{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33803797", "kind": "science-record", "revision": 7, "content_hash": "sha256:e2c44a340948320a275381918c8ee2c919a845e392c87c13b866441f64c3807e", "created_at": "2026-11-01T15:41:31Z", "updated_at": "2026-11-01T22:03:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic Analysis of Mycelial Exudates of Ustilaginoidea virens.", "doi": "10.3390/pathogens10030364", "pmid": "33803797", "authors": ["Haining Wang", "Xiaohe Yang", "Songhong Wei", "Yan Wang"], "journal": "Pathogens (Basel, Switzerland)", "year": 2021, "abstract": "Rice false smut (RFS) disease, which is caused by Ustilaginoidea virens, has been widespread all over the world in recent years, causing irreversible losses. Under artificial culture conditions, exudates will appear on colonies of U. virens during the growth of the hyphae. Exudation of droplets is a common feature in many fungi, but the functions of exudates are undetermined. As the executors of life functions, proteins can intuitively reflect the functions of exudates. Shotgun proteomics were used in this study. A total of 650 proteins were identified in the exudate of U. virens, and the raw data were made available via ProteomeXchange with the identifier PXD019861. There were 57 subcategories and 167 pathways annotated with Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, respectively. Through protein-protein interaction (PPI) network analysis, it was found that 20 proteins participated in the biosynthesis of secondary metabolites. Two separate PPI analyses were performed for carbon metabolism and microbial metabolism in diverse environments. After comparing and annotating the functions of proteins of the exudate, it was speculated that the exudate was involved in the construction and remodeling of the fungal cell wall. Pathogenicity, sporulation, and antioxidant effects might all be affected by the exudate.", "claims": [{"id": "claim-method", "statement": "GO and KEGG enrichment analyses were carried out with Fisher’s exact test and FDR correction for multiple tests was also performed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33803797", "locator": "sections[14] \"4.5. 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Protein Identification", "row_count": 26, "column_count": 3}, "table": {"label": "Table 1", "caption": "List of proteins identified with liquid chromatography–tandem mass spectrometry (LC-MS/MS) in the exudates of Ustilaginoidea virens.", "rows": [["NO a", "Protein Functions b", "Protein IDs c"], ["1", "fungal-type cell wall organization", "KDB16044.1, KDB16026.1, KDB12967.1, KDB17270.1, KDB13423.1, KDB12509.1, KDB10968.1, KDB12449.1"], ["2", "pathogenesis", "KDB16026.1, KDB18474.1, KDB18473.1, KDB13423.1, KDB13264.1, KDB17801.1, KDB14282.1, KDB12970.1, KDB12705.1, KDB12369.1, KDB12341.1, KDB12056.1, KDB12863.1, KDB14729.1, KDB12463.1, KDB18714.1, KDB11931.1, KDB11462.1"], ["3", "response to oxidative stress", "KDB14292.1, KDB12590.1, KDB18386.1, KDB17179.1, KDB13850.1, KDB15471.1, KDB13484.1, KDB11596.1, KDB11345.1, KDB11441.1, KDB15626.1, KDB16892.1, KDB13523.1, KDB15731.1, KDB18611.1, KDB16877.1, KDB17534.1"], ["4", "sporulation resulting in formation of a cellular spore", "KDB13075.1, KDB17876.1"], ["5", "ascospore formation", "KDB12701.1, KDB11591.1"], ["6", "spore germination", "KDB17080.1"], ["7", "cell wall organization", "KDB16967.1, KDB18910.1, KDB15368.1, KDB12546.1, KDB14267.1, KDB19043.1, KDB12613.1, KDB14252.1, KDB13987.1, KDB18188.1, KDB11503.1, KDB16319.1"], ["8", "cellular response to osmotic stress", "KDB18447.1, KDB11395.1, KDB13915.1, KDB18874.1, KDB17080.1"], ["9", "carbohydrate metabolic process", "KDB14278.1, KDB18474.1, KDB18473.1, KDB18838.1, KDB14575.1, KDB11829.1, KDB14601.1, KDB14600.1, KDB15368.1, KDB12546.1, KDB11271.1, KDB14684.1, KDB12548.1, KDB15611.1, KDB10889.1, KDB14267.1, KDB14320.1, KDB12419.1, KDB18213.1, KDB13612.1, KDB15373.1, KDB13423.1, KDB11780.1"], ["10", "cell redox homeostasis", "KDB16889.1, KDB12590.1, KDB18386.1, KDB17179.1, KDB18140.1"], ["11", "cellulose catabolic process", "KDB12033.1, KDB16140.1, KDB12252.1, KDB16790.1, KDB11955.1, KDB16468.1, KDB13443.1"], ["12", "chitin