" not in n for n in docs[3]["ecological_interactions"])
+
+
+def test_every_node_and_arrow_is_decided_without_unapproved_extension():
+ ledger, rows, docs = records()
+ assert sum(len(r["node_decisions"]) for r in rows) == 12
+ assert sum(len(r["edges_before"]) for r in rows) == 4
+ assert sum(len(r["edges_after"]) for r in rows) == 3
+ assert sum(len(r["removed_edge_decisions"]) for r in rows) == 1
+ assert (
+ ledger["primary_graph_snippet_count"] == ledger["cache_matched_graph_snippet_count"] == 21
+ )
+ for row, doc in zip(rows, docs, strict=True):
+ rename = row["renamed_nodes"]
+ before = {
+ (rename.get(e["source"], e["source"]), rename.get(e["target"], e["target"]))
+ for e in row["edges_before"]
+ }
+ after = {(e["source"], e["target"]) for e in row["edges_after"]}
+ removed = {
+ (rename.get(e["source"], e["source"]), rename.get(e["target"], e["target"]))
+ for e in row["removed_edge_decisions"]
+ }
+ assert after.isdisjoint(removed) and before == after | removed
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ assert names == {n["node"] for n in row["node_decisions"]}
+ assert all(
+ a.split("#", 1)[1] in names
+ for d in doc.get("discussions", [])
+ for a in d["attaches_to"]
+ if a.startswith("ecological_interactions#")
+ )
+
+
+def test_history_and_research_lifecycle_are_explicit():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1652, 1653, 1654, 1655]
+ assert ledger["unresolved_research_issues"] == [1656, 1657]
+ assert ledger["unresolved_non_graph_issues"] == [1658]
+ assert ledger["cache_changes"] == []
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert len(ledger["edison"]["dry_runs"]) == 1
+ assert ledger["edison"]["dry_runs"][0]["query_chars"] == 11815
+ for row, doc in zip(rows, docs, strict=True):
+ assert set(row["allowed_changed_fields"]) == {
+ "ecological_interactions",
+ "discussions",
+ "curation_history",
+ }
+ assert row["curation_events_added"] == 1 and len(row["history_files"]) == 1
+ assert all((ROOT / p).exists() for p in row["history_files"])
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]