diff --git a/docs/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html b/docs/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html index bbdf1a26b..834924f45 100644 --- a/docs/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html +++ b/docs/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html @@ -558,7 +558,7 @@

Ecological Interactions

Ecological interaction network for SynCom BsBv Cigar Tobacco Leaf Fermentation - Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (mutualism, niche partitioning). + Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -566,13 +566,8 @@

Ecological Interactions

Mutualism -
-
- Niche partitioning + aria-hidden="true" data-symbol="symbolTriangle2" + data-color="#929caa"> Other
@@ -580,10 +575,9 @@

Ecological Interactions

-

Cooperative macromolecule degradation by the BsBv SynCom

- MUTUALISM +

Macromolecule degradation after BsBv inoculation

-

Co-inoculation of the two cellulase/amylase/protease-producing Bacillus members on cigar tobacco leaves accelerated the degradation of key macromolecules, reducing cellulose, protein, and starch contents by 52.48 %, 56.36 %, and 68.47 % respectively, markedly greater than the uninoculated control (a community-level, emergent function of the consortium).

+

BsBv inoculation accelerated cellulose, protein and starch loss during the tested leaf fermentation, with reductions of 52.48%, 56.36% and 68.47%, respectively, greater than the uninoculated control. This is a measured consortium-associated process outcome; it does not establish that both bacterial partners benefit or that the mixture exceeds each monoculture.

@@ -621,9 +615,8 @@

Cooperative macromolecule degradation by the BsBv SynCom

Downstream Effects:
- → Volatile Flavor Profile Remodeling -

Faster cellulose, protein, and starch degradation is one SynCom-driven process associated with the volatile flavor-metabolite changes measured during cigar-tobacco leaf fermentation. -

+ → Volatile flavor and sensory-quality outcomes +

HYPOTHESIZED/PARTIAL: macromolecule conversion is proposed to contribute to the altered chemical and sensory outcomes under BsBv inoculation. The abstract reports chemical changes and a path-model interpretation, but does not isolate degradation of any one substrate as the mediator of a specific volatile or sensory change.

@@ -653,9 +646,8 @@

Evidence

SynCom-driven bacterial community succession and Bacillus enrichment

- NICHE_PARTITIONING
-

Inoculation with the SynCom shifted the leaf bacterial community structure, increasing the relative abundance of Firmicutes and significantly enriching the genus Bacillus during fermentation (community-level restructuring driven by the introduced consortium).

+

BsBv inoculation shifted bacterial community structure, including greater relative abundance of Firmicutes and enrichment of Bacillus. The authors also used PLS-PM to infer a microbiome-mediated contribution to sensory quality. Relative abundance and modeled mediation do not establish absolute population increases, niche separation or a Bacillus-specific causal mechanism.

@@ -664,26 +656,14 @@

SynCom-driven bacterial community succession and Bacillus enrichment

-

Biological Processes:

- -
Downstream Effects:
- → Volatile Flavor Profile Remodeling -

BsBv-driven enrichment of Bacillus and Firmicutes is the community succession pattern associated with SynCom flavor metabolism during the 42-day leaf fermentation. -

+ → Volatile flavor and sensory-quality outcomes +

HYPOTHESIZED/PARTIAL: community restructuring is proposed to contribute to the sensory component of the BsBv-associated outcome, consistent with the authors beta-diversity path-model interpretation. This does not identify Bacillus enrichment as the necessary mediator of each volatile change, or equate relative-abundance shifts with the modeled beta-diversity variable.

@@ -706,17 +686,28 @@

Evidence

+
  • +
    + + doi:10.1016/j.indcrop.2025.122621 + + - PARTIAL (COMPUTATIONAL) +
    + +
    "indirectly improved sensory quality by mediating shifts in microbial β-diversity"
    + +
    • +
    -

    Volatile Flavor Profile Remodeling

    - MUTUALISM +

    Volatile flavor and sensory-quality outcomes

    -

    BsBv inoculation remodeled volatile flavor metabolites during the 42-day cigar-tobacco fermentation, increasing honey, floral, and baked aroma contributions while reducing irritancy. -

    +

    Metabolomics identified 31 differentially accumulated volatile compounds after BsBv inoculation. The source associates increased phenylacetic acid, phytol and farnesol with honey, floral and baked aromas and reduced irritancy. These chemical and sensory outcomes are distinct from reciprocal microbial fitness and from direct measurements of the upstream degradation processes.

    @@ -725,35 +716,25 @@

    Volatile Flavor Profile Remodeling

    -

    Biological Processes:

    - +

    Evidence

    +
    @@ -579,11 +569,9 @@

    Ecological Interactions

    -

    Sequential SynCom-Microalga Coupling Construction

    - CROSS_FEEDING +

    Nitrate-Nitrogen and Phosphorus Removal

    -

    A synthetic bacterial pretreatment community was coupled sequentially to an autochthonous Chlorella sorokiniana isolate to improve resource utilization from livestock biogas slurry. -

    +

    The sequential SynCom-microalga system operated stably for 60 days and removed 94.41% of nitrate nitrogen, 81.84% of total phosphorus and 6.31% of chemical oxygen demand. These are system-level removal endpoints, not direct evidence of metabolite transfer between the bacterial pretreatment community and the alga or of which organisms carried each removal flux.

    @@ -616,7 +604,7 @@

    Evidence

    - SUPPORT (IN_VITRO)
    -
    "this study constructed a sequential synthetic microbial community (SynCom)-microalgae coupling system +
    "94.41% removal of nitrate nitrogen, 81.84% removal of total phosphorus, and 6.31% removal of chemical oxygen demand "
    @@ -627,22 +615,16 @@

    Evidence

    -

    Sixty-Day Stable Slurry Operation

    - NICHE_PARTITIONING +

    Chlorella biomass and protein response to SynCom pretreatment

    -

    The sequential coupling system remained stable for 60 days while treating livestock biogas slurry. -

    - +

    C. sorokiniana grown with SynCom-pretreated slurry had 27.15% greater biomass and 488.10% greater soluble protein content than the BG11 comparison. This positive algal response does not isolate bacterial conditioning from all differences between the media, identify an exchanged metabolite, or establish that bacterial fitness was unaffected.

    +

    Participating Taxa: -

    Metabolites: - - nitrate - (CHEBI:17632) + Chlorella sorokiniana

    @@ -650,22 +632,7 @@

    Sixty-Day Stable Slurry Operation

    -
    - Downstream Effects: -
    - → Nitrate-Nitrogen and Phosphorus Removal -

    Stable operation was measured by nitrate-nitrogen, total-phosphorus, and chemical-oxygen-demand removal from biogas slurry. -

    -
    - -
    - → SynCom Pretreatment Facilitates Chlorella Growth -

    The same SynCom pretreatment condition increased downstream Chlorella biomass and soluble protein relative to a BG11 control. -

    -
    - -
    @@ -681,8 +648,7 @@

    Evidence

    - SUPPORT (IN_VITRO)
    -
    "The system operated stably for 60 days and achieved 94.41% removal of nitrate nitrogen -"
    +
    "SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana by 27.15% and 488.10%, respectively"
    @@ -692,22 +658,16 @@

    Evidence

    -

    Nitrate-Nitrogen and Phosphorus Removal

    - CROSS_FEEDING +

    Chlorella carbon- and nitrogen-assimilation transcript response

    -

    During 60 days of operation, the coupling system removed most nitrate-nitrogen, most total phosphorus, and a smaller chemical oxygen demand fraction from livestock biogas slurry. -

    - - +

    Transcriptomic analysis reported upregulated Rubisco and glutamine synthetase genes in C. sorokiniana. This supports a carbon- and nitrogen-assimilation transcriptional response accompanying the biomass and protein phenotype. It does not measure enzyme activity or carbon/nitrogen flux and does not establish that increased growth caused the transcript changes.

    -

    Metabolites: +

    Participating Taxa: - nitrate - (CHEBI:17632) + Chlorella sorokiniana

    @@ -715,66 +675,20 @@

    Nitrate-Nitrogen and Phosphorus Removal

    +

    Biological Processes:

    +
    - -
    -
    -

    SynCom Pretreatment Facilitates Chlorella Growth

    - COMMENSALISM -
    -

    SynCom pretreatment of the biogas slurry enhanced the microalga's growth, increasing C. sorokiniana biomass and soluble protein content relative to the BG11 control. -

    - - - -

    Metabolites: - - nitrate - (CHEBI:17632) - -

    - - - - - -
    - Downstream Effects: - -
    - → Rubisco and Glutamine-Synthetase Up-Regulation -

    The Chlorella growth response was accompanied by increased expression of Rubisco and glutamine synthetase genes. -

    -
    - -
    - -

    Evidence

    -
    "SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana by 27.15% and 488.10%, respectively"
    +
    "Transcriptomic analysis showed that the expression levels of key genes Rubisco and glutamine synthetase were upregulated +"
    @@ -796,63 +711,68 @@

    Evidence

    -
    -
    -

    Rubisco and Glutamine-Synthetase Up-Regulation

    - COMMENSALISM -
    -

    Chlorella sorokiniana in the SynCom-pretreated system upregulated key genes for carbon fixation and nitrogen assimilation, linking the pretreatment to algal biomass and protein gains. -

    + + +
    +

    Knowledge gaps & discussions (1)

    +
    +

    + KNOWLEDGE_GAP + OPEN + Which pretreatment changes mediate the algal growth and transcriptional responses in the sequential slurry system? +

    +

    The positive 60-day removal and BG11-referenced algal outcomes remain. Construction, duration and coincident expression are not separate causal drivers. The reviewed abstract does not resolve exchanged metabolites, reciprocal fitness, organism-specific removal flux or expression-to-growth mediation. The unnamed bacterial membership remains the separate existing issue183 gap.

    +

    Attaches to: ecological_interactions#Nitrate-Nitrogen and Phosphorus Removal, ecological_interactions#Chlorella biomass and protein response to SynCom pretreatment, ecological_interactions#Chlorella carbon- and nitrogen-assimilation transcript response

    -

    Biological Processes:

    -
      +
      + 2 evidence item(s) -
    • - photosynthesis - (GO:0015979) -
      • +
      +
      + IN_VITRO + SUPPORT -
    + PMID:41794300 +
    +

    SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana by 27.15% and 488.10%, respectively

    +

    Supports the algal biomass/protein response; the abstract names BG11 as the comparator, not an otherwise identical untreated-slurry control.

    +
    -

    Evidence

    - + - + - - - @@ -1011,7 +931,7 @@

    Evidence

    (function() { var intId = "interaction:0"; - var intType = "CROSS_FEEDING"; + var intType = "UNKNOWN"; var metabolites = []; @@ -1024,7 +944,7 @@

    Evidence

    nodes.push({ id: intId, - label: "Sequential SynCom-Microalga Coupling Construction", + label: "Nitrate-Nitrogen and Phosphorus Removal", type: "interaction", interactionType: intType, metabolites: metabolites, @@ -1039,20 +959,16 @@

    Evidence

    (function() { var intId = "interaction:1"; - var intType = "NICHE_PARTITIONING"; + var intType = "UNKNOWN"; var metabolites = []; - - metabolites.push("nitrate"); - - var processes = []; var evidenceCount = 1; nodes.push({ id: intId, - label: "Sixty-Day Stable Slurry Operation", + label: "Chlorella biomass and protein response to SynCom pretreatment", type: "interaction", interactionType: intType, metabolites: metabolites, @@ -1063,52 +979,35 @@

    Evidence

    - })(); - - (function() { - var intId = "interaction:2"; - var intType = "CROSS_FEEDING"; - var metabolites = []; - - - metabolites.push("nitrate"); - - - var processes = []; + var participantKeys = [ - var evidenceCount = 1; + "Chlorella sorokiniana" - nodes.push({ - id: intId, - label: "Nitrate-Nitrogen and Phosphorus Removal", - type: "interaction", - interactionType: intType, - metabolites: metabolites, - processes: processes, - evidenceCount: evidenceCount + ]; + participantKeys.forEach(function(key) { + if (taxonNodeIds[key]) { + links.push({ source: taxonNodeIds[key], target: intId }); + } }); - - - })(); (function() { - var intId = "interaction:3"; - var intType = "COMMENSALISM"; + var intId = "interaction:2"; + var intType = "UNKNOWN"; var metabolites = []; + var processes = []; - metabolites.push("nitrate"); + processes.push("photosynthesis"); - var processes = []; var evidenceCount = 1; nodes.push({ id: intId, - label: "SynCom Pretreatment Facilitates Chlorella Growth", + label: "Chlorella carbon- and nitrogen-assimilation transcript response", type: "interaction", interactionType: intType, metabolites: metabolites, @@ -1119,34 +1018,17 @@

    Evidence

    - })(); - - (function() { - var intId = "interaction:4"; - var intType = "COMMENSALISM"; - var metabolites = []; - - var processes = []; + var participantKeys = [ + "Chlorella sorokiniana" - processes.push("photosynthesis"); - - - var evidenceCount = 1; - - nodes.push({ - id: intId, - label: "Rubisco and Glutamine-Synthetase Up-Regulation", - type: "interaction", - interactionType: intType, - metabolites: metabolites, - processes: processes, - evidenceCount: evidenceCount + ]; + participantKeys.forEach(function(key) { + if (taxonNodeIds[key]) { + links.push({ source: taxonNodeIds[key], target: intId }); + } }); - - - })(); @@ -1168,7 +1050,7 @@

    Evidence

    var svg = d3.select("#network-svg"); var width = container.clientWidth - 32; // Dynamic height based on node count: minimum 500px, add 40px per node - var nodeCount = 7; + var nodeCount = 5; var height = Math.max(500, 400 + nodeCount * 20); svg.attr("width", width).attr("height", height); diff --git a/docs/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.html b/docs/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.html index f2c3fae25..0c122e714 100644 --- a/docs/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.html +++ b/docs/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.html @@ -552,7 +552,7 @@

    Ecological Interactions

    Ecological interaction network for SynCom MetG2 Rhizobacteria Sugarcane Stress Resilience - Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (mutualism, colonization facilitation). + Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
    @@ -560,13 +560,8 @@

    Ecological Interactions

    Mutualism -
    -
    - Colonization facilitation + aria-hidden="true" data-symbol="symbolTriangle2" + data-color="#929caa"> Other
    @@ -574,19 +569,14 @@

    Ecological Interactions

    -

    Microbial colonization of sugarcane roots

    - COLONIZATION_FACILITATION +

    Rhizosphere colonization-associated gene expression

    -

    Following MetG2 inoculation, genes for flagellar assembly, chemotaxis, quorum sensing, and biofilm formation were up-regulated (particularly within Proteobacteria), indicating active microbial movement toward and colonization of sugarcane root surfaces.

    +

    After MetG2 inoculation, the rhizosphere showed increased expression of flagellar assembly, chemotaxis, quorum-sensing and biofilm-associated genes, particularly within Proteobacteria. The authors interpret this as movement toward roots; the reviewed evidence is molecular, not direct tracking of cells or proof that one organism facilitates another's colonization. Responding native rhizosphere taxa must not be equated with the defined MetG2 inoculant.

    -

    Source Taxon: Proteobacteria (rhizosphere community members)

    -

    Target Taxon: sugarcane (Saccharum officinarum)

    - - @@ -621,16 +611,6 @@

    Microbial colonization of sugarcane roots

    -
    - Downstream Effects: - -
    - → SynCom-stimulated enhancement of sugarcane stress resilience -

    Root-surface movement and biofilm formation provide the colonization context for MetG2-associated nutrient, hormone, siderophore, and VOC functions that stimulate sugarcane stress-resistance responses.

    -
    - -
    -

    Evidence

    @@ -642,7 +622,7 @@

    Evidence

    doi:10.1016/j.rhisph.2025.101142 - - SUPPORT (IN_VIVO) + - PARTIAL (IN_VIVO)
    "an up-regulation of genes related to flagellar assembly, chemotaxis, quorum sensing, and biofilm formation, particularly within Proteobacteria, indicating active microbial movement toward root surfaces"
    @@ -655,17 +635,12 @@

    Evidence

    -

    SynCom-stimulated enhancement of sugarcane stress resilience

    - MUTUALISM +

    Rhizosphere enrichment of plant-associated functional genes

    -

    Enrichment of microbial genes for nutrient acquisition, hormone synthesis, siderophore production, and VOC synthesis accompanies sugarcane up-regulation of hormone (auxin, cytokinin, salicylic acid) and nutrient-transporter genes and induction of stress-resistance genes, a mutualistic modulation of plant-microbe interactions that enhances stress resilience.

    - - -

    Source Taxon: Proteobacteria (rhizosphere community members)

    +

    Rhizosphere genes associated with nutrient acquisition, hormone synthesis, siderophore production and VOC synthesis were enriched after MetG2 inoculation. The source interprets these changes as potentially beneficial microbial activities. Gene enrichment is not direct measurement of secreted products, transfer to the host or reciprocal fitness, and is not assigned exclusively to the inoculated strains or to one responding phylum.

    -

    Target Taxon: sugarcane (Saccharum officinarum)

    @@ -689,7 +664,7 @@

    SynCom-stimulated enhancement of sugarcane stress resilience

    → Sugarcane hormone and nutrient-transporter response -

    Enriched rhizosphere nutrient-acquisition, hormone, siderophore, and VOC functions precede the host response in which sugarcane up-regulates hormone-related and nutrient-transporter genes.

    +

    HYPOTHESIZED/PARTIAL: the enriched microbial functions are proposed to contribute to the host transcriptional response in the MetG2-associated plant-microbe system. The reviewed omics evidence does not identify a transferred causal signal, establish that gene enrichment precedes the host response, or isolate mediation by the inoculant from the native rhizosphere community.

    @@ -712,19 +687,6 @@

    Evidence

    -
  • -
    - - doi:10.1016/j.rhisph.2025.101142 - - - SUPPORT (IN_VIVO) -
    - -
    "Sugarcane plants also exhibited dynamic responses, including the up-regulation of hormone-related genes (auxin, cytokinin, salicylic acid) and nutrient transporter genes"
    - -
    • - @@ -732,16 +694,11 @@

    Evidence

    Sugarcane hormone and nutrient-transporter response

    - MUTUALISM
    -

    After MetG2 inoculation, sugarcane up-regulates genes for auxin, cytokinin, and salicylic-acid signaling as well as nitrate, phosphate, potassium, and sulfur transport, linking the stimulated rhizosphere functions to a host transcriptional response.

    - - -

    Source Taxon: Proteobacteria (rhizosphere community members)

    +

    Sugarcane showed increased expression of hormone-related and nutrient-transporter genes after MetG2 inoculation, together with stress-response transcription. These are positive molecular responses, not by themselves a quantified stress-tolerance phenotype or reciprocal microbial benefit. The canonical Saccharum officinarum grounding and inoculant membership require separate identity resolution; this observation is stated at the source's sugarcane level.

    -

    Target Taxon: sugarcane (Saccharum officinarum)

    @@ -778,6 +735,19 @@

    Evidence

    +
  • +
    + + doi:10.1016/j.rhisph.2025.101142 + + - SUPPORT (IN_VIVO) +
    + +
    "Stress resistance genes such as trehalose 6-phosphate phosphatase, phenylalanine ammonia-lyase, expansin, and antioxidant-related genes were also induced."
    + +
    • +
    @@ -787,6 +757,56 @@

    Evidence

    +
    +

    Knowledge gaps & discussions (1)

    + +
    +

    + KNOWLEDGE_GAP + OPEN + Which MetG2 members and host identity underlie the observed native-rhizosphere and sugarcane transcriptional responses? +

    +

    The indexed publisher Introduction and experimental-design preview name four MetG2 strains, unlike the record's broad responding-phylum wrapper. They differ in the spelling of one strain designation. The reviewed source also does not verify the current species-level sugarcane grounding. Resolve canonical identities and graph attribution together under issue1847; the record remains needs_research. Preserve the proposed functional contribution without treating co-occurring expression, gene enrichment and host response as a demonstrated causal sequence.

    + +

    Attaches to: ecological_interactions#Rhizosphere colonization-associated gene expression, ecological_interactions#Rhizosphere enrichment of plant-associated functional genes, ecological_interactions#Sugarcane hormone and nutrient-transporter response

    + + + +
    + 2 evidence item(s) + +
    +
    + IN_VIVO + SUPPORT + + + doi:10.1016/j.rhisph.2025.101142 + +
    +

    genes associated with nutrient acquisition, hormone synthesis, siderophore production, and volatile organic compound (VOC) synthesis were enriched, suggesting stimulated beneficial microbial activities

    +

    Supports functional gene enrichment and its proposed beneficial interpretation, not demonstrated mutualism or metabolite transfer.

    +
    + +
    +
    + IN_VIVO + SUPPORT + + + doi:10.1016/j.rhisph.2025.101142 + +
    +

    Sugarcane plants also exhibited dynamic responses, including the up-regulation of hormone-related genes (auxin, cytokinin, salicylic acid) and nutrient transporter genes

    +

    Supports the sugarcane hormone and nutrient-transporter gene response after MetG2 inoculation.

