{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30250588", "kind": "science-record", "revision": 8, "content_hash": "sha256:5dc04f18696c30dc73f06c1bc31edb7d8c6d8e8199a9937fb8de992333ed1a11", "created_at": "2026-11-01T15:40:37Z", "updated_at": "2026-11-01T22:43:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential biomarkers in cervical cancer with combined public mRNA and miRNA expression microarray data analysis.", "doi": "10.3892/ol.2018.9323", "pmid": "30250588", "authors": ["Sizhe Wang", "Xiaojin Chen"], "journal": "Oncology letters", "year": 2018, "abstract": "Cervical cancer is the fourth most prevalent malignancy in females worldwide. Early diagnosis is key to improving survival rates. Molecular biomarkers are an important method for diagnosing a number of types of cancer, including cervical cancer. The present study utilized public data from three mRNA microarray datasets and one microRNA dataset to analyze the key genes involved in cervical cancer. The mRNA and microRNA expression profile datasets (GSE9750, GSE46857, GSE67522 and GSE30656) were downloaded from the Gene Expression Omnibus database (GEO). Differentially expressed genes (DEGs) and microRNAs (DEMs) were screened using the online tool GEO2R. By using the DEGs consistent across the three mRNA datasets, a functional and pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network was constructed and module analysis performed using the Search Tool for the Retrieval of Interacting Genes. Validated target genes of the DEMs were identified using the miRecords website. Using the identified target genes of the DEMs, a survival analysis was performed using the OncoLnc online tool. A total of 73 DEGs and 19 DEMs were screened from the microarray expression profile datasets. 'Integrin-mediated', 'proteolysis' and 'phosphoinositide 3 kinase-protein kinase 3' signaling pathways were the most enriched in the DEGs. Three of the DEGs, including Ras homolog family member B (RhoB), stathmin 1 (STMN1) and cyclin D1 (CCNB1) were validated DEM target genes. The OncoLnc survival analysis identified that RhoB was associated with a significantly longer overall survival, whereas STMN1 was associated with a significantly reduced overall survival time in patients with cervical cancer. Finally, data from The Cancer Genome Atlas revealed an association between the mRNA expression levels of RhoB and STMN1, and the overall survival time for patients with cervical cancer. In conclusion, RhoB and STMN1 were identified as key genes that may provide potential targets for cervical cancer diagnosis and treatment.", "claims": [{"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the GEO repository, (https://www.ncbi.nlm.nih.gov/geo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30250588", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are available in the GEO repository, (https://www.ncbi.nlm.nih.gov/geo)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30250588"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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GSTM5, DCN, BAIAP2, SYNGR1, HOPX, CXCL14, MPZL2, LAMA2, CDH13, CRYAB, MAL, EGR1, ARG1, DUSP1, TGM3, DPT, RGS5, SDPR, SORBS1, FOS, RHOB, CXCL12, JAM2, SPARCL1, AQP1, COL17A1, CAB39L, SLC5A1, GPX3, PTGS1, PTGIS"], [""], ["B, Downregulated DEGs"], [""], ["BRCA1, LAMP3, ASF1B, RYR1, SMC4, AURKA, CKS1B, PCNA, SPP1, TYMS, APOL1, PLOD2, STMN1, CKS2, LYN, AGRN, CCNB2, PRC1, TOP2A, CXCL9, WDHD1, RSAD2, HMMR, MCM6, IFNAR2, PLAUR, CENPF, BIRC3"], [""], ["C, Genes with an inconsistent trend"], [""], ["PEG3, NTRK2, BNIP3, MYH11, SVEP1, TRIM13, UNC93A, ARMCX1, IL17RC, KRT7, SLC6A8"]], "row_count": 10, "column_count": 1, "numeric_cells": 2, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tI-ol-0-0-9323"}}, {"id": "asset:table:pmid:30250588:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e4f21e5faf31bdff08fd0c574d9c25b11942c8df9725b161645c715513634c69", "bytes": 