{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33658475", "kind": "science-record", "revision": 6, "content_hash": "sha256:8743861704ece796f8bf79987550f30af3af99f4bdf2df3e23346d468f146a50", "created_at": "2026-11-01T15:41:26Z", "updated_at": "2026-11-01T22:03:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Biomarkers Based on Bioinformatics Analysis: The Expression of Ubiquitin-Conjugating Enzyme E2T (UBE2T) in the Carcinogenesis and Progression of Hepatocellular Carcinoma.", "doi": "10.12659/MSM.929023", "pmid": "33658475", "authors": ["Xuemiao Zhao", "Wei Weng", "Miao Jin", "Sunjian Li", "Qingwei Chen", "Bingrong Li", "Zhou Zhou", "Chuanqiang Lan", "Yunjun Yang"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2021, "abstract": "BACKGROUND The purpose of this study was to screen and identify key genes in the occurrence and development of hepatocellular carcinoma (HCC) based on bioinformatics analysis. MATERIAL AND METHODS Three Gene Expression Omnibus (GEO) series (GSE) - GSE121248, GSE87630, and GSE84598 - were downloaded from the GEO database. GEO2R was used to screen different genes and a Venn diagram was drawn to screen coexpressed differentially expressed genes (DEGs). Coexpressed DEGs were obtained by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, a protein-protein interaction network diagram was produced by Cytoscape, and module genes were calculated by the Molecular Complex Detection Cytoscape plug-in. Finally, overall survival, progression-free survival, and relapse-free survival analysis of the key genes selected were performed using the online Kaplan-Meier plotter. For the target genes, the online network UCSC Cancer Genome Browser was used to analyze the gene expression profiles of the grade and vascular invasion of HCC. RESULTS A total of 296 coexpressed DEGs were obtained from the 3 GSEs and 12 key genes were obtained from the modular analysis. Survival analysis showed that the upregulated genes UBE2T and FBLN5 were involved in the poor prognosis of HCC. Furthermore, the expression of UBE2T was significantly related to the grade and vascular invasion of HCC. CONCLUSIONS The expression of the UBE2T gene was significantly upregulated in HCC tissue compared to in normal liver tissue. UBE2T may be a new marker for the diagnosis and subsequent therapy of HCC.", "claims": [{"id": "claim-data-access", "statement": "GSE121248 contains 70 HCC tissue samples and 37 normal liver tissue samples adjacent to HCC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33658475", "locator": "sections[3] \"Microarray Data\" paragraph 2", "quote": "GSE121248 contains 70 HCC tissue samples and 37 normal liver tissue samples adjacent to HCC."}], "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:33658475"], "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:GSE121248"], "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:GSE121248"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33658475", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.929023", "sha256": 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"Count", "FDR"], ["Downregulated"], ["GOTERM_BP_DIRECT", "GO: 0019373", "Epoxygenase P450 pathway", "10", "8.46E-10"], ["GOTERM_BP_DIRECT", "GO: 0055114", "Oxidation-reduction process", "30", "1.60E-06"], ["GOTERM_BP_DIRECT", "GO: 0006956", "Complement activation", "11", "5.79E-05"], ["GOTERM_BP_DIRECT", "GO: 0006805", "Xenobiotic metabolic process", "10", "1.74E-04"], ["GOTERM_BP_DIRECT", "GO: 0071356", "Cellular response to tumor necrosis factor", "10", "0.002280078"], ["GOTERM_BP_DIRECT", "GO: 0006508", "Proteolysis", "20", "0.004661937"], ["GOTERM_CC_DIRECT", "GO: 0005576", "Extracellular region", "63", "2.51E-13"], ["GOTERM_CC_DIRECT", "GO: 0031090", "Organelle membrane", "16", "2.80E-11"], ["GOTERM_CC_DIRECT", "GO: 0070062", "Extracellular exosome", "79", "3.65E-10"], ["GOTERM_CC_DIRECT", "GO: 0005615", "Extracellular space", "48", "1.08E-08"], ["GOTERM_CC_DIRECT", "GO: 0072562", "Blood microparticle", "12", "1.30E-04"], ["GOTERM_MF_DIRECT", "GO: 0020037", "Heme binding", "19", 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0007067", "Mitotic nuclear division", "10", "9.83E-06"], ["GOTERM_BP_DIRECT", "GO: 0051301", "Cell division", "11", "9.83E-06"], ["GOTERM_CC_DIRECT", "GO: 0005654", "Nucleoplasm", "22", "1.84E-04"], ["GOTERM_CC_DIRECT", "GO: 0005634", "Nucleus", "30", "7.93E-04"], ["GOTERM_CC_DIRECT", "GO: 0005829", "Cytosol", "21", "0.005534764"]], "row_count": 31, "column_count": 5, "numeric_cells": 85, "header_rows": 1, "locator": "section[10]/table-wrap[1]#t1-medscimonit-27-e929023"}}, {"id": "asset:table:pmid:33658475:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:10bfea0a6c000c07898136693d3caae47f8453046a0005054ba70f0f00d98075", "bytes": 709, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#t2-medscimonit-27-e929023", "version": null, "note": "GO and KEGG pathway enrichment analysis of DEGs in the most significant module.", "structure": {"pmcid": "PMC7941760", "section_index": 11, "section_title": "PPI Network Construction and Module Analysis", "row_count": 7, "column_count": 5}, "table": {"label": "Table 2", "caption": "GO and KEGG pathway enrichment analysis of DEGs in the most significant module.", "rows": [["Category", "Term", "Description", "Count", "FDR"], ["GOTERM_BP_DIRECT", "GO: 0051301", "Cell division", "11", "1.66E-08"], ["GOTERM_BP_DIRECT", "GO: 