{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32596394", "kind": "science-record", "revision": 7, "content_hash": "sha256:f93dacbd75bf50bbd08a5ddb5e39b10e626a2acfcd4244309732bb59b0e42a2e", "created_at": "2026-11-01T15:41:04Z", "updated_at": "2026-11-01T22:01:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of an Individualized Prognostic Signature Based on the RWSR Model in Early-Stage Bladder Carcinoma.", "doi": "10.1155/2020/9186546", "pmid": "32596394", "authors": ["Liyang Liu", "Xiaodan Zhong", "Haining Cui", "Hao Zhang", "Linyu Wang", "Yuanning Liu"], "journal": "BioMed research international", "year": 2020, "abstract": "Bladder cancer (BLCA) is the fourth common cancer among males in the United States, which is also the fourth leading cause of cancer-related death in old males. BLCA has a high recurrence rate, with over 50% of patients which has at least one recurrence within five years. Due to the complexity of the molecular mechanisms and heterogeneous cancer feature, BLCA clinicians find it hard to make an efficient management decision as they lack reliable assessment of mortality risk. Meanwhile, there is currently no screening suitable prognostic signature or method recommended for early detection, which is significantly important to early-stage detection and prognosis. In this study, a novel model, named the risk-weighted sparse regression (RWSR) model, is constructed to identify a robust signature for patients of early-stage BLCA. The 17-gene signature is generated and then validated as an independent prognostic factor in BLCA cohorts from GSE13507 and TCGA_BLCA datasets. Meanwhile, a risk score model is developed and validated among the 17-gene signature. The risk score is also considered an independent factor for prognosis prediction, which is confirmed through prognosis analysis. The Kaplan-Meier with the log-rank test is used to assess survival difference. Furthermore, the predictive capacity of the signature is proved through stratification analysis. Finally, an effective patient classification is completed by a combination of the 17-gene signature and stage information, which is for better survival prediction and treatment decisions. Besides, 11 genes in the signature, such as coiled-coil domain containing 73 (CCDC73) and protein kinase, DNA-activated, and catalytic subunit (PRKDC), are proved to be prognosis marker genes or strongly associated with prognosis and progress of other types of cancer in published literature already. As a result, this paper would more accurately predict a patient's prognosis and improve surveillance in the clinical setting, which may provide a quantitative and reliable decision-making basis for the treatment plan.", "claims": [{"id": "claim-method", "statement": "To predict the differences between the two risk BLCA patient groups based on survival time, we use the Kaplan-Meier method and calculate the log-rank value to identify the statistical significance between groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32596394", "locator": "sections[7] \"2.5. Statistical Analysis\" paragraph 2", "quote": "To predict the differences between the two risk BLCA patient groups based on survival time, we use the Kaplan-Meier method and calculate the log-rank value to identify the statistical significance between groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data of RNA-seq and clinical data from TCGA and GEO datasets are available in the Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32596394", "locator": "sections[23] \"Data Availability\" paragraph 2", "quote": "The raw data of RNA-seq and clinical data from TCGA and GEO datasets are available in the Supplemental Files."