{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28103885", "kind": "science-record", "revision": 7, "content_hash": "sha256:5a46cc2d8ee552d380bce7bc7d382130ee2a60fabf664533686dcf99cc153cfb", "created_at": "2026-11-01T15:40:22Z", "updated_at": "2026-11-01T21:59:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Discovery and validation of immune-associated long non-coding RNA biomarkers associated with clinically molecular subtype and prognosis in diffuse large B cell lymphoma.", "doi": "10.1186/s12943-017-0580-4", "pmid": "28103885", "authors": ["Meng Zhou", "Hengqiang Zhao", "Wanying Xu", "Siqi Bao", "Liang Cheng", "Jie Sun"], "journal": "Molecular cancer", "year": 2017, "abstract": "BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is an aggressive and complex disease characterized by wide clinical, phenotypic and molecular heterogeneities. The expression pattern and clinical implication of long non-coding RNAs (lncRNAs) between germinal center B-cell-like (GCB) and activated B-cell-like (ABC) subtypes in DLBCL remain unclear. This study aims to determine whether lncRNA can serve as predictive biomarkers for subtype classification and prognosis in DLBCL.\nMETHODS: Genome-wide comparative analysis of lncRNA expression profiles were performed in a large number of DLBCL patients from Gene Expression Omnibus (GEO), including GSE31312 cohort (N = 426), GSE10846 (N = 350) cohort and GSE4475 cohort (N = 129). Novel lncRNA biomarkers associated with clinically molecular subtype and prognosis were identified in the discovery cohort using differential expression analyses and weighted voting algorithm. The predictive value of the lncRNA signature was then assessed in two independent cohorts. The functional implication of lncRNA signature was also analyzed by integrative analysis of lncRNA and mRNA.\nRESULTS: Seventeen of the 156 differentially expressed lncRNAs between GCB and ABC subtypes were identified as candidate biomarkers and integrated into form a lncRNA-based signature (termed SubSigLnc-17) which was able to discriminate between GCB and ABC subtypes with AUC of 0.974, specificity of 89.6% and sensitivity of 92.5%. Furthermore, subgroups of patients characterized by the SubSigLnc-17 demonstrated significantly different clinical outcome. The reproducible predictive power of SubSigLnc-17 in subtype classification and prognosis was successfully validated in the internal validation cohort and another two independent patient cohorts. Integrative analysis of lncRNA-mRNA suggested that these candidate lncRNA biomarkers were mainly related to immune-associated processes, such as T cell activation, leukocyte activation, lymphocyte activation and Chemokine signaling pathway.\nCONCLUSIONS: Our study uncovered differentiated lncRNA expression pattern between GCB and ABC DLBCL and identified a 17-lncRNA signature for subtype classification and prognosis prediction. With further prospective validation, our study will improve the understanding of underlying molecular heterogeneities in DLBCL and provide candidate lncRNA biomarkers in DLBCL classification and prognosis.", "claims": [{"id": "claim-method", "statement": "To construct a lncRNA-based molecular signature for subtype classification and prognosis prediction, we developed a supervised subgroup predictive classifier using the weighted voting algorithm as previously described [34] based on the weighted votes of a set of informative lncRNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28103885", "locator": "sections[7] \"Formulation of lncRNA-based molecular signature\" paragraph 2", "quote": "To construct a lncRNA-based molecular signature for subtype classification and prognosis prediction, we developed a supervised subgroup predictive classifier using the weighted voting algorithm as previously described [34] based on the weighted votes of a set of informative lncRNAs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression data and clinical data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE31312 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31312), GSE10846 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10846) and GSE4475 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4475).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28103885", "locator": "sections[21] \"ack\" paragraph 1", "quote": "The gene expression data and clinical data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE31312 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31312), GSE10846 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10846) and GSE4475 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4475)."