    +
    + +
    + + +
    + +
    @@ -883,7 +903,7 @@

    Evidence

    (function() { var intId = "interaction:0"; - var intType = "COLONIZATION_FACILITATION"; + var intType = "UNKNOWN"; var metabolites = []; var processes = []; @@ -902,7 +922,7 @@

    Evidence

    nodes.push({ id: intId, - label: "Microbial colonization of sugarcane roots", + label: "Rhizosphere colonization-associated gene expression", type: "interaction", interactionType: intType, metabolites: metabolites, @@ -911,23 +931,13 @@

    Evidence

    }); - var srcKey = "Proteobacteria (rhizosphere community members)"; - if (taxonNodeIds[srcKey]) { - links.push({ source: taxonNodeIds[srcKey], target: intId }); - } - - - var tgtKey = "sugarcane (Saccharum officinarum)"; - if (taxonNodeIds[tgtKey]) { - links.push({ source: intId, target: taxonNodeIds[tgtKey] }); - } })(); (function() { var intId = "interaction:1"; - var intType = "MUTUALISM"; + var intType = "UNKNOWN"; var metabolites = []; var processes = []; @@ -936,11 +946,11 @@

    Evidence

    processes.push("biological process involved in interspecies interaction between organisms"); - var evidenceCount = 2; + var evidenceCount = 1; nodes.push({ id: intId, - label: "SynCom-stimulated enhancement of sugarcane stress resilience", + label: "Rhizosphere enrichment of plant-associated functional genes", type: "interaction", interactionType: intType, metabolites: metabolites, @@ -949,23 +959,13 @@

    Evidence

    }); - var srcKey = "Proteobacteria (rhizosphere community members)"; - if (taxonNodeIds[srcKey]) { - links.push({ source: taxonNodeIds[srcKey], target: intId }); - } - - var tgtKey = "sugarcane (Saccharum officinarum)"; - if (taxonNodeIds[tgtKey]) { - links.push({ source: intId, target: taxonNodeIds[tgtKey] }); - } - })(); (function() { var intId = "interaction:2"; - var intType = "MUTUALISM"; + var intType = "UNKNOWN"; var metabolites = []; var processes = []; @@ -974,7 +974,7 @@

    Evidence

    processes.push("biological process involved in interspecies interaction between organisms"); - var evidenceCount = 1; + var evidenceCount = 2; nodes.push({ id: intId, @@ -987,18 +987,8 @@

    Evidence

    }); - var srcKey = "Proteobacteria (rhizosphere community members)"; - if (taxonNodeIds[srcKey]) { - links.push({ source: taxonNodeIds[srcKey], target: intId }); - } - - var tgtKey = "sugarcane (Saccharum officinarum)"; - if (taxonNodeIds[tgtKey]) { - links.push({ source: intId, target: taxonNodeIds[tgtKey] }); - } - })(); diff --git a/docs/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.html b/docs/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.html index f7c42c316..242dc9870 100644 --- a/docs/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.html +++ b/docs/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.html @@ -558,7 +558,7 @@

    Ecological Interactions

    Ecological interaction network for Pseudomonas-Rahnella native rhizosphere SynCom for Artemisia argyi phytoremediation - Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (mutualism, niche partitioning). + Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
    @@ -566,13 +566,8 @@

    Ecological Interactions

    Mutualism -
    -
    - Niche partitioning + aria-hidden="true" data-symbol="symbolTriangle2" + data-color="#929caa"> Other
    @@ -580,10 +575,9 @@

    Ecological Interactions

    -

    Cd-tolerant Pseudomonas-Rahnella SynCom co-selection

    - NICHE_PARTITIONING +

    Cadmium tolerance of the Pseudomonas-Rahnella pair

    -

    The simplified SynCom pairs the Pseudomonas and Rahnella isolates after selection for joint tolerance of approximately 2 mM Cd, retaining both members under the heavy-metal stress targeted by the phytoremediation design.

    +

    The selected Pseudomonas-Rahnella pair was reported to tolerate approximately 2 mM cadmium. This is a trait of the tested pair, not a causal co-selection step or evidence that the partners occupy distinct niches. The reviewed abstract does not resolve the assay setting or each member's quantitative contribution.

    @@ -632,7 +626,7 @@

    Evidence

    doi:10.1016/j.indcrop.2025.122518 - - SUPPORT (IN_VIVO) + - SUPPORT (OTHER)
    "The selected Pseudomonas-Rahnella pair exhibited strong Cd tolerance (~ 2 mM), Plant growth promotion (PGP) traits, and carbon fixation capacity."
    @@ -646,9 +640,8 @@

    Evidence

    Functionally complementary Pseudomonas-Rahnella pairing with minimal antagonism

    - NICHE_PARTITIONING
    -

    The two members were selected by a top-down design strategy to be functionally complementary while minimizing antagonism, allowing stable coexistence in the simplified SynCom.

    +

    The source describes top-down assembly of a functionally complementary Pseudomonas-Rahnella SynCom with minimal antagonism. This supports the reported compatibility/design rationale, not demonstrated spatial or temporal niche separation, reduced resource competition, or stable reciprocal fitness benefits. No causal direction between the two members is resolved.

    Source Taxon: Pseudomonas (rhizosphere isolate)

    @@ -685,7 +678,7 @@

    Evidence

    doi:10.1016/j.indcrop.2025.122518 - - SUPPORT (IN_VIVO) + - PARTIAL (OTHER)
    "A top-down design strategy guided the assembly of a simplified, yet functionally complementary SynCom with minimal antagonism."
    @@ -699,9 +692,8 @@

    Evidence

    Joint PGP and carbon-fixation capacity

    - MUTUALISM
    -

    The selected Pseudomonas-Rahnella SynCom pair carries plant-growth-promotion traits together with carbon-fixation capacity, linking the two-member community to phytoremediation, productivity, and carbon sequestration goals.

    +

    The selected pair was reported to possess plant-growth-promoting traits and carbon-fixation capacity. These positive traits do not establish mutualism between the bacteria or quantify their contribution to plant benefit and persistent soil-carbon storage. The capacity claim is retained without turning it into a measured sequestration flux.

    @@ -742,7 +734,7 @@

    Evidence

    doi:10.1016/j.indcrop.2025.122518 - - SUPPORT (IN_VIVO) + - SUPPORT (OTHER)
    "The selected Pseudomonas-Rahnella pair exhibited strong Cd tolerance (~ 2 mM), Plant growth promotion (PGP) traits, and carbon fixation capacity."
    @@ -758,6 +750,56 @@

    Evidence

    +
    +

    Knowledge gaps & discussions (1)

    + +
    +

    + KNOWLEDGE_GAP + OPEN + How do the reported pair-level traits contribute to the observed plant and soil outcomes? +

    +

    The whole indexed publisher abstract reports positive plant and soil outcomes, but the committed cache contains only the two trait/design sentences used here. Preserve these supported traits and the prior removal of screening-order arrows. Low antagonism does not establish niche partitioning, and carbon-fixation capacity does not isolate a durable soil-carbon contribution. No new causal topology or unsupported assay provenance is introduced.

    + +

    Attaches to: ecological_interactions#Cadmium tolerance of the Pseudomonas-Rahnella pair, ecological_interactions#Functionally complementary Pseudomonas-Rahnella pairing with minimal antagonism, ecological_interactions#Joint PGP and carbon-fixation capacity

    + + + +
    + 2 evidence item(s) + +
    +
    + OTHER + PARTIAL + + + doi:10.1016/j.indcrop.2025.122518 + +
    +

    A top-down design strategy guided the assembly of a simplified, yet functionally complementary SynCom with minimal antagonism.

    +

    Supports the reported design rationale and minimal antagonism, not proof of the ecological mechanism or its assay setting.

    +
    + +
    +
    + OTHER + SUPPORT + + + doi:10.1016/j.indcrop.2025.122518 + +
    +

    The selected Pseudomonas-Rahnella pair exhibited strong Cd tolerance (~ 2 mM), Plant growth promotion (PGP) traits, and carbon fixation capacity.

    +

    Supports the reported pair-level traits and capacity; the abstract does not specify the assay setting or quantify persistent carbon storage from bacterial fixation.

    +
    + +
    + + +
    + +
    @@ -854,7 +896,7 @@

    Evidence

    (function() { var intId = "interaction:0"; - var intType = "NICHE_PARTITIONING"; + var intType = "UNKNOWN"; var metabolites = []; @@ -871,7 +913,7 @@

    Evidence

    nodes.push({ id: intId, - label: "Cd-tolerant Pseudomonas-Rahnella SynCom co-selection", + label: "Cadmium tolerance of the Pseudomonas-Rahnella pair", type: "interaction", interactionType: intType, metabolites: metabolites, @@ -899,7 +941,7 @@

    Evidence

    (function() { var intId = "interaction:1"; - var intType = "NICHE_PARTITIONING"; + var intType = "UNKNOWN"; var metabolites = []; var processes = []; @@ -937,7 +979,7 @@