}], "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:32596394"], "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:GSE13507"], "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:GSE13507"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32596394", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/9186546", "sha256": 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Prognostic Signature Generation", "row_count": 19, "column_count": 5}, "table": {"label": "Table 2", "caption": "Univariate Cox regression analysis of 17 genes and overall survival of BLCA in two databases.", "rows": [["Gene name", "GEO", "TCGA"], ["HR (95% CI for HR)", "P value", "HR (95% CI for HR)", "P value"], ["ATP4A", "13 (1.1-140)", "3.92E-02", "1.2 (1-1.4)", "4.51E-02"], ["CCDC73", "29 (2.4-360)", "8.45E-03", "2.1 (1.3-3.5)", "3.69E-03"], ["CNTNAP4", "35 (1.5-850)", "2.75E-02", "1.1 (1-1.3)", "4.09E-02"], ["CRB1", "0.014 (0.00019-0.98)", "4.88E-02", "0.83 (0.68-1)", "4.85E-02"], ["EWSR1", "5.4 (1.7-18)", "5.05E-03", "10 (1.9-54)", "6.87E-03"], ["FCGR3B", "0.2 (0.043-0.9)", "3.59E-02", "0.77 (0.62-0.95)", "1.37E-02"], ["FRYL", "0.053 (0.005-0.56)", "1.48E-02", "0.24 (0.083-0.7)", "9.17E-03"], ["GDF7", "42 (1.6-1100)", "2.44E-02", "1.4 (1.1-1.9)", "2.3E-02"], ["GSG1L", "520 (19-14000)", "2.14E-04", "1.2 (1-1.4)", "3.33E-02"], ["PRDM14", "20 (1.4-270)", "2.58E-02", "1.2 (1-1.4)", "2.3E-02"], ["PRKDC", "0.59 (0.4-0.86)", "6.62E-03", "0.41 (0.21-0.8)", "9.25E-03"], ["RER1", "3.3 (1.2-8.9)", "1.91E-02", "6 (1.5-24)", "1.12E-02"], ["SYNPO", "0.02 (0.00046-0.86)", "4.15E-02", "0.46 (0.26-0.81)", "7.35E-03"], ["XKR8", "21 (1.4-300)", "2.71E-02", "3.7 (1.2-12)", "2.55E-02"], ["ZNF284", "54 (1.4-2200)", "3.37E-02", "2.5 (1-6.1)", "4.38E-02"], ["ZNF680", "2.3 (1.1-4.7)", "2.48E-02", "2.1 (1-4)", "3.65E-02"], ["ZNF780B", "27 (1.8-390)", "1.63E-02", "2.7 (1.3-5.6)", "9.42E-03"]], "row_count": 19, "column_count": 5, "numeric_cells": 75, "header_rows": 2, "locator": "section[9]/table-wrap[2]#tab2"}}, {"id": "asset:table:pmid:32596394:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:757dad9a84fc11f901f9593bc22dec25451ca10aae45bfd49d54de858d466aa1", "bytes": 2043, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#tab3", "version": null, "note": "Univariate and multivariate Cox regression analyses of the signature genes and overall survival.", "structure": {"pmcid": "PMC7293744", "section_index": 11, "section_title": "3.3. The 17-Gene Prognostic Signature Is Independent of Other Clinicopathological Factors", "row_count": 23, "column_count": 6}, "table": {"label": "Table 3", "caption": "Univariate and multivariate Cox regression analyses of the signature genes and overall survival.", "rows": [["Characters", "Ch.description", "Univariate analysis", "Multivariate analysis"], ["HR (95% CI for HR)", "P value", "HR (95% CI for HR)", "P value"], ["GEO", "", "", "", "", ""], ["Sex", "Female/male", "1.43 (0.76-2.7)", "2.58E-01", "1.13 (0.82-1.55)", "3.92E-02"], ["Age", ">70/<=70", "1.15 (1.02-1.14)", "9.03E-03", "1.17 (1.06-1.59)", "2.91E-02"], ["Invasiveness", "Yes/no", "2.32 (1.46-3.92)", "1.64E-03", "1.35 (0.65-2.83)", "4.23E-02"], ["Intravesical therapy", "Yes/no", "0.67 (0.48-0.93)", "1.59E-02", "0.91 (0.66-1.25)", "4.57E-01"], ["Stage", "0-III", "1.79 (1.37-2.23)", "2.23E-04", "1.39 (1.05-1.86)", "2.38E-03"], ["Grade", "Low/high", "2.76 (1.68-4.57)", "1.97E-03", "1.21 (0.91-1.62)", "3.93E-02"], ["Event", "Yes/no", "0.92 (0.51-1.6)", "7.76E-01", "0.46 (0.37-1.99)", "1.79E-02"], ["Specific survival", "Alive/dead", "13.02 (7.54-24)", "6.62E-04", "11.79 (10.94-17.38)", "2.32E-03"], ["Risk score", "Low/high", "4.45 (4.32-5.32)", "3.15E-07", "4.02 (4.99-8.04)", "2.46E-04"], ["TCGA", "", "", "", "", ""], ["Sex", "Female/male", "1.12 (0.73-1.68)", "7.04E-03", "2.95 (0.72-12.04)", "1.355E-02"], ["Age", ">70/<=70", "1.36 (0.76-2.35)", "3.77E-02", "1.22 (0.53-2.79)", "6.42E-02"], ["Height", ">170/≤170 cm", "1.24 (0.99-2.5)", "2.43E-03", "1.09 (1.03-1.16)", "4.43E-03"], ["Weight", ">80/≤80", "0.99 (0.98-1.07)", "1.49E-02", "0.97 (0.93-1.05)", "2.97E-02"], ["Diagnosis age", "Yes/no", "0.62 (0.33-1.89)", "4.16E-02", "0.83 (0.36-1.90)", "6.64E-02"], ["Stage", "II/III", "1.62 (1.3-2.11)", "2.31E-05", "1.5 (0.92-2.58)", "9.92E-04"], ["Grade", "High/low", "4.75 (3.63-7.91)", "9.92E-02", "3.8 (2.88-8.34)", "1.87E-01"], ["Noninvasive history", "Yes/no", "0.81 (0.63-1.87)", "1.04E-02", "0.83 (0.43-1.57)", "5.68E-02"], ["Smoking", "No/<15 yr/>15 yr", "1.41 (1.12-1.85)", "7.47E-03", "1.20 (0.67-2.15)", "5.53E-03"], ["Risk score", "High/low", "3.93 (3.34-6.35)", "3.57E-06", "3.11 (3.09-4.24)", "8.42E-04"]], "row_count": 23, "column_count": 6, "numeric_cells": 84, "header_rows": 2, "locator": "section[11]/table-wrap[1]#tab3"}}, {"id": "asset:table:pmid:32596394:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1e6ecad77b1e4f6a8218b36d56304f766916cd901093b49f25c669d536da9086", "bytes": 