1040, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tII-ol-0-0-9323", "version": null, "note": "Functional/pathway enrichment analysis of the differentially expressed genes from 3 cervical cancer mRNA expression profiles.", "structure": {"pmcid": "PMC6144068", "section_index": 13, "section_title": "Functional pathway enrichment analysis", "row_count": 14, "column_count": 4}, "table": {"label": "Table II.", "caption": "Functional/pathway enrichment analysis of the differentially expressed genes from 3 cervical cancer mRNA expression profiles.", "rows": [["Term", "Description", "Count", "P-value"], ["hsa05222", "Small cell lung cancer", "5", "3.34×10−3"], ["hsa04620", "Toll-like receptor signaling pathway", "5", "6.45×10−3"], ["hsa04510", "Focal adhesion", "6", "1.59×10−2"], ["hsa04512", "ECM-receptor interaction", "4", "2.42×10−2"], ["hsa05200", "Pathways in cancer", "7", "3.29×10−2"], ["hsa04062", "Chemokine signaling pathway", "5", "4.94×10−2"], ["hsa04150", "mTOR signaling pathway", "3", "5.71×10−2"], ["hsa00590", "Arachidonic acid metabolism", "3", "6.51×10−2"], ["hsa04110", "Cell cycle", "4", "6.56×10−2"], ["hsa05214", "Glioma", "3", "7.99×10−2"], ["hsa04115", "p53 signaling pathway", "3", "9.11×10−2"], ["hsa04730", "Long-term depression", "3", "9.34×10−2"], ["hsa05218", "Melanoma", "3", "9.80×10−2"]], "row_count": 14, "column_count": 4, "numeric_cells": 40, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tII-ol-0-0-9323"}}, {"id": "asset:table:pmid:30250588:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bcc28033e17d1e06fd0a066b3af4c84c24a6288dc6295cabb32ba95236333eb6", "bytes": 1738, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tIII-ol-0-0-9323", "version": null, "note": "Differentially expressed miRNAs in cervical cancer screened out from miRNA expression microarray GSE30656 and their target genes which have been reported and validated using miRecords.", "structure": {"pmcid": "PMC6144068", "section_index": 14, "section_title": "miRNA-DEG pairs", "row_count": 22, "column_count": 4}, "table": {"label": "Table III.", "caption": "Differentially expressed miRNAs in cervical cancer screened out from miRNA expression microarray GSE30656 and their target genes which have been reported and validated using miRecords.", "rows": [["miRNA", "Adjusted P-value", "Log fold change", "Validated target genes"], ["miR-106b", "2.05×10−7", "1.02", "E2F1, CDKN1A, VEGFA, E2F1, CDKN1A, ITCH"], ["miR-125b", "4.82×10−4", "−1.44", "ERBB2, ERBB3, LIN28, BAK1, NTRK3, C10orf104, H3F3B, ADAMTS1, PERP"], ["miR-149", "1.04×10−4", "−1.14", "N/A"], ["miR-15b", "1.42×10−3", "1.01", "BCL2, CCNE1, RECK, MKK4, RECK, BMI1"], ["miR-16", "5.47×10−4", "1.06", "TPPP3, BCL2, VEGFA, CCND1, PDCD4, RAB21, CADM1, SKAP2, WT1, BCL2"], ["miR-192", "3.98×10−2", "1.18", "DHFR, WNK1, RB1"], ["miR-193b", "2.69×10−4", "−1.29", "PLAU, ESR1"], ["miR-194", "2.24×10−2", "1.07", "N/A"], ["miR-200a", "9.84×10−3", "1.07", "ZEB2, ZEB1 FOG2, ERBB2IP, BAP1, KLHL20"], ["miR-203", "1.57×10−5", "−3.00", "N/A"], ["miR-205", "2.16×10−2", "−2.26", "ZEB2, ZEB1, VEGFA, INPPL1, ERBB3, PRKCE, MED1"], ["miR-21", "1.69×10−5", "2.10", "TPM1, NFIB, PDCD4, SERPINB5, CDKN1A, FAS, FAM3C, HIPK3, PRRG4, ACTA2"], ["miR-223", "1.38×10−2", "1.04", "NFIA, LMO2, LMO2, STMN1, RHOB, IRS1, FBXW7, EPB41L3"], ["miR-370", "1.04×10−3", "−2.37", "MAP3K8"], ["miR-494", "2.18×10−2", "−1.22", "PTEN"], ["miR-565", "1.61×10−2", "−1.04", "N/A"], ["miR-572", "1.23×10−2", "−1.04", "N/A"], ["miR-575", "1.02×10−3", "−1.46", "N/A"], ["miR-630", "1.34×10−2", "−1.20", "N/A"], ["miR-638", "1.21×10−2", "−1.37", "N/A"], ["miR-99a", "6.46×10−4", "−1.25", "RAVER2, mTOR, IGF-IR, RPTOR, FGFR3"]], "row_count": 22, "column_count": 4, "numeric_cells": 67, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tIII-ol-0-0-9323"}}, {"id": "asset:table:pmid:30250588:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7e132d0bd750cfcf565899a38d38872d93b781bb82cb1cf7bc841ea827692d06", "bytes": 438, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tIV-ol-0-0-9323", "version": null, "note": "The prognostic value of two differentially expressed genes identified in patients with other types of cancer.", "structure": {"pmcid": "PMC6144068", "section_index": 15, "section_title": "Overall survival analysis", "row_count": 5, "column_count": 3}, "table": {"label": "Table IV.", "caption": "The prognostic value of two differentially expressed genes identified in patients with other types of cancer.", "rows": [["Cancer type", "Ras homolog family member B", "Stathmin 1"], ["Breast", "0.158", "0.569"], ["Gastric", "0.046", 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OncoLnc) and pathway enrichment analysis (by DAVID). All cervical cancer data were downloaded from TCGA."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "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": "protein-protein interaction"}}, {"id": "method-5", "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.reader_differs_from_extractor"]}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE9750", "GSE46857", "GSE67522", "GSE30656"], "resolved_accessions": ["GSE9750", "GSE46857", "GSE67522", "GSE30656"], "statements": ["The datasets generated and/or analyzed during the current study are available in the GEO repository, (https://www.ncbi.nlm.nih.gov/geo)."], "basis": "The paper names GSE9750, GSE46857, GSE67522, GSE30656 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:30250588", "data:geo:GSE30656", "asset:table:pmid:30250588:1", "asset:table:pmid:30250588:2", "asset:table:pmid:30250588:3", "asset:table:pmid:30250588:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE30656"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:23Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25927, "completion_tokens": 1828, "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:30250588", "type": "paper", "label": "pmid:30250588"}, {"id": "source:pmid:30250588", "type": "manuscript", "label": "PMID 30250588 full text"}, {"id": "data:geo:GSE30656", "type": "dataset", "label": "GEO GSE30656"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30250588", "type": "paper", "label": "pmid:30250588"}, {"id": "source:pmid:30250588", "type": "manuscript", "label": "PMID 30250588 full text"}, {"id": "data:geo:GSE30656", "type": "dataset", "label": "GEO GSE30656"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30250588", "type": "extraction", "used": ["source:pmid:30250588"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE30656", "type": "accession_resolution", "used": ["data:geo:GSE30656"], "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:30250588", "parent_hash": "sha256:d9d7696d92b00ec58164a407af158a41a8ce6d86d1c7c74619b77233733d372e", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE30656 licence not read", "asset:data:geo:GSE30656 not downloaded", "asset:data:geo:GSE46857 licence not read", "asset:data:geo:GSE46857 not downloaded", "asset:data:geo:GSE67522 licence not read", "asset:data:geo:GSE67522 not downloaded", "asset:data:geo:GSE9750 licence not read", "asset:data:geo:GSE9750 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["th combined public mRNA and miRNA expression microarray data analysis.", "t study utilized public data from three mRNA microarray datasets and one microRNA dataset to analyze", "f 73 DEGs and 19 DEMs were screened from the microarray expression profile datasets. 'Integrin-media", "Materials and methods Microarray datasets and data processing A total of 3 hu"], "order_basis": "paper_text_order:60", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan-Meier analysis and log-rank test were used in overall survival analysis (by OncoLnc) and pathway enrichment analysis (by DAVID). All cervical cancer data were downloaded from TCGA."], "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. 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":"2026-11-04T01:50:08+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}}}