    Evidence

    (function() { var intId = "interaction:2"; - var intType = "MUTUALISM"; + var intType = "UNKNOWN"; var metabolites = []; var processes = []; diff --git a/history/records/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation/2026-10-08T041040Z-codex-dd5f0e.yaml b/history/records/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation/2026-10-08T041040Z-codex-dd5f0e.yaml new file mode 100644 index 000000000..afa20cb2f --- /dev/null +++ b/history/records/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation/2026-10-08T041040Z-codex-dd5f0e.yaml @@ -0,0 +1,28 @@ +history_version: 1 +target: + kind: record + path: kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml + slug: SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation +session: + id: 2026-10-08T041040Z-codex-dd5f0e + timestamp: '2026-10-08T04:10:40Z' + actors: + - type: ai_agent + name: codex + model: unspecified + agent_tool: codex +links: + issues: + - https://github.com/CultureBotAI/CommunityMech/issues/1843 +events: +- type: EDIT + outcome: changed + sections: + - interactions + - discussions + summary: Preserve quantified substrate loss versus the control without reciprocal-benefit + or monoculture-synergy claims; qualify its existing outcome contribution.; Preserve community + shifts and the PLS-PM hypothesis with bounded statistical provenance, not niche separation + or a taxon-specific mediator.; Preserve volatile and sensory outcomes; remove mutualism + and misplaced upstream degradation-process annotations. + details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml diff --git a/history/records/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System/2026-10-08T041041Z-codex-cc3e7e.yaml b/history/records/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System/2026-10-08T041041Z-codex-cc3e7e.yaml new file mode 100644 index 000000000..54d348d45 --- /dev/null +++ b/history/records/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System/2026-10-08T041041Z-codex-cc3e7e.yaml @@ -0,0 +1,28 @@ +history_version: 1 +target: + kind: record + path: kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml + slug: SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System +session: + id: 2026-10-08T041041Z-codex-cc3e7e + timestamp: '2026-10-08T04:10:41Z' + actors: + - type: ai_agent + name: codex + model: unspecified + agent_tool: codex +links: + issues: + - https://github.com/CultureBotAI/CommunityMech/issues/1844 +events: +- type: EDIT + outcome: changed + sections: + - interactions + - discussions + summary: Preserve all three quantified removal endpoints and stable 60-day context without + inferring cross-feeding or organism-specific flux.; Preserve the positive algal biomass/protein + response and explicit BG11 comparator; remove unsupported commensalism and nitrate mediation.; + Preserve transcript upregulation with algal participant scope, not measured enzymatic + flux or growth-to-expression causation. + details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml diff --git a/history/records/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience/2026-10-08T041041Z-codex-ab21b2.yaml b/history/records/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience/2026-10-08T041041Z-codex-ab21b2.yaml new file mode 100644 index 000000000..c7ae1263d --- /dev/null +++ b/history/records/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience/2026-10-08T041041Z-codex-ab21b2.yaml @@ -0,0 +1,29 @@ +history_version: 1 +target: + kind: record + path: kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml + slug: SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience +session: + id: 2026-10-08T041041Z-codex-ab21b2 + timestamp: '2026-10-08T04:10:41Z' + actors: + - type: ai_agent + name: codex + model: unspecified + agent_tool: codex +links: + issues: + - https://github.com/CultureBotAI/CommunityMech/issues/1845 +events: +- type: EDIT + outcome: changed + sections: + - interactions + - discussions + summary: Preserve colonization-associated expression but distinguish inferred movement from + direct colonization/facilitation; remove the context-only arrow.; Preserve functional + gene enrichment and its qualified existing contribution to host responses; remove mutualism + and exclusive inoculant attribution.; Preserve hormone, nutrient and stress transcription + without asserting measured stress tolerance; keep the unresolved host/member identity + boundary explicit. + details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml diff --git a/history/records/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation/2026-10-08T041041Z-codex-ab8e2d.yaml b/history/records/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation/2026-10-08T041041Z-codex-ab8e2d.yaml new file mode 100644 index 000000000..b6b680506 --- /dev/null +++ b/history/records/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation/2026-10-08T041041Z-codex-ab8e2d.yaml @@ -0,0 +1,28 @@ +history_version: 1 +target: + kind: record + path: kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml + slug: SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation +session: + id: 2026-10-08T041041Z-codex-ab8e2d + timestamp: '2026-10-08T04:10:41Z' + actors: + - type: ai_agent + name: codex + model: unspecified + agent_tool: codex +links: + issues: + - https://github.com/CultureBotAI/CommunityMech/issues/1846 +events: +- type: EDIT + outcome: changed + sections: + - interactions + - discussions + summary: Recast co-selection as the reported tolerance phenotype; remove niche-partitioning + typing and unsupported in-vivo assay assignment.; Preserve complementarity/minimal-antagonism + context without stable coexistence, directional causation or niche separation.; Preserve + plant-growth-promoting and carbon-fixation capacity without reciprocal-benefit or sequestration-flux + claims. + details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml diff --git a/kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml b/kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml index 48d711fca..99ef00954 100644 --- a/kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml +++ b/kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml @@ -74,12 +74,11 @@ taxonomy: protease activities were screened out, and synthetic communities were constructed. explanation: Identifies Bacillus velezensis as a member of the constructed SynCom. ecological_interactions: -- name: Cooperative macromolecule degradation by the BsBv SynCom - description: Co-inoculation of the two cellulase/amylase/protease-producing Bacillus members on - cigar tobacco leaves accelerated the degradation of key macromolecules, reducing cellulose, - protein, and starch contents by 52.48 %, 56.36 %, and 68.47 % respectively, markedly greater than - the uninoculated control (a community-level, emergent function of the consortium). - interaction_type: MUTUALISM +- name: Macromolecule degradation after BsBv inoculation + description: BsBv inoculation accelerated cellulose, protein and starch loss during the tested leaf fermentation, + with reductions of 52.48%, 56.36% and 68.47%, respectively, greater than the uninoculated control. This is a + measured consortium-associated process outcome; it does not establish that both bacterial partners benefit or + that the mixture exceeds each monoculture. scope: COMMUNITY_LEVEL biological_processes: - preferred_term: cellulose catabolic process @@ -95,72 +94,70 @@ ecological_interactions: id: GO:0030163 label: protein catabolic process downstream: - - target: Volatile Flavor Profile Remodeling - description: > - Faster cellulose, protein, and starch degradation is one SynCom-driven - process associated with the volatile flavor-metabolite changes measured - during cigar-tobacco leaf fermentation. + - target: Volatile flavor and sensory-quality outcomes + description: 'HYPOTHESIZED/PARTIAL: macromolecule conversion is proposed to contribute to the altered chemical + and sensory outcomes under BsBv inoculation. The abstract reports chemical changes and a path-model interpretation, + but does not isolate degradation of any one substrate as the mediator of a specific volatile or sensory change.' evidence: - reference: doi:10.1016/j.indcrop.2025.122621 supports: SUPPORT evidence_source: IN_VITRO - snippet: The SynCom significantly accelerated the degradation of key macromolecules, reducing - cellulose, protein, and starch contents by 52.48 %, 56.36 %, and 68.47 %, respectively, which - were markedly greater reductions than those observed in the uninoculated control. - explanation: Measured community-level macromolecule degradation by the two-member SynCom versus - control. + snippet: The SynCom significantly accelerated the degradation of key macromolecules, reducing cellulose, protein, + and starch contents by 52.48 %, 56.36 %, and 68.47 %, respectively, which were markedly greater reductions + than those observed in the uninoculated control. + explanation: Measured community-level macromolecule degradation by the two-member SynCom versus control. - name: SynCom-driven bacterial community succession and Bacillus enrichment - description: Inoculation with the SynCom shifted the leaf bacterial community structure, increasing - the relative abundance of Firmicutes and significantly enriching the genus Bacillus during - fermentation (community-level restructuring driven by the introduced consortium). - interaction_type: NICHE_PARTITIONING + description: BsBv inoculation shifted bacterial community structure, including greater relative abundance of Firmicutes + and enrichment of Bacillus. The authors also used PLS-PM to infer a microbiome-mediated contribution to sensory + quality. Relative abundance and modeled mediation do not establish absolute population increases, niche separation + or a Bacillus-specific causal mechanism. scope: COMMUNITY_LEVEL - biological_processes: - - preferred_term: biological process involved in interspecies interaction between organisms - term: - id: GO:0044419 - label: biological process involved in interspecies interaction between organisms downstream: - - target: Volatile Flavor Profile Remodeling - description: > - BsBv-driven enrichment of Bacillus and Firmicutes is the community - succession pattern associated with SynCom flavor metabolism during the - 42-day leaf fermentation. + - target: Volatile flavor and sensory-quality outcomes + description: 'HYPOTHESIZED/PARTIAL: community restructuring is proposed to contribute to the sensory component + of the BsBv-associated outcome, consistent with the authors beta-diversity path-model interpretation. This + does not identify Bacillus enrichment as the necessary mediator of each volatile change, or equate relative-abundance + shifts with the modeled beta-diversity variable.' evidence: - reference: doi:10.1016/j.indcrop.2025.122621 supports: SUPPORT evidence_source: IN_VITRO - snippet: inoculation shifted the bacterial community structure, increasing the relative abundance - of Firmicutes and significantly enriching the genus Bacillus. + snippet: inoculation shifted the bacterial community structure, increasing the relative abundance of Firmicutes + and significantly enriching the genus Bacillus. explanation: SynCom inoculation restructured the resident bacterial community, enriching Bacillus. -- name: Volatile Flavor Profile Remodeling - description: > - BsBv inoculation remodeled volatile flavor metabolites during the 42-day - cigar-tobacco fermentation, increasing honey, floral, and baked aroma - contributions while reducing irritancy. - interaction_type: MUTUALISM + - reference: doi:10.1016/j.indcrop.2025.122621 + supports: PARTIAL + evidence_source: COMPUTATIONAL + snippet: indirectly improved sensory quality by mediating shifts in microbial β-diversity + explanation: Reports the authors statistical mediation interpretation, not an experimentally isolated taxon + effect. + computational_provenance: + prediction_type: STATISTICAL_INFERENCE + model_source: Chemical components, microbial community variation and sensory measurements from the BsBv fermentation + study + parameters: Partial least squares path modeling (PLS-PM); software, version and model specification are not + supplied in the reviewed abstract. +- name: Volatile flavor and sensory-quality outcomes + description: Metabolomics identified 31 differentially accumulated volatile compounds after BsBv inoculation. + The source associates increased phenylacetic acid, phytol and farnesol with honey, floral and baked aromas and + reduced irritancy. These chemical and sensory outcomes are distinct from reciprocal microbial fitness and from + direct measurements of the upstream degradation processes. scope: COMMUNITY_LEVEL - biological_processes: - - preferred_term: cellulose catabolic process - term: - id: GO:0030245 - label: cellulose catabolic process - - preferred_term: starch catabolic process - term: - id: GO:0005983 - label: starch catabolic process - - preferred_term: protein catabolic process - term: - id: GO:0030163 - label: protein catabolic process evidence: - reference: doi:10.1016/j.indcrop.2025.122621 supports: SUPPORT evidence_source: IN_VITRO snippet: Metabolomic profiling identified 31 differentially accumulated volatile flavor compounds - explanation: > - Supports volatile flavor-metabolite remodeling by the two-member BsBv - SynCom after application to cigar tobacco leaves. + explanation: 'Supports volatile flavor-metabolite remodeling by the two-member BsBv SynCom after application + to cigar tobacco leaves. + + ' + - reference: doi:10.1016/j.indcrop.2025.122621 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: phenylacetic acid, phytol, and farnesol, which were upregulated in the BsBv group and contributed to + enhanced honey, floral, and baked aromas, while reducing irritancy. + explanation: Supports the reported volatile/sensory association without establishing a specific causal mediator. growth_media: - name: Solid-state fermentation on cigar tobacco leaves (cultivar QX204) composition: @@ -180,3 +177,32 @@ growth_media: 42-day fermentation. explanation: States the fermentation substrate (cigar tobacco leaves, cultivar QX204) and the 42-day incubation duration. +discussions: +- discussion_id: bsbv-outcomes-versus-modeled-mediation + prompt: Which components of the BsBv-associated fermentation response mediate the volatile and sensory outcomes? + kind: KNOWLEDGE_GAP + status: OPEN + attaches_to: + - ecological_interactions#Macromolecule degradation after BsBv inoculation + - ecological_interactions#SynCom-driven bacterial community succession and Bacillus enrichment + - ecological_interactions#Volatile flavor and sensory-quality outcomes + rationale: Keep the positive degradation, community and flavor observations and the source path-model hypothesis. + The reviewed abstract does not isolate substrate conversion or Bacillus enrichment as the causal mediator. Reciprocal + bacterial benefit and spatial or temporal niche separation are not established. + evidence: + - reference: doi:10.1016/j.indcrop.2025.122621 + supports: PARTIAL + evidence_source: COMPUTATIONAL + snippet: indirectly improved sensory quality by mediating shifts in microbial β-diversity + explanation: Reports the authors statistical mediation interpretation, not an experimentally isolated taxon + effect. + posed_by: codex +curation_history: +- timestamp: '2026-10-08T04:10:38Z' + curator: codex + action: REVIEW_CAUSAL_GRAPH + changes: Preserve quantified substrate loss versus the control without reciprocal-benefit or monoculture-synergy + claims; qualify its existing outcome contribution.; Preserve community shifts and the PLS-PM hypothesis with + bounded statistical provenance, not niche separation or a taxon-specific mediator.; Preserve volatile and sensory + outcomes; remove mutualism and misplaced upstream degradation-process annotations. Issue#1843; reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml + llm_assisted: true diff --git a/kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml b/kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml index 89dba6a86..a205b6056 100644 --- a/kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml +++ b/kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml @@ -63,63 +63,12 @@ taxonomy: system explanation: Identifies an unnamed constructed SynCom as the bacterial pretreatment component. ecological_interactions: -- name: Sequential SynCom-Microalga Coupling Construction - description: > - A synthetic bacterial pretreatment community was coupled sequentially to an - autochthonous Chlorella sorokiniana isolate to improve resource utilization - from livestock biogas slurry. - scope: COMMUNITY_LEVEL - interaction_type: CROSS_FEEDING - metabolites: - - preferred_term: nitrate - term: - id: CHEBI:17632 - label: nitrate - evidence: - - reference: PMID:41794300 - supports: SUPPORT - evidence_source: IN_VITRO - snippet: > - this study constructed a sequential synthetic microbial community - (SynCom)-microalgae coupling system - explanation: > - Supports construction of the sequential SynCom-microalga system. -- name: Sixty-Day Stable Slurry Operation - description: > - The sequential coupling system remained stable for 60 days while treating - livestock biogas slurry. - scope: COMMUNITY_LEVEL - interaction_type: NICHE_PARTITIONING - metabolites: - - preferred_term: nitrate - term: - id: CHEBI:17632 - label: nitrate - downstream: - - target: Nitrate-Nitrogen and Phosphorus Removal - description: > - Stable operation was measured by nitrate-nitrogen, total-phosphorus, and - chemical-oxygen-demand removal from biogas slurry. - - target: SynCom Pretreatment Facilitates Chlorella Growth - description: > - The same SynCom pretreatment condition increased downstream Chlorella - biomass and soluble protein relative to a BG11 control. - evidence: - - reference: PMID:41794300 - supports: SUPPORT - evidence_source: IN_VITRO - snippet: > - The system operated stably for 60 days and achieved 94.41% removal of - nitrate nitrogen - explanation: > - Supports stable 60-day operation and nitrate-nitrogen removal. - name: Nitrate-Nitrogen and Phosphorus Removal - description: > - During 60 days of operation, the coupling system removed most - nitrate-nitrogen, most total phosphorus, and a smaller chemical oxygen - demand fraction from livestock biogas slurry. + description: The sequential SynCom-microalga system operated stably for 60 days and removed 94.41% of nitrate + nitrogen, 81.84% of total phosphorus and 6.31% of chemical oxygen demand. These are system-level removal endpoints, + not direct evidence of metabolite transfer between the bacterial pretreatment community and the alga or of which + organisms carried each removal flux. scope: COMMUNITY_LEVEL - interaction_type: CROSS_FEEDING metabolites: - preferred_term: nitrate term: @@ -129,43 +78,38 @@ ecological_interactions: - reference: PMID:41794300 supports: SUPPORT evidence_source: IN_VITRO - snippet: > - 94.41% removal of nitrate nitrogen, 81.84% removal of total phosphorus, - and 6.31% removal of chemical oxygen demand - explanation: > - Supports the reported nitrate-nitrogen, phosphorus, and COD removal - endpoints. -- name: SynCom Pretreatment Facilitates Chlorella Growth - description: > - SynCom pretreatment of the biogas slurry enhanced the microalga's growth, - increasing C. sorokiniana biomass and soluble protein content relative to - the BG11 control. + snippet: '94.41% removal of nitrate nitrogen, 81.84% removal of total phosphorus, and 6.31% removal of chemical + oxygen demand + + ' + explanation: 'Supports the reported nitrate-nitrogen, phosphorus, and COD removal endpoints. + + ' +- name: Chlorella biomass and protein response to SynCom pretreatment + description: C. sorokiniana grown with SynCom-pretreated slurry had 27.15% greater biomass and 488.10% greater + soluble protein content than the BG11 comparison. This positive algal response does not isolate bacterial conditioning + from all differences between the media, identify an exchanged metabolite, or establish that bacterial fitness + was unaffected. scope: COMMUNITY_LEVEL - interaction_type: COMMENSALISM - metabolites: - - preferred_term: nitrate - term: - id: CHEBI:17632 - label: nitrate - downstream: - - target: Rubisco and Glutamine-Synthetase Up-Regulation - description: > - The Chlorella growth response was accompanied by increased expression of - Rubisco and glutamine synthetase genes. evidence: - reference: PMID:41794300 supports: SUPPORT evidence_source: IN_VITRO - snippet: SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana - by 27.15% and 488.10%, respectively - explanation: Measured facilitation of C. sorokiniana biomass and protein by SynCom pretreatment. -- name: Rubisco and Glutamine-Synthetase Up-Regulation - description: > - Chlorella sorokiniana in the SynCom-pretreated system upregulated key genes - for carbon fixation and nitrogen assimilation, linking the pretreatment to - algal biomass and protein gains. + snippet: SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana by 27.15% and + 488.10%, respectively + explanation: Supports the algal biomass/protein response; the abstract names BG11 as the comparator, not an + otherwise identical untreated-slurry control. + participating_taxa: + - preferred_term: Chlorella sorokiniana + term: + id: NCBITaxon:3076 + label: Chlorella sorokiniana +- name: Chlorella carbon- and nitrogen-assimilation transcript response + description: Transcriptomic analysis reported upregulated Rubisco and glutamine synthetase genes in C. sorokiniana. + This supports a carbon- and nitrogen-assimilation transcriptional response accompanying the biomass and protein + phenotype. It does not measure enzyme activity or carbon/nitrogen flux and does not establish that increased + growth caused the transcript changes. scope: COMMUNITY_LEVEL - interaction_type: COMMENSALISM biological_processes: - preferred_term: photosynthesis term: @@ -175,12 +119,18 @@ ecological_interactions: - reference: PMID:41794300 supports: SUPPORT evidence_source: IN_VITRO - snippet: > - Transcriptomic analysis showed that the expression levels of key genes - Rubisco and glutamine synthetase were upregulated - explanation: > - Supports the carbon- and nitrogen-assimilation transcriptional response - in the coupled system. + snippet: 'Transcriptomic analysis showed that the expression levels of key genes Rubisco and glutamine synthetase + were upregulated + + ' + explanation: 'Supports the carbon- and nitrogen-assimilation transcriptional response in the coupled system. + + ' + participating_taxa: + - preferred_term: Chlorella sorokiniana + term: + id: NCBITaxon:3076 + label: Chlorella sorokiniana growth_media: - name: livestock biogas slurry (SynCom-pretreated); BG11 (control) incubation_time: '60' @@ -206,7 +156,47 @@ curation_history: - timestamp: '2026-10-02T06:04:09Z' curator: codex action: REPAIR_CAUSAL_GRAPH - changes: Removed one construction-to-operation workflow edge and one - coincident nutrient-removal-to-transcript edge from the sequential - SynCom-Chlorella slurry record. + changes: Removed one construction-to-operation workflow edge and one coincident nutrient-removal-to-transcript + edge from the sequential SynCom-Chlorella slurry record. + llm_assisted: true +- timestamp: '2026-10-08T04:10:39Z' + curator: codex + action: REVIEW_CAUSAL_GRAPH + changes: Preserve all three quantified removal endpoints and stable 60-day context without inferring cross-feeding + or organism-specific flux.; Preserve the positive algal biomass/protein response and explicit BG11 comparator; + remove unsupported commensalism and nitrate mediation.; Preserve transcript upregulation with algal participant + scope, not measured enzymatic flux or growth-to-expression causation. Issue#1844; reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml llm_assisted: true +discussions: +- discussion_id: sequential-slurry-endpoints-and-mediation + prompt: Which pretreatment changes mediate the algal growth and transcriptional responses in the sequential slurry + system? + kind: KNOWLEDGE_GAP + status: OPEN + attaches_to: + - ecological_interactions#Nitrate-Nitrogen and Phosphorus Removal + - ecological_interactions#Chlorella biomass and protein response to SynCom pretreatment + - ecological_interactions#Chlorella carbon- and nitrogen-assimilation transcript response + rationale: The positive 60-day removal and BG11-referenced algal outcomes remain. Construction, duration and coincident + expression are not separate causal drivers. The reviewed abstract does not resolve exchanged metabolites, reciprocal + fitness, organism-specific removal flux or expression-to-growth mediation. The unnamed bacterial membership + remains the separate existing issue183 gap. + evidence: + - reference: PMID:41794300 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana by 27.15% and + 488.10%, respectively + explanation: Supports the algal biomass/protein response; the abstract names BG11 as the comparator, not an + otherwise identical untreated-slurry control. + - reference: PMID:41794300 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'Transcriptomic analysis showed that the expression levels of key genes Rubisco and glutamine synthetase + were upregulated + + ' + explanation: 'Supports the carbon- and nitrogen-assimilation transcriptional response in the coupled system. + + ' + posed_by: codex diff --git a/kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml b/kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml index b69b80e06..d6912b8eb 100644 --- a/kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml +++ b/kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml @@ -69,22 +69,13 @@ taxonomy: explanation: Identifies Proteobacteria as the microbial group with up-regulated motility/colonization genes. ecological_interactions: -- name: Microbial colonization of sugarcane roots - description: Following MetG2 inoculation, genes for flagellar assembly, chemotaxis, quorum sensing, - and biofilm formation were up-regulated (particularly within Proteobacteria), indicating active - microbial movement toward and colonization of sugarcane root surfaces. - interaction_type: COLONIZATION_FACILITATION +- name: Rhizosphere colonization-associated gene expression + description: After MetG2 inoculation, the rhizosphere showed increased expression of flagellar assembly, chemotaxis, + quorum-sensing and biofilm-associated genes, particularly within Proteobacteria. The authors interpret this + as movement toward roots; the reviewed evidence is molecular, not direct tracking of cells or proof that one + organism facilitates another's colonization. Responding native rhizosphere taxa must not be equated with the + defined MetG2 inoculant. scope: COMMUNITY_LEVEL - source_taxon: - preferred_term: Proteobacteria (rhizosphere community members) - term: - id: NCBITaxon:1224 - label: Pseudomonadota - target_taxon: - preferred_term: sugarcane (Saccharum officinarum) - term: - id: NCBITaxon:4547 - label: Saccharum officinarum biological_processes: - preferred_term: bacterial-type flagellum assembly term: @@ -102,37 +93,21 @@ ecological_interactions: term: id: GO:0042710 label: biofilm formation - downstream: - - target: SynCom-stimulated enhancement of sugarcane stress resilience - description: Root-surface movement and biofilm formation provide the - colonization context for MetG2-associated nutrient, hormone, siderophore, - and VOC functions that stimulate sugarcane stress-resistance responses. evidence: - reference: doi:10.1016/j.rhisph.2025.101142 - supports: SUPPORT + supports: PARTIAL evidence_source: IN_VIVO - snippet: an up-regulation of genes related to flagellar assembly, chemotaxis, quorum sensing, and - biofilm formation, particularly within Proteobacteria, indicating active microbial movement toward - root surfaces - explanation: Motility, chemotaxis and biofilm genes up-regulated in Proteobacteria