}], "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:28103885"], "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:GSE10846"], "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:GSE10846"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28103885", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12943-017-0580-4", "sha256": 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accession numbers GSE31312 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31312), GSE10846 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10846) and GSE4475 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4475).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression data and clinical data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE31312 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31312), GSE10846 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10846) and GSE4475 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4475).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM274895", "GSM274896", "GSM274897", "GSM274898", "GSM274899", "GSM274900", "GSM274901", "GSM274902", "GSM274903", "GSM274904", "GSM274905", "GSM274906", "GSM274907", "GSM274908", "GSM274909", "GSM274910", "GSM274911", 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["Unknown", "20"], ["Subtype"], ["GCB", "106", "121", "227", "183", "74"], ["ABC", "107", "92", "199", "167", "55"], ["Unclassified"], ["Survival status"], ["Dead", "80", "74", "154", "143", "51"], ["Alive", "133", "139", "272", "207", "42"], ["Unknown", "36"]], "row_count": 33, "column_count": 6, "numeric_cells": 101, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:28103885:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:606313c643d97a56edc2a61112cbfc94098f5409468d84131f03802ddc7577f9", "bytes": 2080, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab2", "version": null, "note": "Candidate lncRNAs biomarkers associated with clinically molecular subtype and prognosis of DLBCL", "structure": {"pmcid": "PMC5248456", "section_index": 12, "section_title": "Identification of lncRNA 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["ENSG00000236901.4", "MIR600HG", "Chr 9: 123,109,494-123,115,477 (−)", "9.02E-07", "1.4E-04", "0.359"], ["ENSG00000279130.1", "RP11-278 J6.4", "Chr 5: 143,406,959-143,407,420 (+)", "2.57E-06", "3.737E-04", "0.341"], ["ENSG00000260303.1", "RP11-203B7.2", "Chr 4: 146,052,604-146,056,762 (−)", "1.33E-07", "2.57E-05", "0.395"], ["ENSG00000231163.4", "CSMD2-AS1", "Chr 1: 33,868,953-33,885,458 (+)", "2.76E-10", "1.29E-07", "0.493"], ["ENSG00000245864.2", "CTC-467 M3.1", "Chr 5: 88,676,218-88,722,831 (+)", "1.12E-07", "2.36E-05", "0.379"], ["ENSG00000223479.3", "RP4-788P17.1", "Chr 1: 73,635,216-73,715,214 (+)", "2.91E-12", "3.39E-09", "0.514"], ["ENSG00000259976.1", "RP11-553 L6.5", "Chr 3: 114,314,501-114,316,179 (−)", "6.09E-08", "1.58E-05", "0.386"], ["ENSG00000245694.7", "CRNDE", "Chr 16: 54,918,863-54,929,189 (−)", "3.49E-06", "4.71E-04", "0.328"], ["ENSG00000259354.4", "RP11-519G16.3", "Chr 15: 45,448,427-45,513,767 (+)", "3.7E-10", "1.44E-07", "0.494"], ["ENSG00000254418.1", "RP11-21 L19.1", "Chr 11: 14,262,846-14,273,691 (−)", "2.96E-11", "1.73E-08", "0.507"], ["ENSG00000240666.2", "MME-AS1", "Chr 3: 155,158,370-155,183,285 (−)", "4.33E-15", "1.01E-11", "0.666"]], "row_count": 18, "column_count": 6, "numeric_cells": 96, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:28103885:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6f38212adea253f6e4d7433ce489bc4ebfb1f6c8ba66fd3273037af57050f879", "bytes": 1698, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab3", "version": null, "note": "Univariate and multivariate Cox regression analysis of overall survival in each dataset", "structure": {"pmcid": "PMC5248456", "section_index": 14, "section_title": "Further validation of lncRNA-based molecular signature in the internal validation cohort and entire GSE31312 cohort", "row_count": 18, "column_count": 7}, "table": {"label": "Table 3", "caption": "Univariate and multivariate Cox regression analysis of overall survival in each dataset", "rows": [["Variables", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI of HR", "P value", "HR", "95% CI of HR", "P value"], ["GSE31312 cohort (n = 426)"], ["SubSigLnc-17 (ABC vs. GCB)", "1.638", "1.19-2.254", "0.002", "1.422", "0.997-2.028", "0.052"], ["Age (> = 60 vs. <60)", "2.01", "1.41-2.864", "1.12E-04", "1.946", "1.315-2.881", "8.79E-04"], ["Gender (Male vs. Female)", "0.959", "0.697-1.32", "0.798", "0.843", "0.597-1.189", "0.331"], ["Stage (III/IV vs. I/II)", "2.314", "1.646-3.251", "1.35E-06", "1.707", "1.135-2.567", "0.01"], ["LDH (High vs. Normal)", "2.035", "1.362-3.04", "5.19 E-04", "1.475", "0.973-2.236", "0.067"], ["No. of extranodal sites (≥2 vs. < 2)", "2.247", "1.598-3.16", "3.23E-06", "1.778", "1.213-2.605", "0.003"], ["ECOG (≥2 vs. < 2)", "2.195", "1.556-3.097", "7.48E-06", "1.584", "1.065-2.355", "0.023"], ["GSE10846 cohort (n = 350)"], ["SubSigLnc-17 (ABC vs. GCB)", "2.364", "1.673-3.341", "1.10E-06", "2.093", "1.391-3.149", "3.94E-04"], ["Age (> = 60 vs. <60)", "2.099", "1.464-3.009", "5.50E-05", "1.988", "1.31-3.016", "0.001"], ["Gender (Male vs. Female)", "1.017", "0.724-1.429", "0.922", "0.993", "0.676-1.46", "0.972"], ["Stage (III/IV vs. I/II)", "1.747", "1.239-2.464", "0.001", "1.147", "0.762-1.727", "0.51"], ["LDH (High vs. Normal)", "2.643", "1.791-3.899", "9.72E-07", "2.038", "1.341-3.096", "8.59E-04"], ["No. of extranodal sites (≥2 vs. < 2)", "1.899", "1.087-3.317", "0.024", "1.183", "0.58-2.415", "0.644"], ["ECOG (≥2 vs. < 2)", "2.968", "2.091-4.214", "1.19E-09", "1.907", "1.246-2.918", "0.003"]], "row_count": 18, "column_count": 7, "numeric_cells": 96, "header_rows": 2, "locator": "section[14]/table-wrap[1]#Tab3"}}], "gaps": ["asset:data:geo:GSE10846 not downloaded", "asset:data:geo:GSE10846 licence not read", "asset:data:geo:GSE31312 not 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analysis"}}, {"id": "method-6", "family": null, "specific": null, "label": "weighted voting algorithm", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To construct a lncRNA-based molecular signature for subtype classification and prognosis prediction, we developed a supervised subgroup predictive classifier using the weighted voting algorithm as previously described [34] based on the weighted votes of a set of informative lncRNAs."}}], "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": ["GSE31312", "GSE10846", "GSE4475"], "resolved_accessions": ["GSE31312", "GSE10846", "GSE4475"], "statements": ["The gene expression data and clinical data in this study can be found online at the Gene Expression Omnibus under accession numbers GSE31312 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31312), GSE10846 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10846) and GSE4475 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4475)."], "basis": "The paper names GSE31312, GSE10846, GSE4475 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:28103885", "data:geo:GSE10846", "asset:table:pmid:28103885:1", "asset:table:pmid:28103885:2", "asset:table:pmid:28103885:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10846"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:28103885", "type": "paper", "label": "pmid:28103885"}, {"id": "source:pmid:28103885", "type": "manuscript", "label": "PMID 28103885 full text"}, {"id": "data:geo:GSE10846", "type": "dataset", "label": "GEO GSE10846"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28103885", "type": "paper", "label": "pmid:28103885"}, {"id": "source:pmid:28103885", "type": "manuscript", "label": "PMID 28103885 full text"}, {"id": "data:geo:GSE10846", "type": "dataset", "label": "GEO GSE10846"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28103885", "type": "extraction", "used": ["source:pmid:28103885"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10846", "type": "accession_resolution", "used": ["data:geo:GSE10846"], "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:28103885", "parent_hash": "sha256:040ef8850c8a9d6a2a707e96be69cf7c00c464c7604202be5f7a63601f332c82", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE10846 licence not read", "asset:data:geo:GSE10846 not downloaded", "asset:data:geo:GSE31312 licence not read", "asset:data:geo:GSE31312 not downloaded", "asset:data:geo:GSE4475 licence not read", "asset:data:geo:GSE4475 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": 0.99, "evidence": ["Methods Patients’ samples Gene expression microarray data and clinical information for DLBCL were", "atients, was based on a different Affymetrix microarray platform (HG-U133A). Therefore, we re-annota", "the Gene Expression Omnibus (GEO) database. Affymetrix gene expression profiles were performed usin", "ene expression profiles were performed using Affymetrix Human Genome U133 Plus 2.0 (HG-U133 Plus_2.0"], "order_basis": "paper_text_order:2583", "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": 0.8, "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":"2026-11-04T01:41:56+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}}}