1340, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tab4", "version": null, "note": "The pathway enriched for the 17-gene signature based on four pathway databases.", "structure": {"pmcid": "PMC7293744", "section_index": 14, "section_title": "3.6. Signature Enrichment Analysis", "row_count": 25, "column_count": 3}, "table": {"label": "Table 4", "caption": "The pathway enriched for the 17-gene signature based on four pathway databases.", "rows": [["Index", "Name of pathway", "P value"], ["1", "BIOCARTA_FAS_PATHWAY", "9.42E-05"], ["2", "BIOCARTA_G_PATHWAY", "2.23E-04"], ["3", "BIOCARTA_G2_PATHWAY", "5.99E-05"], ["4", "BIOCARTA_HIVNEF_PATHWAY", "3.55E-04"], ["5", "BIOCARTA_TNFR_PATHWAY", "2.04E-04"], ["6", "BIOCARTA_TNFR1_PATHWAY", "8.8E-05"], ["7", "KEGG_CELL_CYCLE", "1.61E-03"], ["8", "KEGG_LEISHMANIA_INFECTION", "5.17E-04"], ["9", "KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY", "1.79E-03"], ["10", "KEGG_NON_HOMOLOGOUS_END_JOINING", "1.7E-05"], ["11", "KEGG_OXIDATIVE_PHOSPHORYLATION", "1.77E-03"], ["12", "KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS", "1.9E-03"], ["13", "KEGG_TGF_BETA_SIGNALING_PATHWAY", "7.61E-04"], ["14", "PID_AR_PATHWAY", "3.93E-04"], ["15", "PID_BARD_PATHWAY", "3.36E-07"], ["16", "PID_BARD1PATHWAY", "3.36E-07"], ["17", "PID_DNA_PK_PATHWAY", "2.61E-05"], ["18", "PID_DNAPK_PATHWAY", "2.61E-05"], ["19", "PID_PI3KCIAKTPATHWAY", "1.29E-04"], ["20", "PID_PIKCI_AKT_PATHWAY", "1.29E-04"], ["21", "REACTOME_DNA_REPAIR", "1.16E-03"], ["22", "REACTOME_DOUBLE_STRAND_BREAK_REPAIR", "5.02E-05"], ["23", "REACTOME_ION_CHANNEL_TRANSPORT", "3.08E-04"], ["24", "REACTOME_ION_TRANSPORT_BY_P_TYPE_ATPASES", "1.14E-04"]], "row_count": 25, "column_count": 3, "numeric_cells": 48, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tab4"}}], "gaps": ["asset:data:geo:GSE13507 not downloaded", "asset:data:geo:GSE13507 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To predict the differences between the two risk BLCA patient groups based on survival time, we use the Kaplan-Meier method and calculate the log-rank value to identify the statistical significance between groups."}}, {"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": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-4", "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": 0.8, "band": "high", "quote": "ROC curve"}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE13507"], "resolved_accessions": ["GSE13507"], "statements": ["The raw data of RNA-seq and clinical data from TCGA and GEO datasets are available in the Supplemental Files."], "basis": "The paper names GSE13507 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:32596394", "data:geo:GSE13507", "asset:table:pmid:32596394:1", "asset:table:pmid:32596394:2", "asset:table:pmid:32596394:3", "asset:table:pmid:32596394:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13507"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:54Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 50334, "completion_tokens": 1018, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32596394", "type": "paper", "label": "pmid:32596394"}, {"id": "source:pmid:32596394", "type": "manuscript", "label": "PMID 32596394 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32596394", "type": "paper", "label": "pmid:32596394"}, {"id": "source:pmid:32596394", "type": "manuscript", "label": "PMID 32596394 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32596394", "type": "extraction", "used": ["source:pmid:32596394"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13507", "type": "accession_resolution", "used": ["data:geo:GSE13507"], "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:32596394", "parent_hash": "sha256:0914b31294340d4dcd42f00b95b5abda8f9fb63140bdeeee1fb2709c1a3191d3", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE13507 licence not read", "asset:data:geo:GSE13507 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": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To predict the differences between the two risk BLCA patient groups based on survival time, we use the Kaplan-Meier method and calculate the log-rank value to identify the statistical significance between groups."], "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":"2026-11-04T03:37:33+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}}}