drive colonization - of root surfaces. -- name: SynCom-stimulated enhancement of sugarcane stress resilience - description: Enrichment of microbial genes for nutrient acquisition, hormone synthesis, siderophore - production, and VOC synthesis accompanies sugarcane up-regulation of hormone (auxin, cytokinin, - salicylic acid) and nutrient-transporter genes and induction of stress-resistance genes, a mutualistic - modulation of plant-microbe interactions that enhances stress resilience. - interaction_type: MUTUALISM + snippet: an up-regulation of genes related to flagellar assembly, chemotaxis, quorum sensing, and biofilm formation, + particularly within Proteobacteria, indicating active microbial movement toward root surfaces + explanation: Supports gene upregulation and the authors colonization interpretation; it does not directly observe + root movement or establish facilitation. +- name: Rhizosphere enrichment of plant-associated functional genes + description: Rhizosphere genes associated with nutrient acquisition, hormone synthesis, siderophore production + and VOC synthesis were enriched after MetG2 inoculation. The source interprets these changes as potentially + beneficial microbial activities. Gene enrichment is not direct measurement of secreted products, transfer to + the host or reciprocal fitness, and is not assigned exclusively to the inoculated strains or to one responding + phylum. scope: COMMUNITY_LEVEL - source_taxon: - preferred_term: Proteobacteria (rhizosphere community members) - term: - id: NCBITaxon:1224 - label: Pseudomonadota - target_taxon: - preferred_term: sugarcane (Saccharum officinarum) - term: - id: NCBITaxon:4547 - label: Saccharum officinarum biological_processes: - preferred_term: biological process involved in interspecies interaction between organisms term: @@ -140,41 +115,25 @@ ecological_interactions: label: biological process involved in interspecies interaction between organisms downstream: - target: Sugarcane hormone and nutrient-transporter response - description: Enriched rhizosphere nutrient-acquisition, hormone, siderophore, and VOC functions - precede the host response in which sugarcane up-regulates hormone-related and nutrient-transporter - genes. + description: 'HYPOTHESIZED/PARTIAL: the enriched microbial functions are proposed to contribute to the host + transcriptional response in the MetG2-associated plant-microbe system. The reviewed omics evidence does not + identify a transferred causal signal, establish that gene enrichment precedes the host response, or isolate + mediation by the inoculant from the native rhizosphere community.' evidence: - reference: doi:10.1016/j.rhisph.2025.101142 supports: SUPPORT evidence_source: IN_VIVO - snippet: genes associated with nutrient acquisition, hormone synthesis, siderophore production, and - volatile organic compound (VOC) synthesis were enriched, suggesting stimulated beneficial microbial - activities - explanation: Beneficial microbial activities (nutrient acquisition, hormones, siderophores, VOCs) - stimulated by the SynCom underpin the mutualistic support of the plant. - - reference: doi:10.1016/j.rhisph.2025.101142 - supports: SUPPORT - evidence_source: IN_VIVO - snippet: Sugarcane plants also exhibited dynamic responses, including the up-regulation of - hormone-related genes (auxin, cytokinin, salicylic acid) and nutrient transporter genes - explanation: Plant-side response (hormone and nutrient-transporter genes) to the SynCom completes the - mutualistic modulation. + snippet: genes associated with nutrient acquisition, hormone synthesis, siderophore production, and volatile + organic compound (VOC) synthesis were enriched, suggesting stimulated beneficial microbial activities + explanation: Supports functional gene enrichment and its proposed beneficial interpretation, not demonstrated + mutualism or metabolite transfer. - name: Sugarcane hormone and nutrient-transporter response - description: After MetG2 inoculation, sugarcane up-regulates genes for auxin, cytokinin, and - salicylic-acid signaling as well as nitrate, phosphate, potassium, and sulfur transport, linking the - stimulated rhizosphere functions to a host transcriptional response. - interaction_type: MUTUALISM + description: Sugarcane showed increased expression of hormone-related and nutrient-transporter genes after MetG2 + inoculation, together with stress-response transcription. These are positive molecular responses, not by themselves + a quantified stress-tolerance phenotype or reciprocal microbial benefit. The canonical Saccharum officinarum + grounding and inoculant membership require separate identity resolution; this observation is stated at the source's + sugarcane level. scope: COMMUNITY_LEVEL - source_taxon: - preferred_term: Proteobacteria (rhizosphere community members) - term: - id: NCBITaxon:1224 - label: Pseudomonadota - target_taxon: - preferred_term: sugarcane (Saccharum officinarum) - term: - id: NCBITaxon:4547 - label: Saccharum officinarum biological_processes: - preferred_term: biological process involved in interspecies interaction between organisms term: @@ -184,7 +143,53 @@ ecological_interactions: - reference: doi:10.1016/j.rhisph.2025.101142 supports: SUPPORT evidence_source: IN_VIVO - snippet: Sugarcane plants also exhibited dynamic responses, including the up-regulation of - hormone-related genes (auxin, cytokinin, salicylic acid) and nutrient transporter genes - explanation: Supports the sugarcane hormone and nutrient-transporter gene response after MetG2 - inoculation. + snippet: Sugarcane plants also exhibited dynamic responses, including the up-regulation of hormone-related genes + (auxin, cytokinin, salicylic acid) and nutrient transporter genes + explanation: Supports the sugarcane hormone and nutrient-transporter gene response after MetG2 inoculation. + - reference: doi:10.1016/j.rhisph.2025.101142 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Stress resistance genes such as trehalose 6-phosphate phosphatase, phenylalanine ammonia-lyase, expansin, + and antioxidant-related genes were also induced. + explanation: Supports host stress-response transcription, not a direct stress-challenge performance measurement. +discussions: +- discussion_id: metg2-identity-and-omics-mediation + prompt: Which MetG2 members and host identity underlie the observed native-rhizosphere and sugarcane transcriptional + responses? + kind: KNOWLEDGE_GAP + status: OPEN + attaches_to: + - ecological_interactions#Rhizosphere colonization-associated gene expression + - ecological_interactions#Rhizosphere enrichment of plant-associated functional genes + - ecological_interactions#Sugarcane hormone and nutrient-transporter response + rationale: The indexed publisher Introduction and experimental-design preview name four MetG2 strains, unlike + the record's broad responding-phylum wrapper. They differ in the spelling of one strain designation. The reviewed + source also does not verify the current species-level sugarcane grounding. Resolve canonical identities and + graph attribution together under issue1847; the record remains needs_research. Preserve the proposed functional + contribution without treating co-occurring expression, gene enrichment and host response as a demonstrated causal + sequence. + evidence: + - reference: doi:10.1016/j.rhisph.2025.101142 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: genes associated with nutrient acquisition, hormone synthesis, siderophore production, and volatile + organic compound (VOC) synthesis were enriched, suggesting stimulated beneficial microbial activities + explanation: Supports functional gene enrichment and its proposed beneficial interpretation, not demonstrated + mutualism or metabolite transfer. + - reference: doi:10.1016/j.rhisph.2025.101142 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Sugarcane plants also exhibited dynamic responses, including the up-regulation of hormone-related genes + (auxin, cytokinin, salicylic acid) and nutrient transporter genes + explanation: Supports the sugarcane hormone and nutrient-transporter gene response after MetG2 inoculation. + posed_by: codex +curation_history: +- timestamp: '2026-10-08T04:10:39Z' + curator: codex + action: REVIEW_CAUSAL_GRAPH + changes: Preserve colonization-associated expression but distinguish inferred movement from direct colonization/facilitation; + remove the context-only arrow.; Preserve functional gene enrichment and its qualified existing contribution + to host responses; remove mutualism and exclusive inoculant attribution.; Preserve hormone, nutrient and stress + transcription without asserting measured stress tolerance; keep the unresolved host/member identity boundary + explicit. Issue#1845; reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml + llm_assisted: true diff --git a/kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml b/kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml index 4771aee68..5f54ef766 100644 --- a/kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml +++ b/kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml @@ -81,11 +81,10 @@ taxonomy: explanation: Identifies Rahnella as one member of the SynCom pair with Cd tolerance, PGP, and carbon fixation. ecological_interactions: -- name: Cd-tolerant Pseudomonas-Rahnella SynCom co-selection - description: The simplified SynCom pairs the Pseudomonas and Rahnella isolates after selection for - joint tolerance of approximately 2 mM Cd, retaining both members under the heavy-metal stress - targeted by the phytoremediation design. - interaction_type: NICHE_PARTITIONING +- name: Cadmium tolerance of the Pseudomonas-Rahnella pair + description: The selected Pseudomonas-Rahnella pair was reported to tolerate approximately 2 mM cadmium. This + is a trait of the tested pair, not a causal co-selection step or evidence that the partners occupy distinct + niches. The reviewed abstract does not resolve the assay setting or each member's quantitative contribution. scope: COMMUNITY_LEVEL participating_taxa: - preferred_term: Pseudomonas (rhizosphere isolate) @@ -109,14 +108,16 @@ ecological_interactions: evidence: - reference: doi:10.1016/j.indcrop.2025.122518 supports: SUPPORT - evidence_source: IN_VIVO - snippet: The selected Pseudomonas-Rahnella pair exhibited strong Cd tolerance (~ 2 mM), Plant - growth promotion (PGP) traits, and carbon fixation capacity. - explanation: Identifies the paired Pseudomonas and Rahnella isolates as the Cd-tolerant SynCom. + evidence_source: OTHER + snippet: The selected Pseudomonas-Rahnella pair exhibited strong Cd tolerance (~ 2 mM), Plant growth promotion + (PGP) traits, and carbon fixation capacity. + explanation: Reports tolerance of the selected pair; the abstract does not specify the trait-assay setting, + so in-vivo provenance is not asserted. - name: Functionally complementary Pseudomonas-Rahnella pairing with minimal antagonism - description: The two members were selected by a top-down design strategy to be functionally - complementary while minimizing antagonism, allowing stable coexistence in the simplified SynCom. - interaction_type: NICHE_PARTITIONING + description: The source describes top-down assembly of a functionally complementary Pseudomonas-Rahnella SynCom + with minimal antagonism. This supports the reported compatibility/design rationale, not demonstrated spatial + or temporal niche separation, reduced resource competition, or stable reciprocal fitness benefits. No causal + direction between the two members is resolved. scope: PAIRWISE source_taxon: preferred_term: Pseudomonas (rhizosphere isolate) @@ -135,17 +136,17 @@ ecological_interactions: label: biological process involved in interspecies interaction between organisms evidence: - reference: doi:10.1016/j.indcrop.2025.122518 - supports: SUPPORT - evidence_source: IN_VIVO - snippet: A top-down design strategy guided the assembly of a simplified, yet functionally - complementary SynCom with minimal antagonism. - explanation: Supports functional complementarity and minimal antagonism between the two SynCom - members. + supports: PARTIAL + evidence_source: OTHER + snippet: A top-down design strategy guided the assembly of a simplified, yet functionally complementary SynCom + with minimal antagonism. + explanation: Supports the reported design rationale and minimal antagonism, not proof of the ecological mechanism + or its assay setting. - name: Joint PGP and carbon-fixation capacity - description: The selected Pseudomonas-Rahnella SynCom pair carries plant-growth-promotion traits - together with carbon-fixation capacity, linking the two-member community to phytoremediation, - productivity, and carbon sequestration goals. - interaction_type: MUTUALISM + description: The selected pair was reported to possess plant-growth-promoting traits and carbon-fixation capacity. + These positive traits do not establish mutualism between the bacteria or quantify their contribution to plant + benefit and persistent soil-carbon storage. The capacity claim is retained without turning it into a measured + sequestration flux. scope: COMMUNITY_LEVEL participating_taxa: - preferred_term: Pseudomonas (rhizosphere isolate) @@ -164,15 +165,53 @@ ecological_interactions: evidence: - reference: doi:10.1016/j.indcrop.2025.122518 supports: SUPPORT - evidence_source: IN_VIVO - snippet: The selected Pseudomonas-Rahnella pair exhibited strong Cd tolerance (~ 2 mM), Plant - growth promotion (PGP) traits, and carbon fixation capacity. - explanation: Links the selected two-member SynCom to PGP traits and carbon-fixation capacity. + evidence_source: OTHER + snippet: The selected Pseudomonas-Rahnella pair exhibited strong Cd tolerance (~ 2 mM), Plant growth promotion + (PGP) traits, and carbon fixation capacity. + explanation: Supports the reported pair-level traits and capacity; the abstract does not specify the assay setting + or quantify persistent carbon storage from bacterial fixation. curation_history: - timestamp: '2026-10-02T06:15:13Z' curator: codex action: REVIEW_CAUSAL_GRAPH - changes: Removed two downstream edges that described Cd-tolerance - co-selection and top-down screening order instead of causal links between - the Pseudomonas-Rahnella SynCom phenotypes. + changes: Removed two downstream edges that described Cd-tolerance co-selection and top-down screening order instead + of causal links between the Pseudomonas-Rahnella SynCom phenotypes. llm_assisted: true +- timestamp: '2026-10-08T04:10:39Z' + curator: codex + action: REVIEW_CAUSAL_GRAPH + changes: Recast co-selection as the reported tolerance phenotype; remove niche-partitioning typing and unsupported + in-vivo assay assignment.; Preserve complementarity/minimal-antagonism context without stable coexistence, directional + causation or niche separation.; Preserve plant-growth-promoting and carbon-fixation capacity without reciprocal-benefit + or sequestration-flux claims. Issue#1846; reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml + llm_assisted: true +discussions: +- discussion_id: artemisia-traits-versus-ecological-mechanism + prompt: How do the reported pair-level traits contribute to the observed plant and soil outcomes? + kind: KNOWLEDGE_GAP + status: OPEN + attaches_to: + - ecological_interactions#Cadmium tolerance of the Pseudomonas-Rahnella pair + - ecological_interactions#Functionally complementary Pseudomonas-Rahnella pairing with minimal antagonism + - ecological_interactions#Joint PGP and carbon-fixation capacity + rationale: The whole indexed publisher abstract reports positive plant and soil outcomes, but the committed cache + contains only the two trait/design sentences used here. Preserve these supported traits and the prior removal + of screening-order arrows. Low antagonism does not establish niche partitioning, and carbon-fixation capacity + does not isolate a durable soil-carbon contribution. No new causal topology or unsupported assay provenance + is introduced. + evidence: + - reference: doi:10.1016/j.indcrop.2025.122518 + supports: PARTIAL + evidence_source: OTHER + snippet: A top-down design strategy guided the assembly of a simplified, yet functionally complementary SynCom + with minimal antagonism. + explanation: Supports the reported design rationale and minimal antagonism, not proof of the ecological mechanism + or its assay setting. + - reference: doi:10.1016/j.indcrop.2025.122518 + supports: SUPPORT + evidence_source: OTHER + snippet: The selected Pseudomonas-Rahnella pair exhibited strong Cd tolerance (~ 2 mM), Plant growth promotion + (PGP) traits, and carbon fixation capacity. + explanation: Supports the reported pair-level traits and capacity; the abstract does not specify the assay setting + or quantify persistent carbon storage from bacterial fixation. + posed_by: codex diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md index d55e0cfe4..71a9eb094 100644 --- a/reports/causal_graph_review/README.md +++ b/reports/causal_graph_review/README.md @@ -5,6 +5,28 @@ 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`. +## Batch108: Process Outcomes And Molecular Responses + +[Decisions](decisions/20261008-four-records-batch108.yaml), +[provenance](cache-provenance-20261008-batch108.json), +[validation](validation-20261008-batch108.json), and +[self-adversarial review](adversarial-review-20261008-batch108.yaml) account for +14 original nodes and seven arrows. Twelve nodes and three qualified existing +directions remain; two workflow nodes and four context/coincidence arrows are +removed. Positive fermentation, algal, plant-transcript and pair-level trait +observations remain distinct from demonstrated exchange, reciprocal fitness, +metabolic flux and isolated causal mediation. + +Review is bounded to primary abstracts and indexed publisher previews, not +complete papers. Twenty-two graph/discussion quotations match independently +retrieved primary text and unchanged caches. Four append-only histories retain +prior curation, and three in-memory mutation probes check that regressions +reject inflated claims. All 923 caches and 456 other records are preserved. +Repair issues #1843-#1846 await protected-main merge. MetG2 identity #1847 +remains unresolved and its record stays `needs_research`; existing Chlorella +membership #183 stays open. No new topology or Edison credits were used. +Self-review is not independent approval or whole-corpus completion. + ## Batch94: Exchange And Plant Mechanism Boundaries Four records retain 14 nodes and 13 existing directions; experimental SynCom diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch108.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch108.yaml new file mode 100644 index 000000000..aeb0abfa2 --- /dev/null +++ b/reports/causal_graph_review/adversarial-review-20261008-batch108.yaml @@ -0,0 +1,296 @@ +reviewer: codex +review_mode: source_based_self_adversarial_review +independent_approval: false +base_commit: f1c21708622a610e2dd4208818a38d20472a3114 +scope: +- kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml +- kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml +- kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml +- kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml +decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml +validation_report: reports/causal_graph_review/validation-20261008-batch108.json +findings: +- issue: 1843 + severity: P2 + status: addressed_in_this_change + finding: Separate BsBv fermentation outcomes and modeled mediation from mutualism and niche partitioning + disposition: Close only after protected-main merge. +- issue: 1844 + severity: P2 + status: addressed_in_this_change + finding: Remove workflow and coincidence arrows from the sequential SynCom-Chlorella slurry graph + disposition: Close only after protected-main merge. +- issue: 1845 + severity: P2 + status: addressed_in_this_change + finding: Separate MetG2-associated gene responses from demonstrated root colonization and reciprocal benefit + disposition: Close only after protected-main merge. +- issue: 1846 + severity: P2 + status: addressed_in_this_change + finding: Bound Artemisia SynCom traits and low antagonism without asserting niche separation or mutualism + disposition: Close only after protected-main merge. +- issue: 1847 + severity: P2 + status: open_identity_follow_up + finding: Resolve MetG2 inoculant membership and sugarcane host grounding before certifying graph participants + disposition: Coordinated canonical and graph identity curation required; record remains needs_research. +adversarial_checks: +- 'Whole original targets and changed graph/discussion diffs reviewed. All 14 original nodes and seven directions + have dispositions: retain 12 nodes and three qualified existing directions, remove two workflow nodes and four + context/coincidence arrows, rename seven nodes. No new topology or Edison spend.' +- 'Challenge deletion versus evidence loss: preserve measured tobacco substrate loss and sensory outcomes, Chlorella + removal/growth/transcript responses, MetG2 microbial/host molecular responses, and Artemisia tolerance/compatibility/carbon-fixation + capacity. Positive endpoints and source hypotheses remain.' +- 'Tobacco: the uninoculated comparator does not establish monoculture synergy or reciprocal bacterial fitness. + Relative Bacillus abundance is not absolute growth or the beta-diversity path-model variable. Preserve PLS-PM + as PARTIAL statistical inference without invented software. Keep the two existing outcome contributions hypothetical; + remove degradation-process annotations from the volatile/sensory endpoint.' +- 'Chlorella: construction and 60-day duration are context, not separate biological causal nodes. Preserve all three + removal percentages and the BG11-referenced algal response, without inferring exchanged nitrate, neutral bacterial + fitness or an isolated bacterial conditioning effect. Transcript upregulation is not enzyme activity or measured + flux. Preserve previous October2 edge repairs; give only algal observations canonical identity-only participant + scope. Existing unnamed bacterial membership issue183 remains separate.' +- 'MetG2: distinguish inferred colonization from direct tracking, enriched genes from products/transfer, and stress-response + transcription from measured stress-challenge performance. Retain one hypothetical functional contribution, remove + the context arrow and redundant unverified community-level taxon links. The primary preview names four inoculant + strains with a Chiliseed2/Chileseed2 discrepancy; responding native Proteobacteria is not the inoculant. Generic + sugarcane does not verify the canonical species. Record remains needs_research under1847.' +- 'Artemisia: retain pair-level tolerance and PGP/carbon-fixation capacity, and the partial complementarity/minimal-antagonism + design rationale. None proves niche partitioning, reciprocal fitness or sequestration flux. The abstract does + not identify these trait-assay settings, so OTHER replaces unsupported IN_VIVO. Prior removal of screening-order + arrows is preserved; no new topology is inferred from other positive plant/soil endpoints.' +- Fifteen graph and seven discussion quotations match independently retrieved primary abstracts/indexed publisher + previews and unchanged caches. Literal matching is separate from entailment. Whole indexed tobacco/Artemisia abstracts, + bounded MetG2 Introduction/section previews and the whole EuropePMC Chlorella abstract were read, not complete + papers. Direct publisher403 and public API400 attempts are recorded; two source CC licenses do not imply full-body + retrieval. No supplements, figure pixels or raw datasets were certified. +- Four guarded writes produce four append-only histories. All 456 other records, all 923 caches, non-graph raw blocks + and prior history/decision files remain byte-identical. No schema, validator, census-threshold or runtime-rule + changes. Chlorella identity scopes and removal of redundant MetG2 links leave the global participant census unchanged; + canonical MetG2 identities are not certified. +- Three in-memory control/mutation/restored-control probes reject promoting statistical evidence to SUPPORT or restoring + the Chlorella and MetG2 coincidence/context arrows at scientific assertions. No canonical files changed; these + probes do not inflate the pytest count. +- Eight focused tests and 975 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks + and four histories validate. The network retains 56 baseline warnings and zero structural defects. Deterministic + rendering and exact HTML parsing cover 456 pages, 1370 node descriptions and 539 arrows, not screenshots. +- Repair issues1843-1846 are addressed but remain open until protected-main merge. Identity1847 and non-graph membership183 + stay open. Existing license949, loader1703, DOI-cache case1091 and stub-policy1093 are not certified. Denied and + unanswered Edison scopes remain untouched. Self-review is not independent approval; no artificial CI, protection + bypass or premature branch deletion. +- Corpus status is 344 reviewed, 64 pending and 52 needs_research, not completion. Postcommit docs-current and exact-head + publication require separate receipts and are not preasserted here. +- Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked. +adversarial_regression_proof: + report: + cases: + - mutation: tobacco modeled mediation promoted to SUPPORT + test: test_tobacco_path_model_is_bounded_and_directions_stay_hypotheses + control: PASS + mutation_rejected: true + assertion_line: 34 + assertion: assert model["evidence_source"] == "COMPUTATIONAL" and model["supports"] == "PARTIAL" + restored_control: PASS + - mutation: Chlorella coincidence arrow restored + test: test_chlorella_workflows_are_context_not_graph_nodes_or_arrows + control: PASS + mutation_rejected: true + assertion_line: 48 + assertion: assert all("interaction_type" not in n and not n.get("downstream") for n in nodes) + restored_control: PASS + - mutation: MetG2 context arrow restored + test: test_metg2_omics_and_identity_gaps_are_not_certified_as_mechanisms + control: PASS + mutation_rejected: true + assertion_line: 82 + assertion: assert not colonization.get("downstream") + restored_control: PASS + canonical_files_unchanged: true + checked_file_sha256: + kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml: 53f9cefb513a07926eee79884f4109702e56df3567d93ac65ec56658025d68f4 + kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml: f76054afccd798d444ad3e51a74e13afbed91762384966fb998b842dc54dfeb2 + kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml: a1fe9ffb3e47c18fa4d8ac5abb97a451dc8bffd7940b3b741d682729bb47bfb7 + kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml: 88b173ca8cef1393eedf415783725e0befc985adcf2cc3b2564fb7465df3d279 + tests/test_causal_review_batch108.py: fc8e5c1fdaff00b1b7db98c2b0b6afbc2f9a095fde4892439bd40ea73d509039 + scope: In-memory mutations of already-loaded evidence; no canonical write or added pytest count. + artifact: /private/tmp/communitymech-batch108/adversarial-regression-proof.json + sha256: a28ee1cd7ad7b163ceb93ed9c855628f903bdbc1ef1ea2843c196d695d5b0c11 +verification: + combined_regressions: 975 passed in 301.81s (0:05:01) + new_regression_tests: 8 + total_recorded_gate_outputs: 41 + primary_graph_snippet_proof: + graph_quotations: 15 + new_discussion_quotations: 7 + fresh_primary_literal_matches: 22 + all_cached_literal_matches: 22 + retained_nodes: 12 + removed_nodes: 2 + retained_arrows: 3 + removed_arrows: 4 + new_nodes_or_directions: 0 + scope: All reviewed quotations match fresh primary text and unchanged caches; source entailment separately reviewed. + Bounded primary abstracts/indexed publisher previews,not full-body/supplement/figure/raw-data certification. + references: Four full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal + matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. + Loader1703 