{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34238253", "kind": "science-record", "revision": 7, "content_hash": "sha256:af469121edffc9f1892bf86cb90194cc794b6b351c3875c8a3bb5653f47f91cf", "created_at": "2026-11-01T15:41:42Z", "updated_at": "2026-11-01T22:04:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer.", "doi": "10.1186/s12885-021-08520-1", "pmid": "34238253", "authors": ["Shiyong Gao", "Jian Gang", "Miao Yu", "Guosong Xin", "Huixin Tan"], "journal": "BMC cancer", "year": 2021, "abstract": "BACKGROUND: Liver cancer is the sixth most commonly diagnosed cancer and the fourth most common cause of cancer death. The purpose of this work is to find new diagnostic biomarkers or prognostic biomarkers and explore the biological functions related to the prognosis of liver cancer.\nMETHODS: GSE25097 datasets were firstly obtained and compared with TCGA LICA datasets and an analysis of the overlapping differentially expressed genes (DEGs) was conducted. Cytoscape was used to screen out the Hub Genes among the DEGs. ROC curve analysis was used to screen the Hub Genes to determine the genes that could be used as diagnostic biomarkers. Kaplan-Meier analysis and Cox proportional hazards model screened genes associated with prognosis biomarkers, and further Gene Set Enrichment Analysis was performed on the prognosis genes to explore the mechanism affecting the survival and prognosis of liver cancer patients.\nRESULTS: 790 DEGs and 2162 DEGs were obtained respectively from the GSE25097 and TCGA LIHC data sets, and 102 Common DEGs were identified by overlapping the two DEGs. Further screening identified 22 Hub Genes from 102 Common DEGs. ROC and survival curves were used to analyze these 22 Hub Genes and it was found that there were 16 genes with a value of AUC > 90%. Among these, the expression levels of ESR1,SPP1 and FOSB genes were closely related to the survival time of liver cancer patients. Three common pathways of ESR1, FOBS and SPP1 genes were identified along with seven common pathways of ESR1 and SPP1 genes and four common pathways of ESR1 and FOSB genes.\nCONCLUSIONS: SPP1, AURKA, NUSAP1, TOP2A, UBE2C, AFP, GMNN, PTTG1, RRM2, SPARCL1, CXCL12, FOS, DCN, SOCS3, FOSB and PCK1 can be used as diagnostic biomarkers for liver cancer, among which FOBS and SPP1 genes can also be used as prognostic biomarkers. Activation of the cell cycle-related pathway, pancreas beta cells pathway, and the estrogen signaling pathway, while on the other hand inhibition of the hallmark heme metabolism pathway, hallmark coagulation pathway, and the fat metabolism pathway may promote prognosis in liver cancer patients.", "claims": [{"id": "claim-method", "statement": "The original microarray data of the GSE25097 and TCGA LIHC datasets were respectively analyzed with R language to screen the differentially expressed genes (DEGs). Adj .p-value < 0.05 and |logFC| > 2 were used as the cut-off criteria. The TCGA LIHC dataset was analyzed with R × 64 3.6.1, using the package DEGseq2, Adj. p value < 0.05 and |logFC| > 2 were regarded as the cut-off criteria. The liver cancer dataset was obtained from TCGA (https://portal.gdc.cancer.gov/). Another gene expression profiling dataset (GSE25097) included information on 243 normal samples and 268 tumor samples, which was downloaded from Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/database) and measured in an array (Platform: GPL10687 Rosetta/Merck Human RSTA Affymetrix 1.0 microarray, Custom CDF).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34238253", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "The original microarray data of the GSE25097 and TCGA LIHC datasets were respectively analyzed with R language to screen the differentially expressed genes (DEGs)."}, {"asset": "source:pmid:34238253", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "Adj .p-value < 0.05 and |logFC| > 2 were used as the cut-off criteria."