catabolic process", "KDB15606.1, KDB11464.1, KDB12586.1"], ["13", "oxidation–reduction process", "KDB16889.1, KDB18474.1, KDB18473.1, KDB17420.1, KDB12801.1, KDB15461.1, KDB12059.1"], ["14", "filamentous growth", "KDB16843.1"], ["15", "tricarboxylic acid cycle", "KDB12786.1, KDB14278.1, KDB14601.1, KDB14600.1, KDB10889.1, KDB13150.1, KDB16991.1, KDB17192.1, KDB16006.1, KDB11543.1, KDB10744.1, KDB14658.1, KDB17818.1, KDB11496.1"], ["16", "translation", "KDB17180.1, KDB17178.1, KDB13202.1, KDB17437.1, KDB17624.1, KDB16501.1, KDB12514.1, KDB15720.1, KDB18497.1, KDB13460.1, KDB12690.1, KDB11557.1, KDB18340.1, KDB13903.1, KDB18121.1, KDB17697.1, KDB12335.1, KDB16500.1, KDB11526.1, KDB11525.1, KDB11907.1, KDB15905.1, KDB16255.1, KDB15436.1, KDB14900.1, KDB13937.1, KDB13450.1, KDB11439.1"], ["17", "amino acid metabolism process", "KDB12840.1, KDB18587.1, KDB14255.1, KDB18363.1, KDB16051.1, KDB18484.1, KDB12951.1, KDB13778.1, KDB13915.1, KDB13888.1, KDB14012.1, KDB14608.1, KDB13578.1, KDB16028.1, KDB11789.1, KDB11862.1, KDB16889.1, KDB16190.1, KDB11291.1, KDB12646.1, KDB11239.1, KDB11321.1, KDB12537.1, KDB18031.1, KDB11222.1, KDB17215.1, KDB15208.1, KDB16374.1, KDB18200.1, KDB16669.1, KDB18959.1, KDB10792.1, KDB18706.1, KDB18773.1, KDB11366.1, KDB11543.1, KDB15471.1, KDB15846.1, KDB12825.1, KDB11677.1, KDB18285.1, KDB12314.1, KDB17813.1, KDB15640.1, KDB16843.1, KDB12482.1, KDB17017.1, KDB11426.1, KDB14889.1, KDB11692.1, KDB13308.1, KDB15264.1, KDB18161.1, KDB15909.1, KDB13150.1, KDB12414.1, KDB13272.1, KDB12151.1"], ["18", "fatty acid biosynthetic process", "KDB13931.1, KDB13929.1, KDB16107.1"], ["19", "glycolytic process", "KDB18218.1, KDB19042.1, KDB15252.1, KDB11157.1, KDB14945.1, KDB14792.1, KDB11877.1, KDB13798.1, KDB18458.1, KDB16050.1, KDB15065.1, KDB10987.1"], ["20", "defense response to fungus", "KDB14422.1, KDB11072.1"], ["21", "mannose metabolism process", "KDB12509.1, KDB13367.1, KDB16099.1, KDB15243.1, KDB13380.1"], ["22", "response to toxic substance", "KDB11815.1"], ["23", "protein 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD019861"], "resolved_accessions": ["PXD019861"], "statements": ["There were 650 proteins identified in the exudate; the raw data are available via ProteomeXchange with the identifier PXD019861 (http://proteomecentral.proteomexchange.org)."], "basis": "The paper names PXD019861 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:33803797", "data:geo:PXD019861", "asset:table:pmid:33803797:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD019861"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:42Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 35999, "completion_tokens": 1229, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33803797", "type": "paper", "label": "pmid:33803797"}, {"id": "source:pmid:33803797", "type": "manuscript", "label": "PMID 33803797 full text"}, {"id": "data:geo:PXD019861", "type": "dataset", "label": "GEO PXD019861"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33803797", "type": "paper", "label": "pmid:33803797"}, {"id": "source:pmid:33803797", "type": "manuscript", "label": "PMID 33803797 full text"}, {"id": "data:geo:PXD019861", "type": "dataset", "label": "GEO PXD019861"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33803797", "type": "extraction", "used": ["source:pmid:33803797"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD019861", "type": "accession_resolution", "used": ["data:geo:PXD019861"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33803797", "parent_hash": "sha256:cf65f60ef85ddf143e5b84434ec764a2566752f6f91b8d34a6f1f4075c756001", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD019861 licence not read", "asset:data:geo:PXD019861 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Proteomic Analysis of Mycelial Exudates of Ustilaginoi", "y reflect the functions of exudates. Shotgun proteomics were used in this study. A total of 650 prot", ": Table S1: List of proteins identified with LC-MS/MS in the exudates of Ustilaginoidea virens. Cl"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. 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At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}