{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34532296", "kind": "science-record", "revision": 8, "content_hash": "sha256:01dee43956361254a29abdee10d0b1fedad5c047b1917ce2191a0cbeffae6fab", "created_at": "2026-11-01T15:41:52Z", "updated_at": "2026-11-01T22:47:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Co-Expression Network Reveals the Potential Regulatory Mechanism of lncRNAs in Relapsed Hepatocellular Carcinoma.", "doi": "10.3389/fonc.2021.745166", "pmid": "34532296", "authors": ["Yuan Fang", "Yang Yang", "XiaoLi Zhang", "Na Li", "Bo Yuan", "Li Jin", "Sheng Bao", "MengGe Li", "Dan Zhao", "LingRui Li", "Zhong Zeng", "HanFei Huang"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "BACKGROUND: The mechanistic basis for relapsed hepatocellular carcinoma (HCC) remains poorly understood. Recent research has highlighted the important roles of long non-coding RNAs (lncRNAs) in HCC. However, there are only a few studies on the association between lncRNAs and HCC relapse.\nMETHODS: Differentially expressed lncRNAs and mRNAs between a primary HCC group and relapsed HCC group were identified using the edge R package to analyze the GSE101432 dataset. The differentially expressed lncRNAs and mRNAs were used to construct a lncRNA-mRNA co-expression network. Weighted gene co-expression network analysis followed by Gene Ontology (GO) enrichment analyses were conducted on the database. Furthermore, correlation and survival analyses were performed using The Cancer Genome Atlas database, and expression in the clinical samples was verified by qRT-PCR. Thereafter, we inputted the genes from the two groups into the HCC TNM stage and tumor grade database from TCGA. Finally, we performed Kaplan-Meier survival analysis on the lncRNAs related to relapsed HCC.\nRESULTS: In this study, lncRNAs and mRNAs associated with HCC relapse were identified. Two gene modules were found to be closely linked to this. The GO terms in the yellow and black modules were related to cell proliferation, differentiation, and survival, as well as some transcription-related biological processes. Through qRT-PCR, we found that the expression levels of LINC00941 and LINC00668 in relapsed HCC were higher than those in primary HCC. Further, mRNA levels of LOX, OTX1, MICB, NDUFA4L2, BAIAP2L2, and KCTD17 were changed in relapsed HCC compared to levels in primary HCC. In addition, we verified that these genes could predict the overall survival and recurrence-free survival of HCC. Moreover, we found that LINC00668 and LINC00941 could affect tumor grade and TNM stages. In total, we identified and validated two lncRNAs (LINC00941 and LINC00668) and six mRNAs (LOX, MICB, OTX1, BAIAP2L2, KCTD17, NDUFA4L2) associated with HCC relapse.\nCONCLUSION: In summary, we identified the key gene modules and central genes associated with relapsed HCC and constructed lncRNA-mRNA networks related to this. These genes are likely to have potential prognostic value for relapsed HCC and might shed new light on novel biomarkers or diagnostic targets for relapsed HCC.", "claims": [{"id": "claim-method", "statement": "The software edgeR (18), which is specifically applied to analyze the differential expression of genes, was used to screen the RNA-seq data for DEGs. The expression profile of genes associated with HCC (GSE101432) was obtained from the NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34532296", "locator": "sections[4] \"Read Alignments and Analysis of Differentially Expressed Genes (DEGs)\" paragraph 2", "quote": "The software edgeR (18), which is specifically applied to analyze the differential expression of genes, was used to screen the RNA-seq data for DEGs."