{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41618008", "kind": "science-record", "revision": 3, "content_hash": "sha256:05b28920a68acac6776a674244c04ac6cb45a3c45af7822357e4c04e51596878", "created_at": "2026-11-01T20:31:43Z", "updated_at": "2026-11-01T22:15:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the mechanism and therapeutic potential of BUB1 in regulating esophageal cancer progression based on 5-FU target prediction.", "doi": "10.1007/s12672-026-04486-3", "pmid": "41618008", "authors": ["Liangqin Luo", "ZhiWu Lin", "Zitong Xiong", "Peiquan Zhu", "Xinglan Wang", "Jiaan Lu", "Ruixiang Li", "Jiangtao Pu", "Qi Song"], "journal": "Discover oncology", "year": 2026, "abstract": "BACKGROUND: Esophageal cancer is the seventh most common and sixth deadliest cancer globally, threatening human health, especially among vulnerable groups. It is also a major cause of global cancer burden, and as a malignant tumor with high mortality and poor prognosis, its 5-year survival rate is less than 25%; currently, surgical resection, radiotherapy and chemotherapy are the main clinical treatments for esophageal cancer. However, conventional treatment outcomes are unsatisfactory, and only a limited number of individuals are able to achieve lasting benefits due to the elusive chemoresistance. Newly developed targeted therapies for esophageal cancer have been available over the past few decades, but have not had a meaningful clinical impact, resulting in minimal improvement in patient survival. Nevertheless, scientists still believe that novel treatments for esophageal cancer hold great promise, and it is therefore important to identify new drug targets from existing chemotherapy regimens for new drug development.\nMETHODS: In this study, we screened potential targets of 5-FU by a multi-omics approach: predicting drug-acting genes based on PubChem, CTD, SwissTargetPrediction and TargetNet databases; differential expression analysis and pathway enrichment of esophageal cancer using GEO dataset GSE17351, and constructing a co-expression network by WGCNA to analyze the clinical and gene module correlations. clinical and gene module correlation. Finally, cell subpopulation distribution was analyzed based on GSE196756 single-cell sequencing data. For the experimental validation part, the KYSE150/TE1 human esophageal cancer cell line was used, with an untreated control group (NC) and a si-BUB1 interference group (two independent siRNA sequences), and the BUB1 function was detected by Western blot, cell scratch/Transwell and clone formation assays.\nRESULTS: KEGG enrichment significantly associated with the p53/PI3K-Akt pathway. Differential analysis showed that genes such as MMP10 and MYBL2 were up-regulated and SLC6A1 was down-regulated in esophageal cancer tissues, and GSEA based on the results of differential analysis suggested activation of the cancer cell cycle/DNA replication pathway. Subsequent drug-disease intersection screening identified 29 core genes, and PPI network and MCODE analysis targeted key nodes such as BUB1, CCNA2, CDK1, etc. TCGA data confirmed that BUB1 was highly expressed in esophageal cancers (p < 0.001) but had no correlation with TNM stage progression. The results showed inhibition of BUB1 protein expression, reduction of clone formation, significant reduction of scratch healing rate and Transwell migration number in the si-BUB1 group (p < 0.01).\nCONCLUSIONS: This study revealed the important role of BUB1, one of the potential targets of 5-FU, in the development of esophageal cancer. Through bioinformatics analysis and experimental validation, we found that the high expression of BUB1 in esophageal cancer tissues was closely related to the biological properties of the tumor. the regulation of cell cycle by BUB1 and its role in the invasion and migration ability of the cells marked its potential as a new target for the treatment of esophageal cancer.", "claims": [{"id": "claim-method", "statement": "Next, BUB1 was used as the target, and the Wilcoxon rank-sum test was used to compare the expression differences between tumor tissues and normal tissues, as well as the mRNA expression differences in different clinical stages (T, N, M, and stage).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41618008", "locator": "sections[10] \"Quantitative mRNA analysis based on the cancer genome atlas esophageal cancer dataset (TCGA-ESCA)\" paragraph 2", "quote": "Next, BUB1 was used as the target, and the Wilcoxon rank-sum test was used to compare the expression differences between tumor tissues and normal tissues, as well as the mRNA expression differences in different clinical stages (T, N, M, and stage)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data are provided within the manuscript and supporting files.All data used in this study were obtained from publicly available datasets, specifically as follows: The 5-fluorouracil (5-FU) predicted target gene sets were sourced from the SwissTargetPrediction database (http://www.swisstargetprediction.ch/) and the TargetNet database (http://targetnet.scbdd.com/home/index/).The esophageal cancer gene set for differential expression analysis was obtained from GEO database entry GSE17351 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE17351).Protein interaction network analysis data originated from the STRING database (https://string-db.org/), with the protein molecular network subsequently constructed using Cytoscape.The single-cell sequencing dataset comparing esophageal cancer with adjacent normal tissue was obtained from GEO database entry GSE196756 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196756).