not certified. + snippet_counts_by_record: + kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml: + MATCH: 9 + RENDERING: 0 + ASSEMBLED: 0 + WEAK: 0 + MISMATCH: 0 + NOCONTENT: 0 + kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml: + MATCH: 9 + RENDERING: 0 + ASSEMBLED: 0 + WEAK: 0 + MISMATCH: 0 + NOCONTENT: 0 + kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml: + MATCH: 8 + RENDERING: 0 + ASSEMBLED: 0 + WEAK: 0 + MISMATCH: 0 + NOCONTENT: 0 + kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml: + MATCH: 7 + RENDERING: 0 + ASSEMBLED: 0 + WEAK: 0 + MISMATCH: 0 + NOCONTENT: 0 + full_corpus_snippet_audit: + counts: + records: 460 + total: 8984 + categories: + MATCH: 8847 + RENDERING: 21 + ASSEMBLED: 1 + WEAK: 0 + MISMATCH: 39 + NOCONTENT: 76 + caveat: Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment. + network: + existing_findings_preserved: 56 + added_findings: {} + removed_findings: {} + interpretation: Twelve nodes and three qualified existing directions retained,two workflow nodes and four context/coincidence + arrows removed. All56existing warnings unchanged;zero structural defects. MetG2 identity remains unresolved1847 + despite structural validity. + tested_file_sha256: + reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml: 4004aaf9719161201cb0135d82c2f0ba2e7231ef9f7473ec99760465993bdaeb + tests/test_causal_review_batch108.py: fc8e5c1fdaff00b1b7db98c2b0b6afbc2f9a095fde4892439bd40ea73d509039 + tests/test_participating_taxa.py: 3a97ee16d14fa2cf1fb8dbb1dedc4cd0dbe89c06e1948247003a05f5c9b31c74 + tests/test_community_level_connectivity_credit.py: 383a0f5904085a5cda800b5102923fc99301831f5769d8d4821e000773d2ea4c + reports/causal_graph_review/cache-provenance-20261008-batch108.json: 94021e82e614fa11c4e8dc2b50d490f9233a514fa7c2664c8e8e53bc3c159512 + kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml: 53f9cefb513a07926eee79884f4109702e56df3567d93ac65ec56658025d68f4 + kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml: f76054afccd798d444ad3e51a74e13afbed91762384966fb998b842dc54dfeb2 + kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml: a1fe9ffb3e47c18fa4d8ac5abb97a451dc8bffd7940b3b741d682729bb47bfb7 + kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml: 88b173ca8cef1393eedf415783725e0befc985adcf2cc3b2564fb7465df3d279 + history_sha256: + history/records/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation/2026-10-08T041040Z-codex-dd5f0e.yaml: 6e0376aee12c70d8a30c704fdcfdee1fa5a90fe0ff3de74bb5b586b312d26963 + history/records/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System/2026-10-08T041041Z-codex-cc3e7e.yaml: 725253c5978d1dc827b5744e55d40c62d0db96fec123f4acac40e32c1d97ae35 + history/records/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience/2026-10-08T041041Z-codex-ab21b2.yaml: 3f95efad304d902ed9b2fe0697d82a4b5e8dd9dedcc454e11163ef3d2fe31fd7 + history/records/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation/2026-10-08T041041Z-codex-ab8e2d.yaml: 9048ae3a67a348abd19e101c1d01ef550520c00c12b35de72e8bab1f677b859f + unchanged_records: 456 + unchanged_caches: 923 + immutable_prior_history_and_decision_files: 828 + cache_changes: [] + edison: + required_for_this_repair: false + required_for_unresolved_extensions: false + provider_submissions: 0 + credits_spent: 0 + dry_runs: [] + repair_scope: Existing-node repair and retention/qualification of three existing directions; no new causal structure. + Identity1847 requires coordinated curation, not topology generation. + post_commit_docs_current: Separate publication gate, not preasserted. +participant_census: + measurements: + baseline: + records: 460 + with_community_level: 403 + mixed: 128 + community_level_only: 275 + taxa: 1544 + credited_solely_by_the_rule: 1270 + current: + records: 460 + with_community_level: 403 + mixed: 128 + community_level_only: 275 + taxa: 1544 + credited_solely_by_the_rule: 1270 + delta: + records: 0 + with_community_level: 0 + mixed: 0 + community_level_only: 0 + taxa: 0 + credited_solely_by_the_rule: 0 + interpretation: Chlorella growth/transcript observations gain canonical identity-only scope;the system removal + endpoint stays community-level. Redundant MetG2 source/target links are removed without changing COMMUNITY_LEVEL + scope;global census unchanged. MetG2 canonical identities are explicitly uncertified. No census thresholds or + audit rules changed. +corpus: + records: 460 + nodes: 1384 + edges: 547 + review_status_counts: + needs_research: 52 + pending: 64 + reviewed: 344 +lint_limitation: Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked. +lint_environment: + path: /private/tmp/communitymech-batch100/lint-env + scope: Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies + unchanged. Not a complete embedding runtime. +limitations: +- 'Fresh both-root baseline precedes source reads: 460 records, 923 caches, 56 existing warnings, zero structural + defects. Whole four records and all 14 original nodes/seven directions reviewed. Retain 12 nodes/three qualified + existing directions; remove two workflow nodes/four context or coincidence arrows; rename seven nodes. No new + topology or Edison spend.' +- Tobacco and Artemisia whole indexed publisher abstracts/highlights read; MetG2 whole indexed abstract/Introduction + and the displayed bounded experimental-design, metagenome, discussion/conclusion previews read. Chlorella whole + independently retrieved EuropePMC abstract read, plus an indexed publisher preview lead. These are not complete + papers. Direct ScienceDirect requests returned HTTP403; Crossref-advertised public API links for the two CC-licensed + articles returned HTTP400. No bypass or whole-paper/supplement/figure-pixel/raw-data certification. Publisher + index was crawled earlier; retrieval is fresh, not a claim that the publisher page was fetched live. +- Crossref version-of-record metadata identifies tobacco as CC BY4.0 and Artemisia as CC BY-NC4.0 despite local + historical paywall wording. That metadata does not mean their complete bodies were retrieved. No cache or license949 + repair is claimed. The four cited Markdown caches were read whole; Artemisia contains two trait/design sentences, + not its full abstract. Existing cache content is unchanged and sufficient for every retained/new literal quotation. +- 'Tobacco: preserve measured substrate loss, community shifts and volatile/sensory outcomes. Remove mutualism and + niche partitioning, qualify the existing directions and preserve PLS-PM mediation as a statistical hypothesis. + No invented software/version, taxon-specific mediator or monoculture-synergy claim. Endpoint process annotations + are removed because they describe upstream degradation, not volatile/sensory measurement.' +- 'Chlorella: preserve 60-day removal, algal biomass/protein versus BG11 and transcript responses. Remove construction/duration + nodes and three remaining noncausal arrows while preserving prior October2 repairs. No demonstrated cross-feeding, + neutral bacterial fitness, isolated medium effect or measured metabolic flux. Only the algal observations gain + canonical identity-only participant scope; unnamed bacterial membership remains existing issue183.' +- 'MetG2: preserve microbial and host molecular responses and one qualified source-proposed functional contribution. + Remove the context-only arrow, unestablished interaction types and redundant community-level source/target links. + The indexed source names four inoculant strains and has a Chiliseed2/Chileseed2 spelling discrepancy; broad native + rhizosphere Proteobacteria is not a resolved inoculant identity. Generic sugarcane is not verified as the canonical + species. Record remains needs_research under1847; no new identifiers or canonical-taxonomy edits.' +- 'Artemisia: preserve the pair-level tolerance, complementarity and PGP/carbon-fixation capacity. Remove niche + partitioning and mutualism; source assay setting is not specified in the reviewed abstract, so OTHER replaces + unsupported IN_VIVO assignment on these trait/design items. Preserve previous removal of screening-order arrows. + Positive whole-abstract plant/soil outcomes are not rejected, but no new graph mechanism or sequestration-flux + claim is introduced.' +- Repair issues1843-1846 await protected-main merge; identity1847 and existing membership183 remain open. Fresh + all-state issue titles/bodies and ignored/hidden local search matched1093,1091,184,183; all four bodies read. + The122 local matching paths were inspected as an index, not all read; focused prior access/missing-PDF/author-request + leads were inspected without contacting anyone. No reusable taxon match found in ignored/hidden-inclusive kb/taxa + searches for the target names/IDs. PRs/comments not exhaustively searched. +- Only existing graphs, focused discussions and curation events change. All456 other records,923 caches, non-graph + raw blocks and prior histories/decisions preserved. No schema, validator, runtime, census threshold or configuration + changes. Non-graph membership, abundance, growth and role claims are not recertified. Loader1703, DOI-case1091 + and stub-policy1093 remain separate. Self-review is not independent approval or corpus completion. Denied AM_AB000444 + and unanswered Edison scopes untouched; validation/publication not preasserted. diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch108.json b/reports/causal_graph_review/cache-provenance-20261008-batch108.json new file mode 100644 index 000000000..15e2d15f7 --- /dev/null +++ b/reports/causal_graph_review/cache-provenance-20261008-batch108.json @@ -0,0 +1,471 @@ +{ + "changes": [], + "unchanged_cache_files": 923, + "primary_artifacts": { + "/private/tmp/communitymech-batch108/artemisia-crossref.json": "aa3d46d5415e9269fae708d23a873e97b70706a44abc0d7d511f56cc7642ca1c", + "/private/tmp/communitymech-batch108/artemisia-indexed-primary.txt": "aa4e6f4c440cc36385db0570e5fb5456c3c9081d7341b28c8204d63b289372fd", + "/private/tmp/communitymech-batch108/baseline.json": "924874048322ec9dc575fb31ed77c1019f28be5ec616afb66734d957285a1b83", + "/private/tmp/communitymech-batch108/chlorella-abstract.txt": "8ad94da0200fad04401b2803e09013f11c622b3a32c34b4c6eeff98175fc665b", + "/private/tmp/communitymech-batch108/chlorella-crossref.json": "dfc2234defea0730f238bf424d0d59d362cb87f7d08ad3297dc38d7f8a4022a0", + "/private/tmp/communitymech-batch108/chlorella-metadata.json": "3c34294fe8a42ed0d2435e804db167bd9278c2d341543fbeaf0eebf329b20be0", + "/private/tmp/communitymech-batch108/dedup-local-current.txt": "07595e8b54dca3146eb1c7a6c869ea7bb6045d50754eff282828bd9db20374c5", + "/private/tmp/communitymech-batch108/issue-dedup-current.json": "ac8cf6accf97387b4df7978a0bb8fc8ce23c134ecd1ca519167db22ac6c97958", + "/private/tmp/communitymech-batch108/oa-retrieval.json": "8b62745386f0d5d5d48040eaa6f4feb8577504015ecad601aeaf53085ace2e87", + "/private/tmp/communitymech-batch108/primary-manifest.json": "b8632441c8967d86414502369971c2e59c09b387c570280f1b49bb4d95a3ca42", + "/private/tmp/communitymech-batch108/sugarcane-crossref.json": "a90002c6c38efda7a580a424df215bf60134a14d6238e537192125a911a2e326", + "/private/tmp/communitymech-batch108/sugarcane-indexed-primary.txt": "636790da7efc988cb2752c481269d5023a29a47dca35bb0831e0b7238e4e9cc2", + "/private/tmp/communitymech-batch108/tobacco-crossref.json": "70e60a1af78a9fc68cda93c83e7165b06c7428bbe039c4884b055de5d71ae6eb", + "/private/tmp/communitymech-batch108/tobacco-indexed-primary.txt": "15ad1fdb873c4e3067087870798192d6e40e3fabfcb441889474c6588ecbb8a9", + "references_cache/PMID_41794300.md": "b91c82802329ca0b23f96532e035e1b0ad5517f52ad5bb6e68a143508e356b20", + "references_cache/doi_10.1016_j.indcrop.2025.122518.md": "2012eb359a1c680913d435c8af619b3c69fb09ec29a90c6cdec66e066e4f1395", + "references_cache/doi_10.1016_j.indcrop.2025.122621.md": "8a4a5fd6472f2216776ed2c26e139f85ffa5fe8c79dbd14ed61b4838f51694ac", + "references_cache/doi_10.1016_j.rhisph.2025.101142.md": "2651ef5f596a41fc8a30d3f77b706f806b9867e7aa5ff132911e396968be3c60" + }, + "source_access": { + "retrieval_manifest": { + "tobacco": { + "reference": "doi:10.1016/j.indcrop.2025.122621", + "doi": "10.1016/j.indcrop.2025.122621", + "pmid": null, + "pii": "S0926669025021685", + "title": "Synthetic microbial communities enhance tobacco quality by driving bacterial community succession and modulating metabolite profiles", + "publisher_url": "https://www.sciencedirect.com/science/article/pii/S0926669025021685", + "crossref": "/private/tmp/communitymech-batch108/tobacco-crossref.json", + "crossref_sha256": "70e60a1af78a9fc68cda93c83e7165b06c7428bbe039c4884b055de5d71ae6eb", + "license": [ + { + "start": { + "date-parts": [ + [ + 2026, + 2, + 1 + ] + ], + "date-time": "2026-02-01T00:00:00Z", + "timestamp": 1769904000000 + }, + "content-version": "tdm", + "delay-in-days": 0, + "URL": "https://www.elsevier.com/tdm/userlicense/1.0/" + }, + { + "start": { + "date-parts": [ + [ + 2026, + 2, + 1 + ] + ], + "date-time": "2026-02-01T00:00:00Z", + "timestamp": 1769904000000 + }, + "content-version": "tdm", + "delay-in-days": 0, + "URL": "https://www.elsevier.com/legal/tdmrep-license" + }, + { + "start": { + "date-parts": [ + [ + 2025, + 12, + 31 + ] + ], + "date-time": "2025-12-31T00:00:00Z", + "timestamp": 1767139200000 + }, + "content-version": "vor", + "delay-in-days": 0, + "URL": "http://creativecommons.org/licenses/by/4.0/" + } + ], + "retrievals": [ + { + "url": "https://www.sciencedirect.com/science/article/pii/S0926669025021685", + "status": "direct_retrieval_failed", + "error": "HTTP Error 403: Forbidden", + "scope": "No access bypass; 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indexed publisher preview separately reviewed through web tool." + } + ] + } + }, + "oa_public_api_attempts": [ + { + "key": "tobacco", + "doi": "10.1016/j.indcrop.2025.122621", + "url": "https://api.elsevier.com/content/article/PII:S0926669025021685?httpAccept=text/plain", + "license": "http://creativecommons.org/licenses/by/4.0/", + "status": "failed_no_bypass", + "error": "HTTP Error 400: Bad Request" + }, + { + "key": "artemisia", + "doi": "10.1016/j.indcrop.2025.122518", + "url": "https://api.elsevier.com/content/article/PII:S0926669025020655?httpAccept=text/plain", + "license": "http://creativecommons.org/licenses/by-nc/4.0/", + "status": "failed_no_bypass", + "error": "HTTP Error 400: Bad Request" + } + ], + "actual_read_scope": [ + "Tobacco and Artemisia whole indexed publisher abstracts/highlights read; MetG2 whole indexed abstract/Introduction and the displayed bounded experimental-design, metagenome, discussion/conclusion previews read. Chlorella whole independently retrieved EuropePMC abstract read, plus an indexed publisher preview lead. These are not complete papers. Direct ScienceDirect requests returned HTTP403; Crossref-advertised public API links for the two CC-licensed articles returned HTTP400. No bypass or whole-paper/supplement/figure-pixel/raw-data certification. Publisher index was crawled earlier; retrieval is fresh, not a claim that the publisher page was fetched live.", + "Crossref version-of-record metadata identifies tobacco as CC BY4.0 and Artemisia as CC BY-NC4.0 despite local historical paywall wording. That metadata does not mean their complete bodies were retrieved. No cache or license949 repair is claimed. The four cited Markdown caches were read whole; Artemisia contains two trait/design sentences, not its full abstract. Existing cache content is unchanged and sufficient for every retained/new literal quotation." + ] + }, + "limitations": [ + "Fresh both-root baseline precedes source reads: 460 records, 923 caches, 56 existing warnings, zero structural defects. Whole four records and all 14 original nodes/seven directions reviewed. Retain 12 nodes/three qualified existing directions; remove two workflow nodes/four context or coincidence arrows; rename seven nodes. No new topology or Edison spend.", + "Tobacco and Artemisia whole indexed publisher abstracts/highlights read; MetG2 whole indexed abstract/Introduction and the displayed bounded experimental-design, metagenome, discussion/conclusion previews read. Chlorella whole independently retrieved EuropePMC abstract read, plus an indexed publisher preview lead. These are not complete papers. Direct ScienceDirect requests returned HTTP403; Crossref-advertised public API links for the two CC-licensed articles returned HTTP400. No bypass or whole-paper/supplement/figure-pixel/raw-data certification. Publisher index was crawled earlier; retrieval is fresh, not a claim that the publisher page was fetched live.", + "Crossref version-of-record metadata identifies tobacco as CC BY4.0 and Artemisia as CC BY-NC4.0 despite local historical paywall wording. That metadata does not mean their complete bodies were retrieved. No cache or license949 repair is claimed. The four cited Markdown caches were read whole; Artemisia contains two trait/design sentences, not its full abstract. Existing cache content is unchanged and sufficient for every retained/new literal quotation.", + "Tobacco: preserve measured substrate loss, community shifts and volatile/sensory outcomes. Remove mutualism and niche partitioning, qualify the existing directions and preserve PLS-PM mediation as a statistical hypothesis. No invented software/version, taxon-specific mediator or monoculture-synergy claim. Endpoint process annotations are removed because they describe upstream degradation, not volatile/sensory measurement.", + "Chlorella: preserve 60-day removal, algal biomass/protein versus BG11 and transcript responses. Remove construction/duration nodes and three remaining noncausal arrows while preserving prior October2 repairs. No demonstrated cross-feeding, neutral bacterial fitness, isolated medium effect or measured metabolic flux. Only the algal observations gain canonical identity-only participant scope; unnamed bacterial membership remains existing issue183.", + "MetG2: preserve microbial and host molecular responses and one qualified source-proposed functional contribution. Remove the context-only arrow, unestablished interaction types and redundant community-level source/target links. The indexed source names four inoculant strains and has a Chiliseed2/Chileseed2 spelling discrepancy; broad native rhizosphere Proteobacteria is not a resolved inoculant identity. Generic sugarcane is not verified as the canonical species. Record remains needs_research under1847; no new identifiers or canonical-taxonomy edits.", + "Artemisia: preserve the pair-level tolerance, complementarity and PGP/carbon-fixation capacity. Remove niche partitioning and mutualism; source assay setting is not specified in the reviewed abstract, so OTHER replaces unsupported IN_VIVO assignment on these trait/design items. Preserve previous removal of screening-order arrows. Positive whole-abstract plant/soil outcomes are not rejected, but no new graph mechanism or sequestration-flux claim is introduced.", + "Repair issues1843-1846 await protected-main merge; identity1847 and existing membership183 remain open. Fresh all-state issue titles/bodies and ignored/hidden local search matched1093,1091,184,183; all four bodies read. The122 local matching paths were inspected as an index, not all read; focused prior access/missing-PDF/author-request leads were inspected without contacting anyone. No reusable taxon match found in ignored/hidden-inclusive kb/taxa searches for the target names/IDs. PRs/comments not exhaustively searched.", + "Only existing graphs, focused discussions and curation events change. All456 other records,923 caches, non-graph raw blocks and prior histories/decisions preserved. No schema, validator, runtime, census threshold or configuration changes. Non-graph membership, abundance, growth and role claims are not recertified. Loader1703, DOI-case1091 and stub-policy1093 remain separate. Self-review is not independent approval or corpus completion. Denied AM_AB000444 and unanswered Edison scopes untouched; validation/publication not preasserted." + ] +} diff --git a/reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml new file mode 100644 index 000000000..915b3787f --- /dev/null +++ b/reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml @@ -0,0 +1,892 @@ +reviewer: codex +review_mode: source_based_self_adversarial_review +independent_approval: false +base_commit: f1c21708622a610e2dd4208818a38d20472a3114 +baseline_commit: f1c21708622a610e2dd4208818a38d20472a3114 +base_tree: f67514fe657a504bbfbe4825943558b24b7f50e5 +pre_source_baseline_sha256: 924874048322ec9dc575fb31ed77c1019f28be5ec616afb66734d957285a1b83 +issues: +- 1843 +- 1844 +- 1845 +- 1846 +unresolved_research_issues: +- 1847 +unresolved_non_graph_issues: +- 183 +issue_deduplication: + all_state_issue_titles_and_bodies: 1092 + matching_issues: + - 1093 + - 1091 + - 184 + - 183 + ignored_hidden_local_search: true +source_access: + retrieval_manifest: + tobacco: + reference: doi:10.1016/j.indcrop.2025.122621 + doi: 10.1016/j.indcrop.2025.122621 + pmid: null + pii: S0926669025021685 + title: Synthetic microbial communities enhance tobacco quality by driving bacterial community succession and + modulating metabolite profiles + publisher_url: https://www.sciencedirect.com/science/article/pii/S0926669025021685 + crossref: /private/tmp/communitymech-batch108/tobacco-crossref.json + crossref_sha256: 70e60a1af78a9fc68cda93c83e7165b06c7428bbe039c4884b055de5d71ae6eb + license: + - start: + date-parts: + - - 2026 + - 2 + - 1 + date-time: '2026-02-01T00:00:00Z' + timestamp: 1769904000000 + content-version: tdm + delay-in-days: 0 + URL: https://www.elsevier.com/tdm/userlicense/1.0/ + - start: + date-parts: + - - 2026 + - 2 + - 1 + date-time: '2026-02-01T00:00:00Z' + timestamp: 1769904000000 + content-version: tdm + delay-in-days: 0 + URL: https://www.elsevier.com/legal/tdmrep-license + - start: + date-parts: + - - 2025 + - 12 + - 31 + date-time: '2025-12-31T00:00:00Z' + timestamp: 1767139200000 + content-version: vor + delay-in-days: 0 + URL: http://creativecommons.org/licenses/by/4.0/ + retrievals: + - url: https://www.sciencedirect.com/science/article/pii/S0926669025021685 + status: direct_retrieval_failed + error: 'HTTP Error 403: Forbidden' + scope: No access bypass; indexed publisher preview separately reviewed through web tool. + chlorella: + reference: PMID:41794300 + doi: 10.1016/j.biortech.2026.134355 + pmid: '41794300' + pii: S0960852426004360 + title: Resource utilization of livestock biogas slurry using a sequential synthetic microbial community-microalga + Chlorella sorokiniana coupling system + publisher_url: https://www.sciencedirect.com/science/article/pii/S0960852426004360 + crossref: /private/tmp/communitymech-batch108/chlorella-crossref.json + crossref_sha256: dfc2234defea0730f238bf424d0d59d362cb87f7d08ad3297dc38d7f8a4022a0 + license: + - start: + date-parts: + - - 2026 + - 6 + - 1 + date-time: '2026-06-01T00:00:00Z' + timestamp: 1780272000000 + content-version: tdm + delay-in-days: 0 + URL: https://www.elsevier.com/tdm/userlicense/1.0/ + - start: + date-parts: + - - 2026 + - 6 + - 1 + date-time: '2026-06-01T00:00:00Z' + timestamp: 1780272000000 + content-version: tdm + delay-in-days: 0 + URL: https://www.elsevier.com/legal/tdmrep-license + - start: + date-parts: + - - 2026 + - 6 + - 1 + date-time: '2026-06-01T00:00:00Z' + timestamp: 1780272000000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-017 + - start: + date-parts: + - - 2026 + - 6 + - 1 + date-time: '2026-06-01T00:00:00Z' + timestamp: 1780272000000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-037 + - start: + date-parts: + - - 2026 + - 6 + - 1 + date-time: '2026-06-01T00:00:00Z' + timestamp: 1780272000000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-012 + - start: + date-parts: + - - 2026 + - 6 + - 1 + date-time: '2026-06-01T00:00:00Z' + timestamp: 1780272000000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-029 + - start: + date-parts: + - - 2026 + - 6 + - 1 + date-time: '2026-06-01T00:00:00Z' + timestamp: 1780272000000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-004 + retrievals: + - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A41794300+AND+SRC%3AMED&format=json&resultType=core + status: retrieved + scope: Primary indexed abstract; not full text. + - url: https://www.sciencedirect.com/science/article/pii/S0960852426004360 + status: direct_retrieval_failed + error: 'HTTP Error 403: Forbidden' + scope: No access bypass; indexed publisher preview separately reviewed through web tool. + pmcid: null + primary_abstract: /private/tmp/communitymech-batch108/chlorella-abstract.txt + primary_abstract_sha256: 8ad94da0200fad04401b2803e09013f11c622b3a32c34b4c6eeff98175fc665b + metadata: /private/tmp/communitymech-batch108/chlorella-metadata.json + metadata_sha256: 3c34294fe8a42ed0d2435e804db167bd9278c2d341543fbeaf0eebf329b20be0 + sugarcane: + reference: doi:10.1016/j.rhisph.2025.101142 + doi: 10.1016/j.rhisph.2025.101142 + pmid: null + pii: S2452219825001272 + title: Inoculation with a rhizobacteria synthetic community enhances sugarcane stress resilience through targeted + modulation of plant-microbe interactions + publisher_url: https://www.sciencedirect.com/science/article/pii/S2452219825001272 + crossref: /private/tmp/communitymech-batch108/sugarcane-crossref.json + crossref_sha256: a90002c6c38efda7a580a424df215bf60134a14d6238e537192125a911a2e326 + license: + - start: + date-parts: + - - 2025 + - 9 + - 1 + date-time: '2025-09-01T00:00:00Z' + timestamp: 1756684800000 + content-version: tdm + delay-in-days: 0 + URL: https://www.elsevier.com/tdm/userlicense/1.0/ + - start: + date-parts: + - - 2025 + - 9 + - 1 + date-time: '2025-09-01T00:00:00Z' + timestamp: 1756684800000 + content-version: tdm + delay-in-days: 0 + URL: https://www.elsevier.com/legal/tdmrep-license + - start: + date-parts: + - - 2025 + - 9 + - 1 + date-time: '2025-09-01T00:00:00Z' + timestamp: 1756684800000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-017 + - start: + date-parts: + - - 2025 + - 9 + - 1 + date-time: '2025-09-01T00:00:00Z' + timestamp: 1756684800000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-037 + - start: + date-parts: + - - 2025 + - 9 + - 1 + date-time: '2025-09-01T00:00:00Z' + timestamp: 1756684800000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-012 + - start: + date-parts: + - - 2025 + - 9 + - 1 + date-time: '2025-09-01T00:00:00Z' + timestamp: 1756684800000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-029 + - start: + date-parts: + - - 2025 + - 9 + - 1 + date-time: '2025-09-01T00:00:00Z' + timestamp: 1756684800000 + content-version: stm-asf + delay-in-days: 0 + URL: https://doi.org/10.15223/policy-004 + retrievals: + - url: https://www.sciencedirect.com/science/article/pii/S2452219825001272 + status: direct_retrieval_failed + error: 'HTTP Error 403: Forbidden' + scope: No access bypass; indexed publisher preview separately reviewed through web tool. + artemisia: + reference: doi:10.1016/j.indcrop.2025.122518 + doi: 10.1016/j.indcrop.2025.122518 + pmid: null + pii: S0926669025020655 + title: Simplified native SynCom enhances phytoremediation, carbon sequestration, and productivity of Artemisia + argyi in heavy metal-contaminated soils + publisher_url: https://www.sciencedirect.com/science/article/pii/S0926669025020655 + crossref: /private/tmp/communitymech-batch108/artemisia-crossref.json + crossref_sha256: aa3d46d5415e9269fae708d23a873e97b70706a44abc0d7d511f56cc7642ca1c + license: + - start: + date-parts: + - - 2026 + - 1 + - 1 + date-time: '2026-01-01T00:00:00Z' + timestamp: 1767225600000 + content-version: tdm + delay-in-days: 0 + URL: https://www.elsevier.com/tdm/userlicense/1.0/ + - start: + date-parts: + - - 2026 + - 1 + - 1 + date-time: '2026-01-01T00:00:00Z' + timestamp: 1767225600000 + content-version: tdm + delay-in-days: 0 + URL: https://www.elsevier.com/legal/tdmrep-license + - start: + date-parts: + - - 2025 + - 12 + - 15 + date-time: '2025-12-15T00:00:00Z' + timestamp: 