0007067", "Mitotic nuclear division", "10", "1.66E-08"], ["GOTERM_CC_DIRECT", "GO: 0005654", "Nucleoplasm", "19", "3.33E-07"], ["GOTERM_CC_DIRECT", "GO: 0005634", "Nucleus", "24", "4.13E-07"], ["GOTERM_MF_DIRECT", "GO: 0005515", "Protein binding", "26", "0.001379194"], ["GOTERM_MF_DIRECT", "GO: 0005524", "ATP binding", "11", "0.002387081"]], "row_count": 7, "column_count": 5, "numeric_cells": 18, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t2-medscimonit-27-e929023"}}, {"id": "asset:table:pmid:33658475:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4ca56d29806a4b7230870a12ceca6ab55275f60f824118c858e0a3e2a9f5b249", "bytes": 1830, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#t3-medscimonit-27-e929023", "version": null, "note": "Functional roles of 16 hub genes with degree ≥10.", "structure": {"pmcid": "PMC7941760", "section_index": 12, "section_title": "Hub Gene Selection and Analysis", "row_count": 13, "column_count": 3}, "table": {"label": "Table 3", "caption": "Functional roles of 16 hub genes with degree ≥10.", "rows": [["Gene symbol", "Full name", "Function"], ["UBE2T", "Ubiquitin-conjugating enzyme E2 T", "Catalyzes the covalent attachment of ubiquitin to protein substrates"], ["HABP2", "Hyaluronan binding protein 2", "Encodes a member of the peptidase S1 family of serine proteases"], ["MT1M", "Metallothionein 1M", "Encodes a member of the metallothionein superfamily, type 1 family"], ["CFP", "Complement factor properdin", "Encodes a plasma glycoprotein that positively regulates the alternative complement pathway of the innate immune system"], ["ENO3", "Enolase 3", "Encodes 1 of the 3 enolase isoenzymes found in vertebrates"], ["CYP2C18", "Cytochrome P450 family 2 subfamily C member 18", "Encodes a member of the cytochrome P450 superfamily of enzymes."], ["CCL2", "C-C motif chemokine ligand 2", "1 of several cytokine genes clustered on the q-arm of chromosome 17"], ["FBLN5", "Fibulin 5", "Protein encoded is a secreted, extracellular matrix protein containing an Arg-Gly-Asp motif and calcium-binding EGF-like domains"], ["KMO", "Kynurenine 3-monooxygenase", "Encodes a mitochondrion outer membrane protein that catalyzes the hydroxylation of L-tryptophan metabolite, L-kynurenine, to form L-3-hydroxykynurenine"], ["ACMSD", "Aminocarboxymuconate semialdehyde decarboxylase", "Converts alpha-amino-beta-carboxymuconate-epsilon-semialdehyde to alpha-aminomuconate semialdehyde"], ["PTGS2", "Prostaglandin-endoperoxide synthase 2", "Encodes an enzyme that is a member of the prostaglandin G/H synthase family"], ["CLEC1B", "C-type lectin domain family 1, member b", "CLEC2 is a C-type lectin-like receptor expressed in myeloid cells and NK cells"]], "row_count": 13, "column_count": 3, "numeric_cells": 15, "header_rows": 1, "locator": "section[12]/table-wrap[1]#t3-medscimonit-27-e929023"}}], "gaps": ["asset:data:geo:GSE121248 not downloaded", "asset:data:geo:GSE121248 licence not read", "asset:data:geo:GSE84598 not downloaded", "asset:data:geo:GSE84598 licence not read", "asset:data:geo:GSE87630 not downloaded", "asset:data:geo:GSE87630 licence not read"]}, "analysis": {"state": "complete", "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": "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"}}], "targets": [], "gaps": []}, "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": ["GSE121248", "GSE87630", "GSE84598"], "resolved_accessions": ["GSE121248", "GSE87630", "GSE84598"], "statements": ["GSE121248 contains 70 HCC tissue samples and 37 normal liver tissue samples adjacent to HCC."], "basis": "The paper names GSE121248, GSE87630, GSE84598 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:33658475", "data:geo:GSE121248", "asset:table:pmid:33658475:1", "asset:table:pmid:33658475:2", "asset:table:pmid:33658475:3", "asset:table:pmid:33658475:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE121248"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:26:27Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 20623, "completion_tokens": 1231, "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:33658475", "type": "paper", "label": "pmid:33658475"}, {"id": "source:pmid:33658475", "type": "manuscript", "label": "PMID 33658475 full text"}, {"id": "data:geo:GSE121248", "type": "dataset", "label": "GEO GSE121248"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33658475", "type": "paper", "label": "pmid:33658475"}, {"id": "source:pmid:33658475", "type": "manuscript", "label": "PMID 33658475 full text"}, {"id": "data:geo:GSE121248", "type": "dataset", "label": "GEO GSE121248"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33658475", "type": "extraction", "used": ["source:pmid:33658475"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE121248", "type": "accession_resolution", "used": ["data:geo:GSE121248"], "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:33658475", "parent_hash": "sha256:c447800b3b33e0b85a70c6362507ad636494e56ee6275b46595402f26552fbe3", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE121248 licence not read", "asset:data:geo:GSE121248 not downloaded", "asset:data:geo:GSE84598 licence not read", "asset:data:geo:GSE84598 not downloaded", "asset:data:geo:GSE87630 licence not read", "asset:data:geo:GSE87630 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T00:36:21+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}}}