}, {"asset": "source:pmid:34532296", "locator": "sections[3] \"Data Downloading and Preprocessing\" paragraph 2", "quote": "The expression profile of genes associated with HCC (GSE101432) was obtained from the NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE101432"], "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:GSE101432"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34532296", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2021.745166", "sha256": "sha256:20f32116cb4404fae453222fcc47f9db20763bb1d6c049b6e8d1c322e92d9ae3", "bytes": 49032, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2021.745166", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8438305", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE101432", "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=GSE101432", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101432", "version": null, "note": "Publicly available datasets were analyzed in this study. 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"platform": "11154", "taxon": "Homo sapiens", "title": "Comprehensive transcriptome analysis in human liver", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34532296:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5d76c6b9caef1e4182bd1915c78e956579e257120d9a62f356b8236f100384b4", "bytes": 914, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T1", "version": null, "note": "Clinical sample information.", "structure": {"pmcid": "PMC8438305", "section_index": 8, "section_title": "Sample Collection", "row_count": 28, "column_count": 2}, "table": {"label": "Table 1", "caption": "Clinical sample information.", "rows": [["Clinical information", "Sample"], ["Primary Tumor", "5"], ["Relapse Tumor", "3"], ["Age, median, (mean)", "54"], ["Gender, male", "4 (50%)"], ["Length of hospital stay (days) (mean)", "10-14 (12.875)"], ["Liver cirrhosis", "4 (50%)"], ["Classification of liver cancer", ""], ["Hepatocellular carcinoma", "8 (100%)"], ["Intrahepatic cholangiocarcinoma", "0"], ["Tumor diameter", ""], ["<2cm", "1 (12.5%)"], ["2cm-5cm", "5 (62.5%)"], [">5cm", "2 (25.0%)"], ["HBV", ""], ["Positive", "4 (50%)"], ["Negative", "4 (50%)"], ["AFP", ""], ["<400", "4 (50%)"], [">400", "4 (50%)"], ["Tumor location", ""], ["Left liver", "5 (62.5%)"], ["Right liver", "3 (37.5%)"], ["Tumor recurrence time (months)", "18,27,76"], ["Outcome", ""], ["Cure", "1 (12.5%)"], ["Improve", "6 (75%)"], ["Death", "1 (12.5%)"]], "row_count": 28, "column_count": 2, "numeric_cells": 26, "header_rows": 1, "locator": "section[8]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34532296:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:926bd425ed864b04393e3a8f9111cfdeb7e0847969cf562f07948c74d125aef7", "bytes": 1722, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T2", "version": null, "note": "Primers of lncRNA and mRNA for qRT-PCR.", "structure": {"pmcid": "PMC8438305", "section_index": 9, "section_title": "qRT-PCR", "row_count": 23, "column_count": 4}, "table": {"label": "Table 2", "caption": "Primers of lncRNA and mRNA for qRT-PCR.", "rows": [["Primers for Validated Genes"], ["Gene", "lncRNA ID/GENE ID", "Prime sequence (5’-3’)"], ["Forward", "Reverse"], ["RP11-334A14.8", "NONHSAT003288.2", "AGGGAACCCCATTCTTCCAA", "AGAGGTCTCAAGGCACAGAT"], ["LINC00668", "NONHSAT057143.2", "GGGTCCAAGGGATCTGCAAG", "CCGCCCAAGATTCCTCTAGC"], ["CTD-2369P2.5", "NONHSAT061043.2", "GCACTTTCCCAAGGGTACAA", "CCCTTGACCCTAACCTCTGA"], ["LINC00941", "NONHSAT027514.2", "CATGTACGTTGCTATCCAGGC", "CTCCTTAATGTCACGCACGAT"], ["AF124730.4", "NONHSAT081627.2", "GCCACACAAATGTTCACCAC", "GAGCAGAAGGACTCAGTGTG"], ["RP13-143G15.4", "NONHSAT115109.2", "ACCCTTGCAACCTTTCTCAG", "TGGCCACCTTGTAGGTTAGA"], ["RP11-973F15.2", "NONHSAT128496.2", "GACAGCCCCCAAAGAACC", "ATCCCCGGACTGCTGC"], ["RP5-967N21.11", "NONHSAT188398.1", "TGGTATGTTTGTGTTCCATTTGC", "AATGCGAGCACAAGATAATTTTT"], ["RASAL1", "8437", "CAGCTCCCTGAATGTTCGC", "TCCTCATCCAGCACGTAGAAG"], ["NDUFA4L2", "56901", "CCTGAGCCCCAATGACCAATA", "TCTGGCCGGTCCTTCTTCA"], ["KCTD17", "79734", "AGTCGGACCGGGATGAGAC", "CCATGCCGGAGGAAGTTCA"], ["BAIAP2L2", "80115", "GCCGAGGTCTACTTCAGTGC", "GCTGGGTGTCAGACATCTGC"], ["MDFI", "4188", "CCACCGGAAGTTGCAGACA", "GGAACTCGCAGAACAGGCA"], ["SLC44A5", "204962", "GACTTTGGTGATCCAAGGACAT", "GTCTGTAGGATAGGCTGCTCT"], ["GPR160", "26996", "CCAGCCATCTACCAAAGCCTG", "GCCAGTAACTCTGAATGCTGACA"], ["LOX", "4015", "GCCGACCAAGATATTCCTGGG", "GCAGGTCATAGTGGCTAAACTC"], ["NXPH4", "11247", "AAGGTCTTCGGACGGCCTA", "GCAGCGAAAACTTGAGGGTAT"], ["OTX1", "5013", "GCGTCGTCGCTGAGTACAC", "ACATGGGATAAGAGGCTGCTG"], ["GMNN", "51053", "GCCCTGGGGTTATTGTCCC", "AGCGCCTTTCTCCGTTTTTCT"], ["MICB", "4277", "TCTTCGTTACAACCTCATGGTG", "TCCCAGGTCTTAGCTCCCAG"]], "row_count": 