1765756800000 + content-version: vor + delay-in-days: 0 + URL: http://creativecommons.org/licenses/by-nc/4.0/ + retrievals: + - url: https://www.sciencedirect.com/science/article/pii/S0926669025020655 + status: direct_retrieval_failed + error: 'HTTP Error 403: Forbidden' + scope: No access bypass; indexed publisher preview separately reviewed through web tool. + oa_public_api_attempts: + - key: tobacco + doi: 10.1016/j.indcrop.2025.122621 + url: https://api.elsevier.com/content/article/PII:S0926669025021685?httpAccept=text/plain + license: http://creativecommons.org/licenses/by/4.0/ + status: failed_no_bypass + error: 'HTTP Error 400: Bad Request' + - key: artemisia + doi: 10.1016/j.indcrop.2025.122518 + url: https://api.elsevier.com/content/article/PII:S0926669025020655?httpAccept=text/plain + license: http://creativecommons.org/licenses/by-nc/4.0/ + status: failed_no_bypass + error: 'HTTP Error 400: Bad Request' + actual_read_scope: + - Tobacco and Artemisia whole indexed publisher abstracts/highlights read; MetG2 whole indexed abstract/Introduction + and the displayed bounded experimental-design, metagenome, discussion/conclusion previews read. Chlorella whole + independently retrieved EuropePMC abstract read, plus an indexed publisher preview lead. These are not complete + papers. Direct ScienceDirect requests returned HTTP403; Crossref-advertised public API links for the two CC-licensed + articles returned HTTP400. No bypass or whole-paper/supplement/figure-pixel/raw-data certification. Publisher + index was crawled earlier; retrieval is fresh, not a claim that the publisher page was fetched live. + - Crossref version-of-record metadata identifies tobacco as CC BY4.0 and Artemisia as CC BY-NC4.0 despite local + historical paywall wording. That metadata does not mean their complete bodies were retrieved. No cache or license949 + repair is claimed. The four cited Markdown caches were read whole; Artemisia contains two trait/design sentences, + not its full abstract. Existing cache content is unchanged and sufficient for every retained/new literal quotation. +primary_artifacts: + /private/tmp/communitymech-batch108/artemisia-crossref.json: aa3d46d5415e9269fae708d23a873e97b70706a44abc0d7d511f56cc7642ca1c + /private/tmp/communitymech-batch108/artemisia-indexed-primary.txt: aa4e6f4c440cc36385db0570e5fb5456c3c9081d7341b28c8204d63b289372fd + /private/tmp/communitymech-batch108/baseline.json: 924874048322ec9dc575fb31ed77c1019f28be5ec616afb66734d957285a1b83 + /private/tmp/communitymech-batch108/chlorella-abstract.txt: 8ad94da0200fad04401b2803e09013f11c622b3a32c34b4c6eeff98175fc665b + /private/tmp/communitymech-batch108/chlorella-crossref.json: dfc2234defea0730f238bf424d0d59d362cb87f7d08ad3297dc38d7f8a4022a0 + /private/tmp/communitymech-batch108/chlorella-metadata.json: 3c34294fe8a42ed0d2435e804db167bd9278c2d341543fbeaf0eebf329b20be0 + /private/tmp/communitymech-batch108/dedup-local-current.txt: 07595e8b54dca3146eb1c7a6c869ea7bb6045d50754eff282828bd9db20374c5 + /private/tmp/communitymech-batch108/issue-dedup-current.json: ac8cf6accf97387b4df7978a0bb8fc8ce23c134ecd1ca519167db22ac6c97958 + /private/tmp/communitymech-batch108/oa-retrieval.json: 8b62745386f0d5d5d48040eaa6f4feb8577504015ecad601aeaf53085ace2e87 + /private/tmp/communitymech-batch108/primary-manifest.json: b8632441c8967d86414502369971c2e59c09b387c570280f1b49bb4d95a3ca42 + /private/tmp/communitymech-batch108/sugarcane-crossref.json: a90002c6c38efda7a580a424df215bf60134a14d6238e537192125a911a2e326 + /private/tmp/communitymech-batch108/sugarcane-indexed-primary.txt: 636790da7efc988cb2752c481269d5023a29a47dca35bb0831e0b7238e4e9cc2 + /private/tmp/communitymech-batch108/tobacco-crossref.json: 70e60a1af78a9fc68cda93c83e7165b06c7428bbe039c4884b055de5d71ae6eb + /private/tmp/communitymech-batch108/tobacco-indexed-primary.txt: 15ad1fdb873c4e3067087870798192d6e40e3fabfcb441889474c6588ecbb8a9 + references_cache/PMID_41794300.md: b91c82802329ca0b23f96532e035e1b0ad5517f52ad5bb6e68a143508e356b20 + references_cache/doi_10.1016_j.indcrop.2025.122518.md: 2012eb359a1c680913d435c8af619b3c69fb09ec29a90c6cdec66e066e4f1395 + references_cache/doi_10.1016_j.indcrop.2025.122621.md: 8a4a5fd6472f2216776ed2c26e139f85ffa5fe8c79dbd14ed61b4838f51694ac + references_cache/doi_10.1016_j.rhisph.2025.101142.md: 2651ef5f596a41fc8a30d3f77b706f806b9867e7aa5ff132911e396968be3c60 +primary_graph_snippet_count: 15 +snippet_checks: +- record: SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation + node: Macromolecule degradation after BsBv inoculation + evidence_index: 0 + reference: doi:10.1016/j.indcrop.2025.122621 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/tobacco-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122621.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation + node: SynCom-driven bacterial community succession and Bacillus enrichment + evidence_index: 0 + reference: doi:10.1016/j.indcrop.2025.122621 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/tobacco-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122621.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation + node: SynCom-driven bacterial community succession and Bacillus enrichment + evidence_index: 1 + reference: doi:10.1016/j.indcrop.2025.122621 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/tobacco-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122621.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation + node: Volatile flavor and sensory-quality outcomes + evidence_index: 0 + reference: doi:10.1016/j.indcrop.2025.122621 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/tobacco-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122621.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation + node: Volatile flavor and sensory-quality outcomes + evidence_index: 1 + reference: doi:10.1016/j.indcrop.2025.122621 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/tobacco-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122621.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System + node: Nitrate-Nitrogen and Phosphorus Removal + evidence_index: 0 + reference: PMID:41794300 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/chlorella-abstract.txt + cache_artifact: references_cache/PMID_41794300.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System + node: Chlorella biomass and protein response to SynCom pretreatment + evidence_index: 0 + reference: PMID:41794300 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/chlorella-abstract.txt + cache_artifact: references_cache/PMID_41794300.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System + node: Chlorella carbon- and nitrogen-assimilation transcript response + evidence_index: 0 + reference: PMID:41794300 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/chlorella-abstract.txt + cache_artifact: references_cache/PMID_41794300.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience + node: Rhizosphere colonization-associated gene expression + evidence_index: 0 + reference: doi:10.1016/j.rhisph.2025.101142 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/sugarcane-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.rhisph.2025.101142.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience + node: Rhizosphere enrichment of plant-associated functional genes + evidence_index: 0 + reference: doi:10.1016/j.rhisph.2025.101142 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/sugarcane-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.rhisph.2025.101142.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience + node: Sugarcane hormone and nutrient-transporter response + evidence_index: 0 + reference: doi:10.1016/j.rhisph.2025.101142 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/sugarcane-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.rhisph.2025.101142.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience + node: Sugarcane hormone and nutrient-transporter response + evidence_index: 1 + reference: doi:10.1016/j.rhisph.2025.101142 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/sugarcane-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.rhisph.2025.101142.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation + node: Cadmium tolerance of the Pseudomonas-Rahnella pair + evidence_index: 0 + reference: doi:10.1016/j.indcrop.2025.122518 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/artemisia-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122518.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation + node: Functionally complementary Pseudomonas-Rahnella pairing with minimal antagonism + evidence_index: 0 + reference: doi:10.1016/j.indcrop.2025.122518 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/artemisia-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122518.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation + node: Joint PGP and carbon-fixation capacity + evidence_index: 0 + reference: doi:10.1016/j.indcrop.2025.122518 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/artemisia-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122518.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +discussion_snippet_checks: +- record: SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation + node: bsbv-outcomes-versus-modeled-mediation + evidence_index: 0 + reference: doi:10.1016/j.indcrop.2025.122621 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/tobacco-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122621.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System + node: sequential-slurry-endpoints-and-mediation + evidence_index: 0 + reference: PMID:41794300 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/chlorella-abstract.txt + cache_artifact: references_cache/PMID_41794300.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System + node: sequential-slurry-endpoints-and-mediation + evidence_index: 1 + reference: PMID:41794300 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/chlorella-abstract.txt + cache_artifact: references_cache/PMID_41794300.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience + node: metg2-identity-and-omics-mediation + evidence_index: 0 + reference: doi:10.1016/j.rhisph.2025.101142 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/sugarcane-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.rhisph.2025.101142.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience + node: metg2-identity-and-omics-mediation + evidence_index: 1 + reference: doi:10.1016/j.rhisph.2025.101142 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/sugarcane-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.rhisph.2025.101142.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation + node: artemisia-traits-versus-ecological-mechanism + evidence_index: 0 + reference: doi:10.1016/j.indcrop.2025.122518 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/artemisia-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122518.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +- record: SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation + node: artemisia-traits-versus-ecological-mechanism + evidence_index: 1 + reference: doi:10.1016/j.indcrop.2025.122518 + cache_matched: true + independent_primary_match: true + matched_artifact: /private/tmp/communitymech-batch108/artemisia-indexed-primary.txt + cache_artifact: references_cache/doi_10.1016_j.indcrop.2025.122518.md + scope: Normalized literal match to independently retrieved primary abstract/indexed publisher preview and unchanged + cache; entailment reviewed separately. +cache_changes: [] +edison: + required_for_this_repair: false + required_for_unresolved_extensions: false + provider_submissions: 0 + credits_spent: 0 + dry_runs: [] + repair_scope: Existing-node repair and retention/qualification of three existing directions; no new causal structure. + Identity1847 requires coordinated curation, not topology generation. +limitations: +- 'Fresh both-root baseline precedes source reads: 460 records, 923 caches, 56 existing warnings, zero structural + defects. Whole four records and all 14 original nodes/seven directions reviewed. Retain 12 nodes/three qualified + existing directions; remove two workflow nodes/four context or coincidence arrows; rename seven nodes. No new + topology or Edison spend.' +- Tobacco and Artemisia whole indexed publisher abstracts/highlights read; MetG2 whole indexed abstract/Introduction + and the displayed bounded experimental-design, metagenome, discussion/conclusion previews read. Chlorella whole + independently retrieved EuropePMC abstract read, plus an indexed publisher preview lead. These are not complete + papers. Direct ScienceDirect requests returned HTTP403; Crossref-advertised public API links for the two CC-licensed + articles returned HTTP400. No bypass or whole-paper/supplement/figure-pixel/raw-data certification. Publisher + index was crawled earlier; retrieval is fresh, not a claim that the publisher page was fetched live. +- Crossref version-of-record metadata identifies tobacco as CC BY4.0 and Artemisia as CC BY-NC4.0 despite local + historical paywall wording. That metadata does not mean their complete bodies were retrieved. No cache or license949 + repair is claimed. The four cited Markdown caches were read whole; Artemisia contains two trait/design sentences, + not its full abstract. Existing cache content is unchanged and sufficient for every retained/new literal quotation. +- 'Tobacco: preserve measured substrate loss, community shifts and volatile/sensory outcomes. Remove mutualism and + niche partitioning, qualify the existing directions and preserve PLS-PM mediation as a statistical hypothesis. + No invented software/version, taxon-specific mediator or monoculture-synergy claim. Endpoint process annotations + are removed because they describe upstream degradation, not volatile/sensory measurement.' +- 'Chlorella: preserve 60-day removal, algal biomass/protein versus BG11 and transcript responses. Remove construction/duration + nodes and three remaining noncausal arrows while preserving prior October2 repairs. No demonstrated cross-feeding, + neutral bacterial fitness, isolated medium effect or measured metabolic flux. Only the algal observations gain + canonical identity-only participant scope; unnamed bacterial membership remains existing issue183.' +- 'MetG2: preserve microbial and host molecular responses and one qualified source-proposed functional contribution. + Remove the context-only arrow, unestablished interaction types and redundant community-level source/target links. + The indexed source names four inoculant strains and has a Chiliseed2/Chileseed2 spelling discrepancy; broad native + rhizosphere Proteobacteria is not a resolved inoculant identity. Generic sugarcane is not verified as the canonical + species. Record remains needs_research under1847; no new identifiers or canonical-taxonomy edits.' +- 'Artemisia: preserve the pair-level tolerance, complementarity and PGP/carbon-fixation capacity. Remove niche + partitioning and mutualism; source assay setting is not specified in the reviewed abstract, so OTHER replaces + unsupported IN_VIVO assignment on these trait/design items. Preserve previous removal of screening-order arrows. + Positive whole-abstract plant/soil outcomes are not rejected, but no new graph mechanism or sequestration-flux + claim is introduced.' +- Repair issues1843-1846 await protected-main merge; identity1847 and existing membership183 remain open. Fresh + all-state issue titles/bodies and ignored/hidden local search matched1093,1091,184,183; all four bodies read. + The122 local matching paths were inspected as an index, not all read; focused prior access/missing-PDF/author-request + leads were inspected without contacting anyone. No reusable taxon match found in ignored/hidden-inclusive kb/taxa + searches for the target names/IDs. PRs/comments not exhaustively searched. +- Only existing graphs, focused discussions and curation events change. All456 other records,923 caches, non-graph + raw blocks and prior histories/decisions preserved. No schema, validator, runtime, census threshold or configuration + changes. Non-graph membership, abundance, growth and role claims are not recertified. Loader1703, DOI-case1091 + and stub-policy1093 remain separate. Self-review is not independent approval or corpus completion. Denied AM_AB000444 + and unanswered Edison scopes untouched; validation/publication not preasserted. +records: +- path: kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml + id: CommunityMech:000278 + original_sha256: ffe0f5e7381d820061ccfe30ec1b71277c3e88866519bcc52389537d4bc85123 + record_sha256: 53f9cefb513a07926eee79884f4109702e56df3567d93ac65ec56658025d68f4 + status: reviewed + outcome: changed + review_file: reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml + scope: Whole record and all existing nodes/directions; graph/evidence repair, not whole-record certification. + summary: Preserve quantified substrate loss versus the control without reciprocal-benefit or monoculture-synergy + claims; qualify its existing outcome contribution.; Preserve community shifts and the PLS-PM hypothesis with + bounded statistical provenance, not niche separation or a taxon-specific mediator.; Preserve volatile and sensory + outcomes; remove mutualism and misplaced upstream degradation-process annotations. + node_decisions: + - node: Macromolecule degradation after BsBv inoculation + rationale: Preserve quantified substrate loss versus the control without reciprocal-benefit or monoculture-synergy + claims; qualify its existing outcome contribution. + - node: SynCom-driven bacterial community succession and Bacillus enrichment + rationale: Preserve community shifts and the PLS-PM hypothesis with bounded statistical provenance, not niche + separation or a taxon-specific mediator. + - node: Volatile flavor and sensory-quality outcomes + rationale: Preserve volatile and sensory outcomes; remove mutualism and misplaced upstream degradation-process + annotations. + removed_node_decisions: [] + renamed_nodes: + Cooperative macromolecule degradation by the BsBv SynCom: Macromolecule degradation after BsBv inoculation + Volatile Flavor Profile Remodeling: Volatile flavor and sensory-quality outcomes + edges_before: + - &id001 + source: Cooperative macromolecule degradation by the BsBv SynCom + target: Volatile Flavor Profile Remodeling + description: 'Faster cellulose, protein, and starch degradation is one SynCom-driven process associated with + the volatile flavor-metabolite changes measured during cigar-tobacco leaf fermentation. + + ' + - &id003 + source: SynCom-driven bacterial community succession and Bacillus enrichment + target: Volatile Flavor Profile Remodeling + description: 'BsBv-driven enrichment of Bacillus and Firmicutes is the community succession pattern associated + with SynCom flavor metabolism during the 42-day leaf fermentation. + + ' + edges_after: + - &id002 + source: Macromolecule degradation after BsBv inoculation + target: Volatile flavor and sensory-quality outcomes + description: 'HYPOTHESIZED/PARTIAL: macromolecule conversion is proposed to contribute to the altered chemical + and sensory outcomes under BsBv inoculation. The abstract reports chemical changes and a path-model interpretation, + but does not isolate degradation of any one substrate as the mediator of a specific volatile or sensory change.' + - &id004 + source: SynCom-driven bacterial community succession and Bacillus enrichment + target: Volatile flavor and sensory-quality outcomes + description: 'HYPOTHESIZED/PARTIAL: community restructuring is proposed to contribute to the sensory component + of the BsBv-associated outcome, consistent with the authors beta-diversity path-model interpretation. This + does not identify Bacillus enrichment as the necessary mediator of each volatile change, or equate relative-abundance + shifts with the modeled beta-diversity variable.' + retained_edge_decisions: + - before: *id001 + after: *id002 + rationale: Existing direction retained as an explicitly hypothetical contribution, not isolated mediation. + - before: *id003 + after: *id004 + rationale: Existing direction retained as an explicitly hypothetical contribution, not isolated mediation. + removed_edge_decisions: [] + references: + - doi:10.1016/j.indcrop.2025.122621 + issues: + - 1843 + allowed_changed_fields: + - curation_history + - discussions + - ecological_interactions + curation_events_added: 1 + history_files: + - history/records/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation/2026-10-08T041040Z-codex-dd5f0e.yaml +- path: kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml + id: CommunityMech:000285 + original_sha256: 6bc229bfcabb16639d9a7ffd085739421b0f38be95cc85cd66aaf80ecc70b9c5 + record_sha256: f76054afccd798d444ad3e51a74e13afbed91762384966fb998b842dc54dfeb2 + status: reviewed + outcome: changed + review_file: reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml + scope: Whole record and all existing nodes/directions; graph/evidence repair, not whole-record certification. + summary: Preserve all three quantified removal endpoints and stable 60-day context without inferring cross-feeding + or organism-specific flux.; Preserve the positive algal biomass/protein response and explicit BG11 comparator; + remove unsupported commensalism and nitrate mediation.; Preserve transcript upregulation with algal participant + scope, not measured enzymatic flux or growth-to-expression causation. + node_decisions: + - node: Nitrate-Nitrogen and Phosphorus Removal + rationale: Preserve all three quantified removal endpoints and stable 60-day context without inferring cross-feeding + or organism-specific flux. + - node: Chlorella biomass and protein response to SynCom pretreatment + rationale: Preserve the positive algal biomass/protein response and explicit BG11 comparator; remove unsupported + commensalism and nitrate mediation. + - node: Chlorella carbon- and nitrogen-assimilation transcript response + rationale: Preserve transcript upregulation with algal participant scope, not measured enzymatic flux or growth-to-expression + causation. + removed_node_decisions: + - node: Sequential SynCom-Microalga Coupling Construction + rationale: System construction is an experimental workflow, not demonstrated cross-feeding; sequential-system + context remains in the record and retained observations. + - node: Sixty-Day Stable Slurry Operation + rationale: The duration/stability statement is operating context, not a biological interaction or niche partitioning; + preserve the 60-day boundary in the removal observation. + renamed_nodes: + SynCom Pretreatment Facilitates Chlorella Growth: Chlorella biomass and protein response to SynCom pretreatment + Rubisco and Glutamine-Synthetase Up-Regulation: Chlorella carbon- and nitrogen-assimilation transcript response + edges_before: + - source: Sixty-Day Stable Slurry Operation + target: Nitrate-Nitrogen and Phosphorus Removal + description: 'Stable operation was measured by nitrate-nitrogen, total-phosphorus, and chemical-oxygen-demand + removal from biogas slurry. + + ' + - source: Sixty-Day Stable Slurry Operation + target: SynCom Pretreatment Facilitates Chlorella Growth + description: 'The same SynCom pretreatment condition increased downstream Chlorella biomass and soluble protein + relative to a BG11 control. + + ' + - source: SynCom Pretreatment Facilitates Chlorella Growth + target: Rubisco and Glutamine-Synthetase Up-Regulation + description: 'The Chlorella growth response was accompanied by increased expression of Rubisco and glutamine + synthetase genes. + + ' + edges_after: [] + retained_edge_decisions: [] + removed_edge_decisions: + - source: Sixty-Day Stable Slurry Operation + target: Nitrate-Nitrogen and Phosphorus Removal + description: 'Stable operation was measured by nitrate-nitrogen, total-phosphorus, and chemical-oxygen-demand + removal from biogas slurry. + + ' + rationale: Stable operation and shared treatment are context, not biological drivers; coincident growth/expression + does not establish growth-to-transcription causation. + - source: Sixty-Day Stable Slurry Operation + target: SynCom Pretreatment Facilitates Chlorella Growth + description: 'The same SynCom pretreatment condition increased downstream Chlorella biomass and soluble protein + relative to a BG11 control. + + ' + rationale: Stable operation and shared treatment are context, not biological drivers; coincident growth/expression + does not establish growth-to-transcription causation. + - source: SynCom Pretreatment Facilitates Chlorella Growth + target: Rubisco and Glutamine-Synthetase Up-Regulation + description: 'The Chlorella growth response was accompanied by increased expression of Rubisco and glutamine + synthetase genes. + + ' + rationale: Stable operation and shared treatment are context, not biological drivers; coincident growth/expression + does not establish growth-to-transcription causation. + references: + - PMID:41794300 + issues: + - 1844 + - 183 + allowed_changed_fields: + - curation_history + - discussions + - ecological_interactions + curation_events_added: 1 + history_files: + - history/records/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System/2026-10-08T041041Z-codex-cc3e7e.yaml +- path: kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml + id: CommunityMech:000302 + original_sha256: 83b3d7091d48bc228128b3266d84d6f9fe3d4d596befb02d76136cbab8d2e24b + record_sha256: a1fe9ffb3e47c18fa4d8ac5abb97a451dc8bffd7940b3b741d682729bb47bfb7 + status: needs_research + outcome: changed + review_file: reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml + scope: Whole record and all existing nodes/directions; graph/evidence repair, not whole-record certification. + summary: Preserve colonization-associated expression but distinguish inferred movement from direct colonization/facilitation; + remove the context-only arrow.; Preserve functional gene enrichment and its qualified existing contribution + to host responses; remove mutualism and exclusive inoculant attribution.; Preserve hormone, nutrient and stress + transcription without asserting measured stress tolerance; keep the unresolved host/member identity boundary + explicit. + node_decisions: + - node: Rhizosphere colonization-associated gene expression + rationale: Preserve colonization-associated expression but distinguish inferred movement from direct colonization/facilitation; + remove the context-only arrow. + - node: Rhizosphere enrichment of plant-associated functional genes + rationale: Preserve functional gene enrichment and its qualified existing contribution to host responses; remove + mutualism and exclusive inoculant attribution. + - node: Sugarcane hormone and nutrient-transporter response + rationale: Preserve hormone, nutrient and stress transcription without asserting measured stress tolerance; + keep the unresolved host/member identity boundary explicit. + removed_node_decisions: [] + renamed_nodes: + Microbial colonization of sugarcane roots: Rhizosphere colonization-associated gene expression + SynCom-stimulated enhancement of sugarcane stress resilience: Rhizosphere enrichment of plant-associated functional + genes + edges_before: + - source: Microbial colonization of sugarcane roots + target: SynCom-stimulated enhancement of sugarcane stress resilience + description: Root-surface movement and biofilm formation provide the colonization context for MetG2-associated + nutrient, hormone, siderophore, and VOC functions that stimulate sugarcane stress-resistance responses. + - &id005 + source: SynCom-stimulated enhancement of sugarcane stress resilience + target: Sugarcane hormone and nutrient-transporter response + description: Enriched rhizosphere nutrient-acquisition, hormone, siderophore, and VOC functions precede the + host response in which sugarcane up-regulates hormone-related and