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41618008", "locator": "sections[28] \"Data availability\" paragraph 2", "quote": "All data are provided within the manuscript and supporting files.All data used in this study were obtained from publicly available datasets, specifically as follows: The 5-fluorouracil (5-FU) predicted target gene sets were sourced from the SwissTargetPrediction database (http://www.swisstargetprediction.ch/) and the TargetNet database (http://targetnet.scbdd.com/home/index/).The esophageal cancer gene set for differential expression analysis was obtained from GEO database entry GSE17351 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE17351).Protein interaction network analysis data originated from the STRING database (https://string-db.org/), with the protein molecular network subsequently constructed using Cytoscape.The single-cell sequencing dataset comparing esophageal cancer with adjacent normal tissue was obtained from GEO database entry GSE196756 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196756)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study revealed the important role of BUB1, one of the potential targets of 5-FU, in the development of esophageal cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41618008", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "This study revealed the important role of BUB1, one of the potential targets of 5-FU, in the development of esophageal cancer."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "This study revealed the important role of BUB1, one of the potential targets of 5-FU, in the development of esophageal cancer.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41618008"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon", "step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41618008", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-026-04486-3", "sha256": "sha256:55c23dd0bf248286b393d37a8ace4facb3bc7c88a10547ae0869f1dad59bf2da", "bytes": 82884, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-026-04486-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12949211", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Next, BUB1 was used as the target, and the Wilcoxon rank-sum test was used to compare the expression differences between tumor tissues and normal tissues, as well as the mRNA expression differences in different clinical stages (T, N, M, and stage)."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-4", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-5", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-6", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["All data are provided within the manuscript and supporting files.All data used in this study were obtained from publicly available datasets, specifically as follows: The 5-fluorouracil (5-FU) predicted target gene sets were sourced from the SwissTargetPrediction database (http://www.swisstargetprediction.ch/) and the TargetNet database (http://targetnet.scbdd.com/home/index/).The esophageal cancer gene set for differential expression analysis was obtained from GEO database entry GSE17351 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE17351).Protein interaction network analysis data originated from the STRING database (https://string-db.org/), with the protein molecular network subsequently constructed using Cytoscape.The single-cell sequencing dataset comparing esophageal cancer with adjacent normal tissue was obtained from GEO database entry GSE196756 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196756)."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41618008"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:12:00Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 20058, "completion_tokens": 3299, "cached_tokens": 256}}, "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:41618008", "type": "paper", "label": "pmid:41618008"}, {"id": "source:pmid:41618008", "type": "manuscript", "label": "PMID 41618008 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41618008", "type": "paper", "label": "pmid:41618008"}, {"id": "source:pmid:41618008", "type": "manuscript", "label": "PMID 41618008 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41618008", "type": "extraction", "used": ["source:pmid:41618008"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:41618008", "parent_hash": "sha256:6bdc9e515e64416034b58cd48b81eaea25baf36db881d1ad2b598979dafa249d", "fork_of": null, "generation": 2}, "gaps": ["execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["si-BUB1 interference group (two independent siRNA sequences), and the BUB1 function was detect", "on of BUB1. Western blot analysis shows that transfection with two independent BUB1-targeting siRNAs (", "n levels of both BUB1 and Cyclin B1.(B) BUB1 knockdown specifically reduced the level of phosphoryl"], "order_basis": "paper_text_order:1848", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nces), and the BUB1 function was detected by Western blot, cell scratch/Transwell and clone formation", "evels following targeted inhibition of BUB1. Western blot analysis shows that transfection with two in"], "order_basis": "paper_text_order:1903", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["d to 5-FU effects were mainly focused on the apoptosis regulation and oxidative stress, and the ana", "1D), among which the p53 signaling pathway, apoptosis, and the PI3K-Akt signaling pathway may play"], "order_basis": "paper_text_order:5435", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Next, BUB1 was used as the target, and the Wilcoxon rank-sum test was used to compare the expression differences between tumor tissues and normal tissues, as well as the mRNA expression differences in different clinical stages (T, N, M, and stage)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]},"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":"2026-11-04T00:36:39+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}}}