23, "column_count": 4, "numeric_cells": 32, "header_rows": 3, "locator": "section[9]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE101432 not downloaded", "asset:data:geo:GSE101432 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The software edgeR (18), which is specifically applied to analyze the differential expression of genes, was used to screen the RNA-seq data for DEGs. The expression profile of genes associated with HCC (GSE101432) was obtained from the NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "Hazard ratios (HR) and 95% confidence int"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "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": "Principal component analysis"}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: edger."}, "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": ["GSE101432"], "resolved_accessions": ["GSE101432"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: Gene Expression Omnibus accession GSE101432 and TCGA (https://portal.gdc.cancer.gov/)."], "basis": "The paper names GSE101432 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34532296", "data:geo:GSE101432", "asset:table:pmid:34532296:1", "asset:table:pmid:34532296:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE101432"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:47Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 39105, "completion_tokens": 1324, "cached_tokens": 792}}, "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:34532296", "type": "paper", "label": "pmid:34532296"}, {"id": "source:pmid:34532296", "type": "manuscript", "label": "PMID 34532296 full text"}, {"id": "data:geo:GSE101432", "type": "dataset", "label": "GEO GSE101432"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34532296", "type": "paper", "label": "pmid:34532296"}, {"id": "source:pmid:34532296", "type": "manuscript", "label": "PMID 34532296 full text"}, {"id": "data:geo:GSE101432", "type": "dataset", "label": "GEO GSE101432"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34532296", "type": "extraction", "used": ["source:pmid:34532296"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE101432", "type": "accession_resolution", "used": ["data:geo:GSE101432"], "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:34532296", "parent_hash": "sha256:dee2ac31501b2e0b040995a7be66aa83097e99151f6ce3647206ef4af7ca0a2f", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE101432 licence not read", "asset:data:geo:GSE101432 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": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["expression of genes, was used to screen the RNA-seq data for DEGs. A fold-change ≥2 or ≤0.5 and"], "order_basis": "paper_text_order:2937", "id": "assay:1"}, {"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["e visualization of next-generation sequence (NGS) data and genomic annotations. The pheatmap"], "order_basis": "paper_text_order:4308", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The software edgeR (18), which is specifically applied to analyze the differential expression of genes, was used to screen the RNA-seq data for DEGs. The expression profile of genes associated with HCC (GSE101432) was obtained from the NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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}}}