nutrient-transporter genes. + edges_after: + - &id006 + source: Rhizosphere enrichment of plant-associated functional genes + target: Sugarcane hormone and nutrient-transporter response + description: 'HYPOTHESIZED/PARTIAL: the enriched microbial functions are proposed to contribute to the host + transcriptional response in the MetG2-associated plant-microbe system. The reviewed omics evidence does not + identify a transferred causal signal, establish that gene enrichment precedes the host response, or isolate + mediation by the inoculant from the native rhizosphere community.' + retained_edge_decisions: + - before: *id005 + after: *id006 + rationale: Existing direction retained as an explicitly hypothetical contribution, not isolated mediation. + removed_edge_decisions: + - source: Microbial colonization of sugarcane roots + target: SynCom-stimulated enhancement of sugarcane stress resilience + description: Root-surface movement and biofilm formation provide the colonization context for MetG2-associated + nutrient, hormone, siderophore, and VOC functions that stimulate sugarcane stress-resistance responses. + rationale: Colonization-associated transcription provides context, not evidence that it causes the separately + enriched functional gene categories. + references: + - doi:10.1016/j.rhisph.2025.101142 + issues: + - 1845 + - 1847 + allowed_changed_fields: + - curation_history + - discussions + - ecological_interactions + curation_events_added: 1 + history_files: + - history/records/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience/2026-10-08T041041Z-codex-ab21b2.yaml + remaining_requirement: Resolve canonical MetG2 member identities, the Chiliseed2/Chileseed2 discrepancy and sugarcane + host grounding; distinguish inoculant from native rhizosphere responses. Issue1847 remains open. +- path: kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml + id: CommunityMech:000292 + original_sha256: 5c99fb8e16eca52dfdb474c9885a8003fd92fe828ff7c4df04b3925dd2f57da9 + record_sha256: 88b173ca8cef1393eedf415783725e0befc985adcf2cc3b2564fb7465df3d279 + status: reviewed + outcome: changed + review_file: reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml + scope: Whole record and all existing nodes/directions; graph/evidence repair, not whole-record certification. + summary: Recast co-selection as the reported tolerance phenotype; remove niche-partitioning typing and unsupported + in-vivo assay assignment.; Preserve complementarity/minimal-antagonism context without stable coexistence, directional + causation or niche separation.; Preserve plant-growth-promoting and carbon-fixation capacity without reciprocal-benefit + or sequestration-flux claims. + node_decisions: + - node: Cadmium tolerance of the Pseudomonas-Rahnella pair + rationale: Recast co-selection as the reported tolerance phenotype; remove niche-partitioning typing and unsupported + in-vivo assay assignment. + - node: Functionally complementary Pseudomonas-Rahnella pairing with minimal antagonism + rationale: Preserve complementarity/minimal-antagonism context without stable coexistence, directional causation + or niche separation. + - node: Joint PGP and carbon-fixation capacity + rationale: Preserve plant-growth-promoting and carbon-fixation capacity without reciprocal-benefit or sequestration-flux + claims. + removed_node_decisions: [] + renamed_nodes: + Cd-tolerant Pseudomonas-Rahnella SynCom co-selection: Cadmium tolerance of the Pseudomonas-Rahnella pair + edges_before: [] + edges_after: [] + retained_edge_decisions: [] + removed_edge_decisions: [] + references: + - doi:10.1016/j.indcrop.2025.122518 + issues: + - 1846 + allowed_changed_fields: + - curation_history + - discussions + - ecological_interactions + curation_events_added: 1 + history_files: + - history/records/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation/2026-10-08T041041Z-codex-ab8e2d.yaml diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv index 56d401549..b017168ce 100644 --- a/reports/causal_graph_review/inventory.tsv +++ b/reports/causal_graph_review/inventory.tsv @@ -392,10 +392,10 @@ kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml CommunityMe kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml CommunityMech:000222 5d3a32811ff6817ac9002bd39f79c53511fa76bc15d97a9adca897220471f235 3 0 65.0 reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml needs_research kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml CommunityMech:000127 3b6f0e648eb199d8139c7d790034e88f471e3fa5a3f0212ed55a60280921a6e6 3 2 91.7 reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml reviewed kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml CommunityMech:000314 8128a35b7336eb6a0e2da4768e456cd12e84db5632b771708a70f07d6bebd5b5 3 2 93.3 reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml reviewed -kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml CommunityMech:000278 ffe0f5e7381d820061ccfe30ec1b71277c3e88866519bcc52389537d4bc85123 3 2 100.0 pending -kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml CommunityMech:000285 6bc229bfcabb16639d9a7ffd085739421b0f38be95cc85cd66aaf80ecc70b9c5 5 3 100.0 pending -kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml CommunityMech:000302 83b3d7091d48bc228128b3266d84d6f9fe3d4d596befb02d76136cbab8d2e24b 3 2 100.0 pending -kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml CommunityMech:000292 5c99fb8e16eca52dfdb474c9885a8003fd92fe828ff7c4df04b3925dd2f57da9 3 0 75.0 pending +kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml CommunityMech:000278 53f9cefb513a07926eee79884f4109702e56df3567d93ac65ec56658025d68f4 3 2 86.7 reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml reviewed +kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml CommunityMech:000285 f76054afccd798d444ad3e51a74e13afbed91762384966fb998b842dc54dfeb2 3 0 63.3 reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml reviewed +kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml CommunityMech:000302 a1fe9ffb3e47c18fa4d8ac5abb97a451dc8bffd7940b3b741d682729bb47bfb7 3 1 80.0 reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml needs_research +kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml CommunityMech:000292 88b173ca8cef1393eedf415783725e0befc985adcf2cc3b2564fb7465df3d279 3 0 65.0 reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml reviewed kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml CommunityMech:000283 7632231bd07c18ef98b01774b24727e9614735db23897194855dae5a791b8b3b 3 2 100.0 pending kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml CommunityMech:000272 caf56231ec4c91150f7679b19fe3de49c892091f7cfa5514b7fe3173945ec418 4 2 100.0 pending kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml CommunityMech:000207 66201890ed3f32317d605338443cdc09ded895b09c58b435184f9e24f8e3f784 3 2 100.0 pending diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json index dedf364d7..868d77a29 100644 --- a/reports/causal_graph_review/summary.json +++ b/reports/causal_graph_review/summary.json @@ -2,14 +2,14 @@ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.", "semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.", "records": 460, - "nodes": 1386, - "edges": 551, + "nodes": 1384, + "edges": 547, "records_without_nodes": 10, - "records_without_edges": 183, + "records_without_edges": 184, "review_status_counts": { - "needs_research": 51, - "pending": 68, - "reviewed": 341 + "needs_research": 52, + "pending": 64, + "reviewed": 344 }, "structural_defects": [], "network_audit": [ diff --git a/reports/causal_graph_review/validation-20261008-batch108.json b/reports/causal_graph_review/validation-20261008-batch108.json new file mode 100644 index 000000000..aae2bf92b --- /dev/null +++ b/reports/causal_graph_review/validation-20261008-batch108.json @@ -0,0 +1,1076 @@ +{ + "base_commit": "f1c21708622a610e2dd4208818a38d20472a3114", + "scope": [ + "kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml", + "kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml", + "kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml", + "kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml" + ], + "results": [ + { + "check": "focused", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "pytest", + "-q", + "tests/test_causal_review_batch108.py" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/focused.log", + "log_sha256": "d1f6c365f27f09506cd4fe2f7b6a8c14f959942474743ac97bb6e4432e5ec987", + "output_tail": "........ [100%]\n8 passed in 1.61s\n" + }, + { + "check": "SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch108/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-strict.tsv", + "kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-strict.log", + "log_sha256": "abd4e41b264b22150512de3050e1d34d4134f23d86938d868924e31618c18cda", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch108/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-batch108/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-strict.tsv\n" + }, + { + "check": "SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-references.log", + "log_sha256": "0923e843126f256497050b5a4226672b52f6e1009c38ac536b31f4490d6a129f", + "output_tail": "Validating kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.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/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.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": "SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-snippets.log", + "log_sha256": "32e79f5bf36e5c97f219c301b9924d6a9da1ff1bf07e2b076f93f0d0ee74a358", + "output_tail": "# 9 evidence snippets scanned across 1 files\n MATCH 9\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": "SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-rank", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/rank_causal_graph_readiness.py", + "kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml", + "--format", + "json" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-rank.log", + "log_sha256": "4d845104c86b739a281a1ebf0e1f61e7742ce14df1c5a9c9a0c131d67f70f3b0", + "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000278\",\n \"name\": \"SynCom BsBv Cigar Tobacco Leaf Fermentation\",\n \"score\": 86.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\"\n }\n]\n" + }, + { + "check": "SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-history-0", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/history.yaml", + "--target-class", + "HistoryRecord", + "history/records/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation/2026-10-08T041040Z-codex-dd5f0e.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation-history-0.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch108/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-strict.tsv", + "kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-strict.log", + "log_sha256": "bd74fd3c28919ef43bcde5a7fdd000c955084e06f60feca6fa387f21da9d9811", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch108/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-batch108/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-strict.tsv\n" + }, + { + "check": "SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-references.log", + "log_sha256": "e2d29c7f477c46346128fe3771dbe30b25ffd6368a8c135b9b6b9f5565958740", + "output_tail": "Validating kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.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/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.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": "SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-snippets.log", + "log_sha256": "32e79f5bf36e5c97f219c301b9924d6a9da1ff1bf07e2b076f93f0d0ee74a358", + "output_tail": "# 9 evidence snippets scanned across 1 files\n MATCH 9\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": "SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-rank", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/rank_causal_graph_readiness.py", + "kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml", + "--format", + "json" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-rank.log", + "log_sha256": "6553122a8e8f23b83256f1eb31768f9a73e1162320987711700b2cb35ea9d604", + "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000285\",\n \"name\": \"SynCom + Chlorella sorokiniana Biogas-slurry Coupling System\",\n \"score\": 63.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\"\n }\n]\n" + }, + { + "check": "SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-history-0", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/history.yaml", + "--target-class", + "HistoryRecord", + "history/records/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System/2026-10-08T041041Z-codex-cc3e7e.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System-history-0.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch108/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-strict.tsv", + "kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-strict.log", + "log_sha256": "b5df9297c19aff2ffd12ba416eb4b24e222330acb29d17fd2ec96d854cb7070f", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch108/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-batch108/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-strict.tsv\n" + }, + { + "check": "SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-references.log", + "log_sha256": "c700e36dc381db97f3fb3cf48f87a960bc62fbc4e048fc1d5afb30d67a61099f", + "output_tail": "Validating kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.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/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.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": "SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-snippets.log", + "log_sha256": "4450b5ff1101bc2d6072d1dbe68983556781062b26a30ff5ad5b7d81a7b14c1b", + "output_tail": "# 8 evidence snippets scanned across 1 files\n MATCH 8\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": "SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-rank", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/rank_causal_graph_readiness.py", + "kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml", + "--format", + "json" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-rank.log", + "log_sha256": "401ed8cce22a04a7f10cb58d742aa30800f234c35a1894f2bb7126370efb7a89", + "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000302\",\n \"name\": \"SynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\",\n \"score\": 80.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\"\n }\n]\n" + }, + { + "check": "SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-history-0", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/history.yaml", + "--target-class", + "HistoryRecord", + "history/records/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience/2026-10-08T041041Z-codex-ab21b2.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience-history-0.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-schema", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/communitymech.yaml", + "kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-schema.log", + "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de", + "output_tail": "No issues found\n" + }, + { + "check": "SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-strict", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3", + "scripts/validate_strict.py", + "--workers", + "1", + "--out", + "/private/tmp/communitymech-batch108/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-strict.tsv", + "kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-strict.log", + "log_sha256": "987c135dc9240859e420f88545e6ef6afb0400bf380a43499b6e8a7330405cfe", + "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch108/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-batch108/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-strict.tsv\n" + }, + { + "check": "SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-terms", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator", + "validate-data", + "kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--labels" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-terms.log", + "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018", + "output_tail": "\u2705 Validation passed\n" + }, + { + "check": "SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-references", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator", + "validate", + "data", + "kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml", + "-s", + "src/communitymech/schema/communitymech.yaml", + "--config", + "conf/reference_validator.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-references.log", + "log_sha256": "28d6185a90440325e55898e93d387e18da3d4785591acd91fa97ab3e134ba345", + "output_tail": "Validating kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.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/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.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": "SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-snippets", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/evidence_snippet_audit.py", + "kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml", + "--list-mismatch", + "--list-nocontent", + "--list-rendering", + "--list-assembled" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-snippets.log", + "log_sha256": "45007c108f9ec8bef530a5471e83cc9e84b78b05e90ad8c19de389a107ed4f60", + "output_tail": "# 7 evidence snippets scanned across 1 files\n MATCH 7\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": "SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-rank", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "scripts/rank_causal_graph_readiness.py", + "kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml", + "--format", + "json" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-rank.log", + "log_sha256": "3e45e3d2f5eff980d0778a2e65b170dbf1f5962f6a8049dab1ef74760fcf2b08", + "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000292\",\n \"name\": \"Pseudomonas-Rahnella native rhizosphere SynCom for Artemisia argyi phytoremediation\",\n \"score\": 65.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml\"\n }\n]\n" + }, + { + "check": "SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-history-0", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate", + "-s", + "src/communitymech/schema/history.yaml", + "--target-class", + "HistoryRecord", + "history/records/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation/2026-10-08T041041Z-codex-ab8e2d.yaml" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation-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-batch108/verification/inventory.log", + "log_sha256": "a602bd6d49984f1b1fc3e9546b5167e9697241726cf701389e40aa40d0a05058", + "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\": 1384,\n \"edges\": 547,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 184,\n \"review_status_counts\": {\n \"needs_research\": 52,\n \"pending\": 64,\n \"reviewed\": 344\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-batch108/verification/network.log", + "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097", + "output_tail": " \"total_genomes\": 17191,\n \"is_reclassified\": false,\n \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n },\n \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"mexZ\"\n },\n \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n \"evidence\": [\n {\n \"reference\": \"PMID:42153623\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n" + }, + { + "check": "just-network-json", + "command": [ + "just", + "audit-network-json" + ], + "exit_code": 2, + "expected_exit_codes": [ + 2 + ], + "log": "/private/tmp/communitymech-batch108/verification/just-network-json.log", + "log_sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff", + "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n" + }, + { + "check": "rank-all", + "command": [ + "just", + "rank-causal-graphs" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/rank-all.log", + "log_sha256": "7aafa585816fbd2d213c0a79e8c446f1012b0b872b5e92e0fc17b35df112c944", + "output_tail": "\tkb/communities/Honeybee_Core20_Defined_Microbiota.yaml\tCommunityMech:000124\tHoneybee Core-20 Defined Microbiota\t1\t1\t0\t3\t2\t3\t\t0\t0\n402\t100.0\tkb/communities/Microbacterium_Terrabacter_Sulfadiazine_CrossFeeding_Coculture.yaml\tCommunityMech:000462\tMicrobacterium-Terrabacter Sulfadiazine Cross-Feeding Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n403\t100.0\tkb/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.yaml\tCommunityMech:000157\tMicrocoleus-Massilia Cyanosphere Urea Mutualism\t2\t2\t0\t3\t2\t5\t\t0\t0\n404\t100.0\tkb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml\tCommunityMech:000119\tMultiomics Corn Straw Degradation SynCom\t1\t1\t0\t4\t3\t9\t\t0\t0\n405\t100.0\tkb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml\tCommunityMech:000156\tNeocallimastix-Methanobrevibacter Xylanolytic Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n406\t100.0\tkb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml\tCommunityMech:000190\tPelotomaculum-Methanocella Propionate RNA-Seq Coculture\t2\t2\t0\t4\t2\t9\t\t0\t0\n407\t100.0\tkb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\tCommunityMech:000052\tPelotomaculum-Methanothermobacter Syntrophic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n408\t100.0\tkb/communities/Phenol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n409\t100.0\tkb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml\tCommunityMech:000290\tPhosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture\t2\t2\t0\t3\t2\t4\t\t0\t0\n410\t100.0\tkb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml\tCommunityMech:000289\tPseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n411\t100.0\tkb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml\tCommunityMech:000092\tRhodopseudomonas-E. coli Cross-Feeding Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n412\t100.0\tkb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml\tCommunityMech:000109\tRice Acid Soil Bioinoculant SynCom\t1\t1\t0\t4\t4\t4\t\t0\t0\n413\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t4\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n417\t100.0\tkb/communities/Synechococcus_Bacillus_SPC.yaml\tCommunityMech:000065\tSynechococcus-Bacillus Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n418\t100.0\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n419\t100.0\tkb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\tCommunityMech:000198\tSynechococcus-Halomonas Light-Driven PHB Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\tCommunityMech:000167\tSynechococcus-Pseudomonas Phototrophic PHA and DNT Coculture\t2\t2\t0\t4\t2\t8\t\t0\t0\n421\t100.0\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n422\t100.0\tkb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\tCommunityMech:000211\tSynechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n424\t100.0\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t8\t\t0\t0\n425\t100.0\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t5\t\t0\t0\n426\t100.0\tkb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml\tCommunityMech:000189\tSyntrophomonas-Methanococcus Butyrate Growth Coordination Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n427\t100.0\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n428\t100.0\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\t\t0\t0\n429\t100.0\tkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml\tCommunityMech:000187\tSyntrophus-Methanospirillum Gentianae Benzoate Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n431\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n432\t100.0\tkb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\tCommunityMech:000100\tTeosinte-Derived Maize Biofertilizer SynCom7\t4\t4\t0\t6\t2\t12\t\t0\t0\n433\t100.0\tkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml\tCommunityMech:000259\tThalassiosira-Marinobacter Marine Snow Coculture\t2\t2\t0\t4\t2\t10\t\t0\t0\n434\t100.0\tkb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml\tCommunityMech:000162\tThalassiosira-Ruegeria Phycosphere Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n435\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n436\t100.0\tkb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\tCommunityMech:000282\tThermophilic Lignocellulose-degrading Composting SynCom\t5\t5\t0\t3\t2\t3\t\t0\t0\n437\t100.0\tkb/communities/Thermophilic_Pyrite_QS_Consortium.yaml\tCommunityMech:000073\tThermophilic Pyrite Quorum Sensing Consortium\t3\t3\t0\t6\t2\t14\t\t0\t0\n438\t100.0\tkb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\tCommunityMech:000186\tThermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\t2\t2\t0\t3\t2\t8\t\t0\t0\n439\t100.0\tkb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml\tCommunityMech:000239\tThiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community\t3\t3\t0\t3\t2\t3\t\t0\t0\n440\t100.0\tkb/communities/Tinto_River_Iron_Cycling_Community.yaml\tCommunityMech:000074\tTinto River Iron Cycling Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n" + }, + { + "check": "render", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "communitymech.render" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/render.log", + "log_sha256": "2e01e63edb873ae54abe991c7ec885d9eca9d100ba4f9a39e76f50911703cb3a", + "output_tail": "unitymech-causal-batch108/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch108/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch108/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch108/docs/index.html\n" + }, + { + "check": "render-repeat", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "communitymech.render" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/render-repeat.log", + "log_sha256": "2e01e63edb873ae54abe991c7ec885d9eca9d100ba4f9a39e76f50911703cb3a", + "output_tail": "unitymech-causal-batch108/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch108/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch108/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch108/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch108/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-batch107')),('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-batch108/verification/connectivity-survey.log", + "log_sha256": "38a12f49cbc88c7b8677195d203bbd2c525ef38242aa0ab91633314f37a45aa7", + "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1544, \"credited_solely_by_the_rule\": 1270}, \"current\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1544, \"credited_solely_by_the_rule\": 1270}}\n" + }, + { + "check": "regressions", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "pytest", + "-q", + "tests/test_causal_review_batch10.py", + "tests/test_causal_review_batch100.py", + "tests/test_causal_review_batch101.py", + "tests/test_causal_review_batch102.py", + "tests/test_causal_review_batch103.py", + "tests/test_causal_review_batch104.py", + "tests/test_causal_review_batch105.py", + "tests/test_causal_review_batch106.py", + "tests/test_causal_review_batch107.py", + "tests/test_causal_review_batch108.py", + "tests/test_causal_review_batch11.py", + "tests/test_causal_review_batch12.py", + "tests/test_causal_review_batch13.py", + "tests/test_causal_review_batch14.py", + "tests/test_causal_review_batch15.py", + "tests/test_causal_review_batch16.py", + "tests/test_causal_review_batch17.py", + "tests/test_causal_review_batch18.py", + "tests/test_causal_review_batch19.py", + "tests/test_causal_review_batch20.py", + "tests/test_causal_review_batch21.py", + "tests/test_causal_review_batch22.py", + "tests/test_causal_review_batch23.py", + "tests/test_causal_review_batch24.py", + "tests/test_causal_review_batch25.py", + "tests/test_causal_review_batch27.py", + "tests/test_causal_review_batch28.py", + "tests/test_causal_review_batch29.py", + "tests/test_causal_review_batch30.py", + "tests/test_causal_review_batch31.py", + "tests/test_causal_review_batch32.py", + "tests/test_causal_review_batch33.py", + "tests/test_causal_review_batch34.py", + "tests/test_causal_review_batch35.py", + "tests/test_causal_review_batch36.py", + "tests/test_causal_review_batch37.py", + "tests/test_causal_review_batch38.py", + "tests/test_causal_review_batch39.py", + "tests/test_causal_review_batch40.py", + "tests/test_causal_review_batch41.py", + "tests/test_causal_review_batch42.py", + "tests/test_causal_review_batch43.py", + "tests/test_causal_review_batch44.py", + "tests/test_causal_review_batch45.py", + "tests/test_causal_review_batch46.py", + "tests/test_causal_review_batch47.py", + "tests/test_causal_review_batch48.py", + "tests/test_causal_review_batch49.py", + "tests/test_causal_review_batch5.py", + "tests/test_causal_review_batch50.py", + "tests/test_causal_review_batch51.py", + "tests/test_causal_review_batch52.py", + "tests/test_causal_review_batch53.py", + "tests/test_causal_review_batch54.py", + "tests/test_causal_review_batch55.py", + "tests/test_causal_review_batch56.py", + "tests/test_causal_review_batch57.py", + "tests/test_causal_review_batch58.py", + "tests/test_causal_review_batch59.py", + "tests/test_causal_review_batch6.py", + "tests/test_causal_review_batch60.py", + "tests/test_causal_review_batch61.py", + "tests/test_causal_review_batch62.py", + "tests/test_causal_review_batch63.py", + "tests/test_causal_review_batch64.py", + "tests/test_causal_review_batch65.py", + "tests/test_causal_review_batch66.py", + "tests/test_causal_review_batch67.py", + "tests/test_causal_review_batch68.py", + "tests/test_causal_review_batch69.py", + "tests/test_causal_review_batch7.py", + "tests/test_causal_review_batch70.py", + "tests/test_causal_review_batch71.py", + "tests/test_causal_review_batch72.py", + "tests/test_causal_review_batch73.py", + "tests/test_causal_review_batch74.py", + "tests/test_causal_review_batch75.py", + "tests/test_causal_review_batch76.py", + "tests/test_causal_review_batch77.py", + "tests/test_causal_review_batch78.py", + "tests/test_causal_review_batch79.py", + "tests/test_causal_review_batch8.py", + "tests/test_causal_review_batch80.py", + "tests/test_causal_review_batch81.py", + "tests/test_causal_review_batch82.py", + "tests/test_causal_review_batch83.py", + "tests/test_causal_review_batch84.py", + "tests/test_causal_review_batch85.py", + "tests/test_causal_review_batch86.py", + "tests/test_causal_review_batch87.py", + "tests/test_causal_review_batch88.py", + "tests/test_causal_review_batch89.py", + "tests/test_causal_review_batch9.py", + "tests/test_causal_review_batch90.py", + "tests/test_causal_review_batch91.py", + "tests/test_causal_review_batch92.py", + "tests/test_causal_review_batch93.py", + "tests/test_causal_review_batch94.py", + "tests/test_causal_review_batch95.py", + "tests/test_causal_review_batch96.py", + "tests/test_causal_review_batch97.py", + "tests/test_causal_review_batch98.py", + "tests/test_causal_review_batch99.py", + "tests/test_site_audit_fixes.py", + "tests/test_causal_review_inventory.py", + "tests/test_rank_causal_graph_readiness.py", + "tests/test_network_auditor.py", + "tests/test_participating_taxa.py", + "tests/test_causal_descriptions_are_published.py", + "tests/test_published_pages_name_real_records.py", + "tests/test_reference_validator_actually_validates.py", + "tests/test_snippet_audit_artefact_classes.py", + "tests/test_reference_error_annotation.py", + "tests/test_community_level_connectivity_credit.py", + "tests/test_no_paywalled_text_in_repo.py" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/regressions.log", + "log_sha256": "07b1bb4e3791f0f27b7f709ac8caa14beba6f4f62a7d8d99643b45fa0f4fa2d4", + "output_tail": "........................................................................ [ 7%]\n........................................................................ [ 14%]\n........................................................................ [ 22%]\n........................................................................ [ 29%]\n........................................................................ [ 36%]\n........................................................................ [ 44%]\n........................................................................ [ 51%]\n........................................................................ [ 59%]\n........................................................................ [ 66%]\n........................................................................ [ 73%]\n........................................................................ [ 81%]\n........................................................................ [ 88%]\n........................................................................ 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[100%]\n975 passed in 301.81s (0:05:01)\n" + }, + { + "check": "just-lint", + "command": [ + "just", + "lint" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/just-lint.log", + "log_sha256": "5fd7f26e1e7a4bb58dbc60ad02ba76259fd13a00d5a4cd38764cdb2d0fc1976e", + "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n361 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n" + }, + { + "check": "mypy-explicit-runtime", + "command": [ + "/private/tmp/communitymech-batch100/lint-env/bin/mypy", + "--no-incremental", + "--python-executable", + "/private/tmp/communitymech-batch100/lint-env/bin/python", + "src/" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/mypy-explicit-runtime.log", + "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875", + "output_tail": "Success: no issues found in 49 source files\n" + }, + { + "check": "audit-snippets-all", + "command": [ + "just", + "audit-snippets" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/audit-snippets-all.log", + "log_sha256": "26d3533ff05842242480f12f223c94a04ca26399763d77d1d1103eb785d1399a", + "output_tail": "# 8984 evidence snippets scanned across 460 files\n MATCH 8847\n RENDERING 21\n ASSEMBLED 1\n WEAK 0\n MISMATCH 39\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\nuv run python scripts/evidence_snippet_audit.py \n" + }, + { + "check": "diff-check", + "command": [ + "git", + "diff", + "--check" + ], + "exit_code": 0, + "expected_exit_codes": [ + 0 + ], + "log": "/private/tmp/communitymech-batch108/verification/diff-check.log", + "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", + "output_tail": "" + } + ], + "limitations": [ + "Fresh both-root baseline precedes source reads: 460 records, 923 caches, 56 existing warnings, zero structural defects. Whole four records and all 14 original nodes/seven directions reviewed. Retain 12 nodes/three qualified existing directions; remove two workflow nodes/four context or coincidence arrows; rename seven nodes. No new topology or Edison spend.", + "Tobacco and Artemisia whole indexed publisher abstracts/highlights read; MetG2 whole indexed abstract/Introduction and the displayed bounded experimental-design, metagenome, discussion/conclusion previews read. Chlorella whole independently retrieved EuropePMC abstract read, plus an indexed publisher preview lead. These are not complete papers. Direct ScienceDirect requests returned HTTP403; Crossref-advertised public API links for the two CC-licensed articles returned HTTP400. No bypass or whole-paper/supplement/figure-pixel/raw-data certification. Publisher index was crawled earlier; retrieval is fresh, not a claim that the publisher page was fetched live.", + "Crossref version-of-record metadata identifies tobacco as CC BY4.0 and Artemisia as CC BY-NC4.0 despite local historical paywall wording. That metadata does not mean their complete bodies were retrieved. No cache or license949 repair is claimed. The four cited Markdown caches were read whole; Artemisia contains two trait/design sentences, not its full abstract. Existing cache content is unchanged and sufficient for every retained/new literal quotation.", + "Tobacco: preserve measured substrate loss, community shifts and volatile/sensory outcomes. Remove mutualism and niche partitioning, qualify the existing directions and preserve PLS-PM mediation as a statistical hypothesis. No invented software/version, taxon-specific mediator or monoculture-synergy claim. Endpoint process annotations are removed because they describe upstream degradation, not volatile/sensory measurement.", + "Chlorella: preserve 60-day removal, algal biomass/protein versus BG11 and transcript responses. Remove construction/duration nodes and three remaining noncausal arrows while preserving prior October2 repairs. No demonstrated cross-feeding, neutral bacterial fitness, isolated medium effect or measured metabolic flux. Only the algal observations gain canonical identity-only participant scope; unnamed bacterial membership remains existing issue183.", + "MetG2: preserve microbial and host molecular responses and one qualified source-proposed functional contribution. Remove the context-only arrow, unestablished interaction types and redundant community-level source/target links. The indexed source names four inoculant strains and has a Chiliseed2/Chileseed2 spelling discrepancy; broad native rhizosphere Proteobacteria is not a resolved inoculant identity. Generic sugarcane is not verified as the canonical species. Record remains needs_research under1847; no new identifiers or canonical-taxonomy edits.", + "Artemisia: preserve the pair-level tolerance, complementarity and PGP/carbon-fixation capacity. Remove niche partitioning and mutualism; source assay setting is not specified in the reviewed abstract, so OTHER replaces unsupported IN_VIVO assignment on these trait/design items. Preserve previous removal of screening-order arrows. Positive whole-abstract plant/soil outcomes are not rejected, but no new graph mechanism or sequestration-flux claim is introduced.", + "Repair issues1843-1846 await protected-main merge; identity1847 and existing membership183 remain open. Fresh all-state issue titles/bodies and ignored/hidden local search matched1093,1091,184,183; all four bodies read. The122 local matching paths were inspected as an index, not all read; focused prior access/missing-PDF/author-request leads were inspected without contacting anyone. No reusable taxon match found in ignored/hidden-inclusive kb/taxa searches for the target names/IDs. PRs/comments not exhaustively searched.", + "Only existing graphs, focused discussions and curation events change. All456 other records,923 caches, non-graph raw blocks and prior histories/decisions preserved. No schema, validator, runtime, census threshold or configuration changes. Non-graph membership, abundance, growth and role claims are not recertified. Loader1703, DOI-case1091 and stub-policy1093 remain separate. Self-review is not independent approval or corpus completion. Denied AM_AB000444 and unanswered Edison scopes untouched; validation/publication not preasserted." + ], + "reference_validator_version": "0.1.7", + "snippet_counts_by_record": { + "kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml": { + "MATCH": 9, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + }, + "kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml": { + "MATCH": 9, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + }, + "kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml": { + "MATCH": 8, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + }, + "kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml": { + "MATCH": 7, + "RENDERING": 0, + "ASSEMBLED": 0, + "WEAK": 0, + "MISMATCH": 0, + "NOCONTENT": 0 + } + }, + "unchanged_record_files": 456, + "unchanged_cache_files": 923, + "unchanged_raw_blocks": 34, + "cache_changes": [], + "edison": { + "required_for_this_repair": false, + "required_for_unresolved_extensions": false, + "provider_submissions": 0, + "credits_spent": 0, + "dry_runs": [], + "repair_scope": "Existing-node repair and retention/qualification of three existing directions; no new causal structure. Identity1847 requires coordinated curation, not topology generation." + }, + "primary_artifacts": { + "/private/tmp/communitymech-batch108/artemisia-crossref.json": "aa3d46d5415e9269fae708d23a873e97b70706a44abc0d7d511f56cc7642ca1c", + "/private/tmp/communitymech-batch108/artemisia-indexed-primary.txt": "aa4e6f4c440cc36385db0570e5fb5456c3c9081d7341b28c8204d63b289372fd", + "/private/tmp/communitymech-batch108/baseline.json": "924874048322ec9dc575fb31ed77c1019f28be5ec616afb66734d957285a1b83", + "/private/tmp/communitymech-batch108/chlorella-abstract.txt": "8ad94da0200fad04401b2803e09013f11c622b3a32c34b4c6eeff98175fc665b", + "/private/tmp/communitymech-batch108/chlorella-crossref.json": "dfc2234defea0730f238bf424d0d59d362cb87f7d08ad3297dc38d7f8a4022a0", + "/private/tmp/communitymech-batch108/chlorella-metadata.json": "3c34294fe8a42ed0d2435e804db167bd9278c2d341543fbeaf0eebf329b20be0", + "/private/tmp/communitymech-batch108/dedup-local-current.txt": "07595e8b54dca3146eb1c7a6c869ea7bb6045d50754eff282828bd9db20374c5", + "/private/tmp/communitymech-batch108/issue-dedup-current.json": "ac8cf6accf97387b4df7978a0bb8fc8ce23c134ecd1ca519167db22ac6c97958", + "/private/tmp/communitymech-batch108/oa-retrieval.json": "8b62745386f0d5d5d48040eaa6f4feb8577504015ecad601aeaf53085ace2e87", + "/private/tmp/communitymech-batch108/primary-manifest.json": "b8632441c8967d86414502369971c2e59c09b387c570280f1b49bb4d95a3ca42", + "/private/tmp/communitymech-batch108/sugarcane-crossref.json": "a90002c6c38efda7a580a424df215bf60134a14d6238e537192125a911a2e326", + "/private/tmp/communitymech-batch108/sugarcane-indexed-primary.txt": "636790da7efc988cb2752c481269d5023a29a47dca35bb0831e0b7238e4e9cc2", + "/private/tmp/communitymech-batch108/tobacco-crossref.json": "70e60a1af78a9fc68cda93c83e7165b06c7428bbe039c4884b055de5d71ae6eb", + "/private/tmp/communitymech-batch108/tobacco-indexed-primary.txt": "15ad1fdb873c4e3067087870798192d6e40e3fabfcb441889474c6588ecbb8a9", + "references_cache/PMID_41794300.md": "b91c82802329ca0b23f96532e035e1b0ad5517f52ad5bb6e68a143508e356b20", + "references_cache/doi_10.1016_j.indcrop.2025.122518.md": "2012eb359a1c680913d435c8af619b3c69fb09ec29a90c6cdec66e066e4f1395", + "references_cache/doi_10.1016_j.indcrop.2025.122621.md": "8a4a5fd6472f2216776ed2c26e139f85ffa5fe8c79dbd14ed61b4838f51694ac", + "references_cache/doi_10.1016_j.rhisph.2025.101142.md": "2651ef5f596a41fc8a30d3f77b706f806b9867e7aa5ff132911e396968be3c60" + }, + "immutable_prior_history_and_decision_files": 828, + "primary_graph_snippet_proof": { + "graph_quotations": 15, + "new_discussion_quotations": 7, + "fresh_primary_literal_matches": 22, + "all_cached_literal_matches": 22, + "retained_nodes": 12, + "removed_nodes": 2, + "retained_arrows": 3, + "removed_arrows": 4, + "new_nodes_or_directions": 0, + "scope": "All reviewed quotations match fresh primary text and unchanged caches; source entailment separately reviewed. Bounded primary abstracts/indexed publisher previews,not full-body/supplement/figure/raw-data certification." + }, + "network_delta": { + "existing_findings_preserved": 56, + "added_findings": {}, + "removed_findings": {}, + "interpretation": "Twelve nodes and three qualified existing directions retained,two workflow nodes and four context/coincidence arrows removed. All56existing warnings unchanged;zero structural defects. MetG2 identity remains unresolved1847 despite structural validity." + }, + "render_determinism": true, + "published_description_coverage": { + "pages": 456, + "nodes": 1370, + "arrows": 539 + }, + "render_scope": "Deterministic rendering and exact HTML-description parser,not screenshots;postcommit docs-current separately required.", + "participant_census": { + "measurements": { + "baseline": { + "records": 460, + "with_community_level": 403, + "mixed": 128, + "community_level_only": 275, + "taxa": 1544, + "credited_solely_by_the_rule": 1270 + }, + "current": { + "records": 460, + "with_community_level": 403, + "mixed": 128, + "community_level_only": 275, + "taxa": 1544, + "credited_solely_by_the_rule": 1270 + } + }, + "delta": { + "records": 0, + "with_community_level": 0, + "mixed": 0, + "community_level_only": 0, + "taxa": 0, + "credited_solely_by_the_rule": 0 + }, + "interpretation": "Chlorella growth/transcript observations gain canonical identity-only scope;the system removal endpoint stays community-level. Redundant MetG2 source/target links are removed without changing COMMUNITY_LEVEL scope;global census unchanged. MetG2 canonical identities are explicitly uncertified. No census thresholds or audit rules changed." + }, + "lint_limitation": "Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.", + "lint_environment": { + "path": "/private/tmp/communitymech-batch100/lint-env", + "scope": "Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies unchanged. Not a complete embedding runtime." + }, + "full_corpus_snippet_counts": { + "records": 460, + "total": 8984, + "categories": { + "MATCH": 8847, + "RENDERING": 21, + "ASSEMBLED": 1, + "WEAK": 0, + "MISMATCH": 39, + "NOCONTENT": 76 + } + }, + "full_corpus_snippet_audit_caveat": "Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment.", + "corpus": { + "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.", + "records": 460, + "nodes": 1384, + "edges": 547, + "records_without_nodes": 10, + "records_without_edges": 184, + "review_status_counts": { + "needs_research": 52, + "pending": 64, + "reviewed": 344 + }, + "structural_defects": [] + }, + "tested_file_sha256": { + "reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml": "4004aaf9719161201cb0135d82c2f0ba2e7231ef9f7473ec99760465993bdaeb", + "tests/test_causal_review_batch108.py": "fc8e5c1fdaff00b1b7db98c2b0b6afbc2f9a095fde4892439bd40ea73d509039", + "tests/test_participating_taxa.py": "3a97ee16d14fa2cf1fb8dbb1dedc4cd0dbe89c06e1948247003a05f5c9b31c74", + "tests/test_community_level_connectivity_credit.py": "383a0f5904085a5cda800b5102923fc99301831f5769d8d4821e000773d2ea4c", + "reports/causal_graph_review/cache-provenance-20261008-batch108.json": "94021e82e614fa11c4e8dc2b50d490f9233a514fa7c2664c8e8e53bc3c159512", + "kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml": "53f9cefb513a07926eee79884f4109702e56df3567d93ac65ec56658025d68f4", + "kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml": "f76054afccd798d444ad3e51a74e13afbed91762384966fb998b842dc54dfeb2", + "kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml": "a1fe9ffb3e47c18fa4d8ac5abb97a451dc8bffd7940b3b741d682729bb47bfb7", + "kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml": "88b173ca8cef1393eedf415783725e0befc985adcf2cc3b2564fb7465df3d279" + }, + "pre_research_baseline": { + "base_commit": "f1c21708622a610e2dd4208818a38d20472a3114", + "base_tree": "f67514fe657a504bbfbe4825943558b24b7f50e5", + "research_worktree": "/private/tmp/communitymech-causal-batch107", + "checks": [ + { + "name": "rank", + "command": [ + "just", + "rank-causal-graphs" + ], + "exit_code": 0, + "expected_exit_code": 0, + "log": "/private/tmp/communitymech-batch108/baseline-rank.log", + "sha256": "4c56af46d790f6da656a55382a12058542527bc825bbd502842ff08a609c53eb" + }, + { + "name": "just-network", + "command": [ + "just", + "audit-network-json" + ], + "exit_code": 2, + "expected_exit_code": 2, + "log": "/private/tmp/communitymech-batch108/baseline-just-network.log", + "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff" + }, + { + "name": "network", + "command": [ + "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3", + "-m", + "communitymech.cli", + "audit-network", + "--json" + ], + "exit_code": 1, + "expected_exit_code": 1, + "log": "/private/tmp/communitymech-batch108/baseline-network.log", + "sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097" + }, + { + "name": "downstream", + "command": [ + "rg", + "--no-ignore", + "--hidden", + "-n", + "downstream:", + "kb/communities", + "data/isolates", + "--glob", + "*.yaml" + ], + "exit_code": 0, + "expected_exit_code": 0, + "log": "/private/tmp/communitymech-batch108/baseline-downstream.log", + "sha256": "e3059d4354d09a4af46a1532ffbbfd9432d96b55645144827b88e0ed0acf0882" + } + ], + "baseline_sha256": "924874048322ec9dc575fb31ed77c1019f28be5ec616afb66734d957285a1b83" + }, + "reference_validator_caveat": "Four full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.", + "status": "verified_existing_graph_repairs_with_source_access_limits", + "total_recorded_gate_outputs": 41 +} diff --git a/tests/test_causal_review_batch108.py b/tests/test_causal_review_batch108.py new file mode 100644 index 000000000..d9a6613bf --- /dev/null +++ b/tests/test_causal_review_batch108.py @@ -0,0 +1,147 @@ +"""Keep process outcomes and omics responses distinct from proven mediation.""" + +import hashlib +from pathlib import Path + +import yaml + +ROOT = Path(__file__).resolve().parents[1] +LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml" + + +def records(): + ledger = yaml.safe_load(LEDGER.read_text()) + rows = ledger["records"] + return ledger, rows, [yaml.safe_load((ROOT / row["path"]).read_text()) for row in rows] + + +def test_tobacco_preserves_measured_outcomes_without_reciprocal_fitness(): + _, _, docs = records() + degradation, succession, outcome = docs[0]["ecological_interactions"] + assert all("interaction_type" not in n for n in [degradation, succession, outcome]) + assert all(value in degradation["description"] for value in ["52.48%", "56.36%", "68.47%"]) + assert "uninoculated control" in degradation["description"] + assert "relative abundance" in succession["description"] + assert "31 differentially" in outcome["evidence"][0]["snippet"] + assert "reducing irritancy" in outcome["evidence"][1]["snippet"] + assert "biological_processes" not in outcome + + +def test_tobacco_path_model_is_bounded_and_directions_stay_hypotheses(): + _, _, docs = records() + degradation, succession, outcome = docs[0]["ecological_interactions"] + model = succession["evidence"][1] + assert model["evidence_source"] == "COMPUTATIONAL" and model["supports"] == "PARTIAL" + provenance = model["computational_provenance"] + assert provenance["prediction_type"] == "STATISTICAL_INFERENCE" + assert "PLS-PM" in provenance["parameters"] and "tools" not in provenance + for node in [degradation, succession]: + assert node["downstream"][0]["target"] == outcome["name"] + assert node["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:") + assert "beta-diversity variable" in succession["downstream"][0]["description"] + + +def test_chlorella_workflows_are_context_not_graph_nodes_or_arrows(): + _, rows, docs = records() + nodes = docs[1]["ecological_interactions"] + assert len(nodes) == 3 + assert all("interaction_type" not in n and not n.get("downstream") for n in nodes) + assert {r["node"] for r in rows[1]["removed_node_decisions"]} == { + "Sequential SynCom-Microalga Coupling Construction", + "Sixty-Day Stable Slurry Operation", + } + assert len(rows[1]["removed_edge_decisions"]) == 3 + assert all( + value in nodes[0]["description"] for value in ["60 days", "94.41%", "81.84%", "6.31%"] + ) + assert len(docs[1]["curation_history"]) == 2 + assert "construction-to-operation workflow edge" in docs[1]["curation_history"][0]["changes"] + + +def test_chlorella_comparator_and_algal_scope_are_explicit(): + _, _, docs = records() + doc = docs[1] + removal, growth, transcript = doc["ecological_interactions"] + assert "BG11 comparison" in growth["description"] + assert "27.15%" in growth["description"] and "488.10%" in growth["description"] + assert "metabolites" not in growth + expected = [{k: doc["taxonomy"][0]["taxon_term"][k] for k in ["preferred_term", "term"]}] + assert growth["participating_taxa"] == transcript["participating_taxa"] == expected + assert "participating_taxa" not in removal + assert "does not measure enzyme activity" in transcript["description"] + + +def test_metg2_omics_and_identity_gaps_are_not_certified_as_mechanisms(): + ledger, rows, docs = records() + colonization, functions, host = docs[2]["ecological_interactions"] + assert rows[2]["status"] == "needs_research" and ledger["unresolved_research_issues"] == [1847] + assert all( + not any(k in n for k in ["interaction_type", "source_taxon", "target_taxon"]) + for n in [colonization, functions, host] + ) + assert not colonization.get("downstream") + assert colonization["evidence"][0]["supports"] == "PARTIAL" + assert len(functions["evidence"]) == 1 + assert functions["downstream"][0]["target"] == host["name"] + assert functions["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:") + assert "antioxidant-related genes were also induced" in host["evidence"][1]["snippet"] + assert "Saccharum officinarum grounding" in host["description"] + assert "four MetG2 strains" in docs[2]["discussions"][-1]["rationale"] + + +def test_artemisia_preserves_traits_without_inventing_niches_or_assay_setting(): + _, _, docs = records() + tolerance, complementarity, capacity = docs[3]["ecological_interactions"] + assert "Cadmium tolerance" in tolerance["name"] and "2 mM" in tolerance["description"] + assert all( + "interaction_type" not in n and not n.get("downstream") + for n in [tolerance, complementarity, capacity] + ) + assert complementarity["scope"] == "PAIRWISE" + assert complementarity["evidence"][0]["supports"] == "PARTIAL" + assert all( + e["evidence_source"] == "OTHER" + for n in [tolerance, complementarity, capacity] + for e in n["evidence"] + ) + assert "carbon fixation capacity" in capacity["evidence"][0]["snippet"] + assert "measured sequestration flux" in capacity["description"] + assert len(docs[3]["curation_history"]) == 2 + assert "Removed two downstream edges" in docs[3]["curation_history"][0]["changes"] + + +def test_every_original_node_and_direction_has_a_disposition_without_extensions(): + ledger, rows, docs = records() + assert sum(len(d["ecological_interactions"]) for d in docs) == 12 + assert sum(len(r["removed_node_decisions"]) for r in rows) == 2 + assert sum(len(r["edges_before"]) for r in rows) == 7 + assert sum(len(r["edges_after"]) for r in rows) == 3 + assert sum(len(r["removed_edge_decisions"]) for r in rows) == 4 + assert sum(len(r["renamed_nodes"]) for r in rows) == 7 + assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0 + assert ledger["unresolved_non_graph_issues"] == [183] + + +def test_hashes_append_only_histories_and_discussion_schema_are_explicit(): + ledger, rows, docs = records() + assert ledger["independent_approval"] is False + assert [r["status"] for r in rows] == ["reviewed", "reviewed", "needs_research", "reviewed"] + for row, doc in zip(rows, docs, strict=True): + assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"] + assert set(row["allowed_changed_fields"]) == { + "ecological_interactions", + "discussions", + "curation_history", + } + assert row["curation_events_added"] == len(row["history_files"]) == 1 + assert (ROOT / row["history_files"][0]).exists() + assert doc["curation_history"][-1]["llm_assisted"] is True + names = {n["name"] for n in doc["ecological_interactions"]} + assert all( + e["target"] in names + for n in doc["ecological_interactions"] + for e in n.get("downstream", []) + ) + assert all( + "computational_provenance" not in e for d in doc["discussions"] for e in d["evidence"] + ) diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py index d45b22057..b6f17b353 100644 --- a/tests/test_participating_taxa.py +++ b/tests/test_participating_taxa.py @@ -416,6 +416,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example): "Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml", "SynComBac10_Chicken_Intestinal_SynCom.yaml", "SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml", + "SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml", "SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml", "SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml", "Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml",