{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33228257", "kind": "science-record", "revision": 6, "content_hash": "sha256:1a2a7d6b4ed33c962a63dc2abe1c1d6f20550fefe9e835b742c013b7bdf44a28", "created_at": "2026-11-01T15:41:17Z", "updated_at": "2026-11-01T21:24:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Efficient Confirmation of Plant Viral Proteins and Identification of Specific Viral Strains by nanoLC-ESI-Q-TOF Using Single-Leaf-Tissue Samples.", "doi": "10.3390/pathogens9110966", "pmid": "33228257", "authors": ["Pavel Cejnar", "Štěpánka Kučková", "Jiří Šantrůček", "Miroslav Glasa", "Petr Komínek", "Daniel Mihálik", "Lucie Slavíková", "Leona Leišová-Svobodová", "Tatiana Smirnova", "Radovan Hynek", "Jiban Kumar Kundu", "Pavel Ryšánek"], "journal": "Pathogens (Basel, Switzerland)", "year": 2020, "abstract": "Plant viruses are important pathogens that cause significant crop losses. A plant protein extraction protocol that combines crushing the tissue by a pestle in liquid nitrogen with subsequent crushing by a roller-ball crusher in urea solution, followed by RuBisCO depletion, reduction, alkylation, protein digestion, and ZipTip purification allowed us to substantially simplify the sample preparation by removing any other precipitation steps and to detect viral proteins from samples, even with less than 0.2 g of leaf tissue, by a medium resolution nanoLC-ESI-Q-TOF. The presence of capsid proteins or polyproteins of fourteen important viruses from seven different families (Geminiviridae, Luteoviridae, Bromoviridae, Caulimoviridae, Virgaviridae, Potyviridae, and Secoviridae) isolated from ten different economically important plant hosts was confirmed through many identified pathogen-specific peptides from a protein database of host proteins and potential pathogen proteins assembled separately for each host and based on existing online plant virus pathogen databases. The presented extraction protocol, combined with a medium resolution LC-MS/MS, represents a cost-efficient virus protein confirmation method that proved to be effective at identifying virus strains (as demonstrated for PPV, WDV) and distinct disease species of BYDV, as well as putative new viral protein sequences from single-plant-leaf tissue samples. Data are available via ProteomeXchange with identifier PXD022456.", "claims": [{"id": "claim-method", "statement": "The peptides in raw spectra were identified and quantified by MaxQuant [11] 1.6.7.0 for Windows using reverse sequences for target-decoy database search strategy [48] and applying a 1% false discovery rate (FDR) for both the peptide spectrum match and protein group levels.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33228257", "locator": "sections[10] \"4.3. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD022456"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD022456"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33228257", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/pathogens9110966", "sha256": "sha256:bc351fe3f5c54aff2a5092775a3a70082dc9cd431c89641235a857bc547243bc", "bytes": 68318, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/pathogens9110966", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7699591", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD022456", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD022456", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD022456", "version": null, "note": "The mass spectrometry proteomics data and search results were deposited to the ProteomeXchange Consortium via the PRIDE partner repository [47] with the dataset identifier PXD022456.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data and search results were deposited to the ProteomeXchange Consortium via the PRIDE partner repository [47] with the dataset identifier PXD022456.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Confirmation of plant viral proteins and identification of specific viral strains by nanoLC-ESI-Q-TOF using single-leaf-tissue samples", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33228257:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0c037edb3e299b61f5aac37b4cd9ea4d75aefab48c386f329de3b3c62c9ee63b", "bytes": 5230, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#pathogens-09-00966-t001", "version": null, "note": "Identified host and virus proteins from single-leaf-tissue samples of virus inoculated plants with strong symptoms.", "structure": {"pmcid": "PMC7699591", "section_index": 4, "section_title": "2.2. Plant Virus Pathogen Capsid Proteins Could Be Efficiently Confirmed in Samples of Plants with Strong Infection Using the Double Crushing Extraction Protocol Followed by nanoLC-ESI-Q-TOF", "row_count": 20, "column_count": 20}, "table": {"label": "Table 1", "caption": "Identified host and virus proteins from single-leaf-tissue samples of virus inoculated plants with strong symptoms.", "rows": [["", "Sample", "01a/barley*1", "01b/barley", "01c/barley", "02/wheat*1", "03a/Chinese cabbage", "03b/Chinese cabbage", "04a/tobacco", "04b/tobacco", "04c/tobacco", "04d/tobacco", "04e/tobacco", "05/apricot", "06a/plum", "06b/plum", "07/bean", "08/goosefoot", "09/sorghum", "10/maize"], ["PREPARATION", "Sample weight (g)", "0.14", "0.34", "0.46", "0.34", "0.52", "0.47", "0.47", "0.46", "0.45", "0.55", "0.63", "0.60", "0.60", "0.97", "0.48", "0.63", "0.32", "0.13"], ["Host taxonomic classification", "Hordeum vulgare", "Hordeum vulgare", "Hordeum vulgare", "Triticum aestivum", "Brassica rapa subsp. pekinensis", "Brassica rapa subsp. pekinensis", "Nicotiana benthamiana", "Nicotiana benthamiana", "Nicotiana benthamiana", "Nicotiana clevelandia x N. glutinosa", "Nicotiana tabacum", "Prunus armeniaca", "Prunus domestica", "Prunus Pdomestica", "Phaseolus vulgaris", "Chenopodium amaranticolor", "Sorghum bicolor", "Zea mays"], ["UniProt reference proteome used", "UP000011116", "UP000019116", "UP000011750", "UP000084051 *2", "*3", "UP000000226", "*4", "UP000000768", "UP000007305"], ["Reference genome proteins", "189,799", "130,673", "40,809", "73,605 + 53,411 + 74,802 *2", "155,017 *3", "30,501", "1063 *4", "41,380", "99,254"], ["Known host viruses in online databases", "66", "63", "29", "369", "17", "227", "378", "22", "69"], ["Tested viruses for sample (UniProt protein sequences available)", "47", "45", "24", "232", "13", "151", "232", "18", "52"], ["RESULTS", "Identified peptides in sample", "3233", "2871", "3963", "3888", "1844", "1094", "3176", "2772", "3412", "3426", "1270", "2344", "1648", "1047", "4364", "346", "1942", "1956"], ["Identified host proteins *", "886", "810", "1082", "1076", "537", "339", "756", "668", "865", "865", "287", "593", "435", "362", "1163", "71", "570", "549"], ["Identified virus", "Wheatdwarf virus(WDV)", "Barley yellow dwarf virus(BYDV)", "Bromemosaic virus(BMV)", "Wheatdwarf virus(WDV)", "Cauliflower mosaic virus (CaMV)", "Turnip vein clearing virus(TVCV)", "Plum pox virus(PPV)", "Turnipmosaic virus(TuMV)", "Tobaccoringspot virus(TRSV)", "Tomatoaspermy virus(TAV)", "Tobaccomosaic virus(TMV)", "Plum pox virus(PPV)", "Plum pox virus(PPV)", "Plum pox virus(PPV)", "Bean common mosaic virus(BCMV)", "Broad BeanWilt Virus 2(BBWV-2)", "Sorghummosaic virus(SrMV)", "Sugarcanemosaic virus(SCMV)"], ["Identified virus family", "Geminiviridae (DNA)", "Luteoviridae (RNA)", "Bromoviridae (RNA)", "Geminiviridae (DNA)", "Caulimoviridae (DNA)", "Virgaviridae (RNA)", "Potyviridae(RNA)", "Potyviridae(RNA)", "Secoviridae(RNA)", "Bromoviridae (RNA)", "Virgaviridae (RNA)", "Potyviridae(RNA)", "Potyviridae(RNA)", "Potyviridae(RNA)", "Potyviridae(RNA)", "Secoviridae(RNA)", "Potyviridae(RNA)", "Potyviridae(RNA)"], ["Identified capsid protein peptides **", "10", "2", "11", "10", "10", "6", "11", "14", "8", "12", "12", "6", "6", "5", "4", "17", "9", "4"], ["Capsid protein sequence coverage (AA) **", "147 of 260", "36 of 199", "147 of 189", "147 of 260", "110 of 489", "82 of 157", "119 of 330", "154 of 286", "104 of 513", "134 of 218", "92 of 159", "86 of 330", "65 of 330", "57 of 330", "71 of 287", "247 of 599", "95 of 320", "59 of 313"], ["(56.5%)", "(18.1%)", "(77.8%)", "(56.5%)", "(22.5%)", "(52.2%)", "(36.1%)", "(53.8%)", "(20.3%)", "(61.5%)", "(57.9%)", "(26.0%)", "(19.7%)", "(17.2%)", "(24.7%)", "(41.2%)", "(29.7%)", "(18.8%)"], ["Capsid protein sequence coverage on ≥ 7 amino acid sequences (AA) **", "147 of 189", "36 of 148", "147 of 152", "147 of 189", "110 of 333", "82 of 142", "119 of 278", "154 of 210", "104 of 437", "134 of 187", "92 of 148", "86 of 278", "65 of 278", "57 of 278", "71 of 232", "247 of 506", "95 of 211", "59 of 247"], ["(77.8%)", "(24.3%)", "(96.7%)", "(77.8%)", "(33.0%)", "(57.7%)", "(42.8%)", "(73.3%)", "(23.8%)", "(71.7%)", "(62.2%)", "(30.1%)", "(23.4%)", "(20.5%)", "(30.6%)", "(48.8%)", "(45.0%)", "(23.9%)"], ["Other viral proteins identified **", "−", "2 fragments of movement protein", "−", "−", "more than 10 fragments of other viral proteins - movement protein, reverse transcriptase, aphid transmission protein, etc.", "−", "other more than 10 fragments of genome polyprotein", "other more than 10 fragments of genome polyprotein", "−", "−", "more than 10 fragments of replication protein", "other more than 10 fragments of genome polyprotein", "other 6 fragments of genome polyprotein", "−", "other more than 10 fragments of genome polyprotein", "one other fragment of genome polyprotein from RNA 1 component", "other more than 10 fragments of genome polyprotein", "other more than 10 fragments of genome polyprotein"], ["Sequence covered (aa) **", "147", "87", "147", "147", "794", "82", "936", "695", "104", "134", "405", "291", "126", "57", "380", "275", "486", "343"], ["Putative sequence covered (aa) ***", "147", "87", "147", "147", "807", "82", "1073", "734", "104", "142", "405", "291", "126", "57", "407", "327", "522", "398"], ["Virus presence also confirmed by ****", "DAS-ELISAqPCR", "DAS-ELISART-PCRRFLP", "DAS-ELISA", "DAS-ELISAqPCR", "DAS-ELISA", "DAS-ELISA", "DAS-ELISAqPCR", "DAS-ELISAqPCR", "DAS-ELISA", "DAS-ELISA", "DAS-ELISA", "DAS-ELISAqPCR", "DAS-ELISAqPCR", "DAS-ELISAqPCR", "DAS-ELISA", "electron microscopyRT-PCR", "DAS-ELISA", "DAS-ELISA"]], "row_count": 20, "column_count": 20, "numeric_cells": 247, "header_rows": 0, "locator": "section[4]/table-wrap[1]#pathogens-09-00966-t001"}}], "gaps": ["asset:data:geo:PXD022456 not downloaded", "asset:data:geo:PXD022456 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Target-decoy database search strategy with a 1% false discovery rate (FDR) applied at both peptide-spectrum-match and protein-group levels", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The peptides in raw spectra were identified and quantified by MaxQuant [11] 1.6.7.0 for Windows using reverse sequences for target-decoy database search strategy [48] and applying a 1% false discovery rate (FDR) for both the peptide spectrum match and protein group levels."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Target-decoy database search strategy with a 1% false discovery rate (FDR) applied at both peptide-spectrum-match and protein-group levels), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD022456"], "resolved_accessions": ["PXD022456"], "statements": ["The mass spectrometry proteomics data and search results were deposited to the ProteomeXchange Consortium via the PRIDE partner repository [47] with the dataset identifier PXD022456."], "basis": "The paper names PXD022456 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33228257", "data:geo:PXD022456", "asset:table:pmid:33228257:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD022456"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:47Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 52180, "completion_tokens": 1676, "cached_tokens": 776}}, "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:33228257", "type": "paper", "label": "pmid:33228257"}, {"id": "source:pmid:33228257", "type": "manuscript", "label": "PMID 33228257 full text"}, {"id": "data:geo:PXD022456", "type": "dataset", "label": "GEO PXD022456"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33228257", "type": "paper", "label": "pmid:33228257"}, {"id": "source:pmid:33228257", "type": "manuscript", "label": "PMID 33228257 full text"}, {"id": "data:geo:PXD022456", "type": "dataset", "label": "GEO PXD022456"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33228257", "type": "extraction", "used": ["source:pmid:33228257"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD022456", "type": "accession_resolution", "used": ["data:geo:PXD022456"], "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:33228257", "parent_hash": "sha256:793d50dc10ae176603dd09ebe41da2394ae848d427ab000d98a5ffbab4fe9f3a", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD022456 licence not read", "asset:data:geo:PXD022456 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": ["protocol, combined with a medium resolution LC-MS/MS, represents a cost-efficient virus protein c", "the 06b/plum sample or 57 AA of 330 AA). For mass spectrometry peptide fragment identification, only fragme"], "order_basis": "paper_text_order:1248", "id": "assay:1"}]},"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. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:44:41+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. 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}}}