}, {"asset": "source:pmid:34238253", "locator": "sections[13] \"Identification of DEGs\" paragraph 2", "quote": "The TCGA LIHC dataset was analyzed with R × 64 3.6.1, using the package DEGseq2, Adj. p value < 0.05 and |logFC| > 2 were regarded as the cut-off criteria."}, {"asset": "source:pmid:34238253", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "The liver cancer dataset was obtained from TCGA (https://portal.gdc.cancer.gov/)."}, {"asset": "source:pmid:34238253", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "Another gene expression profiling dataset (GSE25097) included information on 243 normal samples and 268 tumor samples, which was downloaded from Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/database) and measured in an array (Platform: GPL10687 Rosetta/Merck Human RSTA Affymetrix 1.0 microarray, Custom CDF)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the [https://www.ncbi.nlm.nih.gov/geo/database] and https://portal.gdc.cancer.gov/].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34238253", "locator": "sections[29] \"notes\" paragraph 1", "quote": "The datasets generated and/or analyzed during the current study are available in the [https://www.ncbi.nlm.nih.gov/geo/database] and https://portal.gdc.cancer.gov/]."}], "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:34238253"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE25097"], "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:GSE25097"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34238253", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-021-08520-1", "sha256": 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null, "note": "Top 22 Hub Genes with degree > = 5", "structure": {"pmcid": "PMC8268589", "section_index": 15, "section_title": "PPI network analysis and screening for Hub Genes", "row_count": 23, "column_count": 14}, "table": {"label": "Table 2", "caption": "Top 22 Hub Genes with degree > = 5", "rows": [["Number", "Name", "Betweenness", "BottleNeck", "Closeness", "Clustering Coefficient", "Degree", "DMNC", "EcCentricity", "EPC", "MCC", "MNC", "Radiality", "Stress"], ["1", "ESR1", "2780.97619", "58", "38.78333", "0.16667", "13", "0.2036", "0.15823", "29.27", "28", "11", "8.416", "5698"], ["2", "SPP1", "1519.02063", "30", "35.65", "0.22727", "12", "0.2545", "0.18987", "28.52", "35", "11", "8.1723", "3920"], ["3", "AURKA", "967.42857", "11", "32.02619", "0.4", "11", "0.6415", "0.13562", "24.93", "5045", "8", "7.8002", "1918"], ["4", "CXCL12", "1415.00476", "15", "32.73333", "0.11111", "9", "0.2842", "0.15823", "24.1", "11", "4", "7.9926", "2458"], ["5", "FOS", "617.74127", "17", "33.3", "0.30556", "9", "0.3207", "0.15823", "27.17", "29", "8", "8.0311", "1918"], ["6", "NQO1", "1353", "11", "31.55952", "0.17857", "8", "0.309", "0.13562", "22.39", "12", "3", "7.8515", "2882"], ["7", "NUSAP1", "146", "2", "25.78452", "0.75", "8", "0.7683", "0.11867", "23.93", "5041", "7", "7.0561", "338"], ["8", "TOP2A", "332.07302", "3", "30.27619", "0.78571", "8", "0.6415", "0.13562", "24.54", "5042", "8", "7.7361", "938"], ["9", "UBE2C", "146.37619", "1", "27.25119", "0.75", "8", "0.7683", "0.11867", "24.36", "5041", "7", "7.2229", "264"], ["10", "AFP", "281.74603", "4", "30.05", "0.33333", "7", "0.3328", "0.15823", "26.15", "17", "6", "7.7874", "770"], ["11", "DCN", "303.6", "3", "28.55", "0.28571", "7", "0.2853", "0.15823", "24.75", "13", "6", "7.5308", "782"], ["12", "EGR1", "228.02381", "3", "30.21667", "0.42857", "7", "0.4279", "0.15823", "25.63", "25", "6", "7.8002", "602"], ["13", "GMNN", "0", "1", "25.28452", "1", "7", "0.7683", "0.11867", "24.18", "5040", "7", "7.0433", "0"], ["14", "PTTG1", "0", "1", "25.28452", "1", "7", "0.7683", "0.11867", "23.95", "5040", "7", "7.0433", "0"], ["15", "RRM2", "0", "1", "25.28452", "1", "7", "0.7683", "0.11867", "23.64", "5040", "7", "7.0433", "0"], ["16", "SOCS3", "631.69841", "6", "31.05952", "0.09524", "7", "0.3078", "0.13562", "25.03", "7", "2", "7.8259", "1378"], ["17", "UBE2T", "0", "1", "25.28452", "1", "7", "0.7683", "0.11867", "24.05", "5040", "7", "7.0433", "0"], ["18", "CYP1A2", "577", "5", "29.39286", "0.2", "6", "0.309", "0.13562", "19.57", "7", "3", "7.7361", "822"], ["19", "GPC3", "44.47619", "2", "26.7", "0.53333", "6", "0.3804", "0.15823", "24.62", "20", "6", "7.364", "138"], ["20", "FOSB", "35.46667", "1", "27.55952", "0.7", "5", "0.4538", "0.13562", "24.25", "18", "5", "7.5821", "166"], ["21", "PCK1", "570", "5", "24.21786", "0.1", "5", "0.3078", "0.11867", "10.7", "5", "2", "7.0176", "1074"], ["22", "SPARCL1", "18.43333", "1", "26.53333", "0.6", "5", "0.389", "0.15823", "24.88", "14", "5", "7.3897", "62"]], "row_count": 23, "column_count": 14, "numeric_cells": 287, "header_rows": 1, "locator": "section[15]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:GSE25097 not downloaded", "asset:data:geo:GSE25097 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox proportional hazards"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}, {"id": "method-4", "family": null, "specific": null, "label": "DEGseq2 differential expression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "The original microarray data of the GSE25097 and TCGA LIHC datasets were respectively analyzed with R language to screen the differentially expressed genes (DEGs). Adj .p-value < 0.05 and |logFC| > 2 were used as the cut-off criteria. The TCGA LIHC dataset was analyzed with R × 64 3.6.1, using the package DEGseq2, Adj. p value < 0.05 and |logFC| > 2 were regarded as the cut-off criteria. The liver cancer dataset was obtained from TCGA (https://portal.gdc.cancer.gov/). Another gene expression profiling dataset (GSE25097) included information on 243 normal samples and 268 tumor samples, which was downloaded from Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/database) and measured in an array (Platform: GPL10687 Rosetta/Merck Human RSTA Affymetrix 1.0 microarray, Custom CDF)."}}], "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": "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": ["GSE25097"], "resolved_accessions": ["GSE25097"], "statements": ["The datasets generated and/or analyzed during the current study are available in the [https://www.ncbi.nlm.nih.gov/geo/database] and https://portal.gdc.cancer.gov/]."], "basis": "The paper names GSE25097 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:34238253", "data:geo:GSE25097", "asset:table:pmid:34238253:1", "asset:table:pmid:34238253:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE25097"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:12Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 31628, "completion_tokens": 2428, "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:34238253", "type": "paper", "label": "pmid:34238253"}, {"id": "source:pmid:34238253", "type": "manuscript", "label": "PMID 34238253 full text"}, {"id": "data:geo:GSE25097", "type": "dataset", "label": "GEO GSE25097"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34238253", "type": "paper", "label": "pmid:34238253"}, {"id": "source:pmid:34238253", "type": "manuscript", "label": "PMID 34238253 full text"}, {"id": "data:geo:GSE25097", "type": "dataset", "label": "GEO GSE25097"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34238253", "type": "extraction", "used": ["source:pmid:34238253"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE25097", "type": "accession_resolution", "used": ["data:geo:GSE25097"], "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:34238253", "parent_hash": "sha256:667350c1e533fcaa7fc414cdafb1222143dd486f1e0dbf43b9ea3674c28a514b", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE25097 licence not read", "asset:data:geo:GSE25097 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.93, "evidence": ["Methods Data processing The original microarray data of the GSE25097 and TCGA LIHC datasets"], "order_basis": "paper_text_order:2372", "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": 0.7, "evidence": ["Kaplan-Meier"], "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":"2026-11-04T03:15:03+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}}}