{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31794632", "kind": "science-record", "revision": 8, "content_hash": "sha256:ec78a48b21b4c563620800f903b3a064f9658a8c510954177dcbf1f0137ad790", "created_at": "2026-11-01T15:40:52Z", "updated_at": "2026-11-01T22:01:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome-wide screening of abberant methylated drivers combined with relative risk loci in bladder cancer.", "doi": "10.1002/cam4.2665", "pmid": "31794632", "authors": ["Chuanjie Zhang", "Kangjie Shen", "Yuxiao Zheng", "Feng Qi", "Jun Luo"], "journal": "Cancer medicine", "year": 2020, "abstract": "BACKGROUND: To explore important methylation-driven genes (MDGs) and risk loci to construct risk model for prognosis of bladder cancer (BCa).\nMETHODS: We utilized TCGA-Assembler package to download 450K methylation data and corresponding transcriptome profiles. MethylMix package was used for identifying methylation-driven genes and functional analysis was mainly performed based on ConsensusPathDB database. Then, Cox regression method was utilized to find prognostic MDGs, and we selected 17 hub genes via stepwise regression and multivariate Cox models. Kruskal-Wallis test was implemented for comparisons between risk with other clinical variables. Moreover, we constructed the risk model and validated it in GSE13507. Gene set enrichment analysis was performed using the levels of risk score as the phenotype. Additionally, we further screened out the relative methylation sites associated with the 17 hub genes. Cox regression and Survival analysis were conducted to find the specifically prognostic sites.\nRESULTS: Two hundred and twenty-eight MDGs were chosen by ConsensusPathDB database. Results revealed that most conspicuous pathways were transcriptional mis-regulation pathways in cancer and EMT. After Cox regression analysis, 17 hub epigenetic MDGs were identified. We calculated the risk score and found satisfactory predictive efficiency by ROC curve (AUC = 0.762). In the validation group from GSE13507, 17 hub genes remained higher predictive value with AUC = 0.723 and patients in high-risk group. Meanwhile, Kruskal-Wallis test revealed that higher risk score correlated with a higher level of TNM stage, tumor grade, and advanced pathological stages. Then, identified 38 risk methylated loci that highly associated with prognosis. Last, gene set enrichment analysis revealed that high-risk level of MDGs may correlate with several important pathways, including MAPK signaling pathway and so on.\nCONCLUSION: Our study indicated several hub-MDGs, calculated novel risk score and explored the prognostic value in BCa, which provided a promising approach to BCA prognosis assessment.", "claims": [{"id": "claim-method", "statement": "We conducted the univariate Cox regression analysis to select prognostic MDGs with P < .05 as the threshold.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31794632", "locator": "sections[5] \"Construction and evaluation of epigenetic risk score based on MDGs\" paragraph 2", "quote": "We conducted the univariate Cox regression analysis to select prognostic MDGs with P < .05 as the threshold."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We obtained RNA‐seq data of transcriptome profiles of BCA from TCGA database (https://portal.gdc.cancer.gov/), including 414 tumor tissues and 10 normal tissues. We used edgeR package19 to normalize the raw data. Moreover, we utilized the tool of TCGA‐Assembler to download the DNA methylation data (419 BCA and corresponding 21 normal samples) based on the Illumina Infinium Human Methylation 450 platform, which detecting over 480 K human genome methylated sites. Limma package was applied to do the normalization.20", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31794632", "locator": "sections[3] \"Data acquisitions and integrative analysis\" paragraph 2", "quote": "We obtained RNA‐seq data of transcriptome profiles of BCA from TCGA database (https://portal.gdc.cancer.gov/), including 414 tumor tissues and 10 normal tissues. We used edgeR package19 to normalize the raw data. Moreover, we utilized the tool of TCGA‐Assembler to download the DNA methylation data (419 BCA and corresponding 21 normal samples) based on the Illumina Infinium Human Methylation 450 platform, which detecting over 480 K human genome methylated sites. Limma package was applied to do the normalization.20"}], "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:31794632"], "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:31794632", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/cam4.2665", "sha256": "sha256:b1ee9a0eb1965e73d62f6c2d9a98a71c3c5bfb40990538a76ced55cba266245f", "bytes": 30465, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/cam4.2665", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6970050", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13507", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13507", "version": null, "note": "We obtained RNA‐seq data of transcriptome profiles of BCA from TCGA database (https://portal.gdc.cancer.gov/), including 414 tumor tissues and 10 normal tissues. We used edgeR package19 to normalize the raw data. Moreover, we utilized the tool of TCGA‐Assembler to download the DNA methylation data (419 BCA and corresponding 21 normal samples) based on the Illumina Infinium Human Methylation 450 platform, which detecting over 480 K human genome methylated sites. Limma package was applied to do the normalization.20", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We obtained RNA‐seq data of transcriptome profiles of BCA from TCGA database (https://portal.gdc.cancer.gov/), including 414 tumor tissues and 10 normal tissues. We used edgeR package19 to normalize the raw data. Moreover, we utilized the tool of TCGA‐Assembler to download the DNA methylation data (419 BCA and corresponding 21 normal samples) based on the Illumina Infinium Human Methylation 450 platform, which detecting over 480 K human genome methylated sites. Limma package was applied to do the normalization.20", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM340537", "GSM340538", "GSM340539", "GSM340540", "GSM340541", "GSM340542", "GSM340543", "GSM340544", "GSM340545", "GSM340546", "GSM340547", "GSM340548", "GSM340549", "GSM340550", "GSM340551", "GSM340552", "GSM340553", "GSM340554", "GSM340555", "GSM340556", "GSM340557", "GSM340558", "GSM340559", "GSM340560", "GSM340561", "GSM340562", "GSM340563", "GSM340564", "GSM340565", "GSM340566", "GSM340567", "GSM340568", "GSM340569", "GSM340570", "GSM340571", "GSM340572", "GSM340573", "GSM340574", "GSM340575", "GSM340576", "GSM340577", "GSM340578", "GSM340579", "GSM340580", "GSM340581", "GSM340582", "GSM340583", "GSM340584", "GSM340585", "GSM340586", "GSM340587", "GSM340588", "GSM340589", "GSM340590", "GSM340591", "GSM340592", "GSM340593", "GSM340594", "GSM340595", "GSM340596", "GSM340597", "GSM340598", "GSM340599", "GSM340600", "GSM340601", "GSM340602", 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["Age", "68 ± 10.57", "65.18 ± 11.97", "67.19 ± 11.06"], ["Gender"], ["Female", "106 (26.2)", "30 (18.2)", "136 (23.9)"], ["Male", "299 (73.8)", "135 (81.8)", "434 (76.1)"], ["Race"], ["White", "334 (82.5)", "NA", "NA"], ["Asian", "43 (10.6)", "NA", "NA"], ["Black or African", "28 (6.9)", "NA", "NA"], ["AJCC‐T"], ["T0/Ta", "1 (0.2)", "24 (14.5)", "25 (4.4)"], ["T1", "3 (0.8)", "80 (48.5)", "83 (14.6)"], ["T2", "117 (28.9)", "31 (18.8)", "148 (25.9)"], ["T3", "193 (47.7)", "9 (5.5)", "212 (37.2)"], ["T4", "58 (14.3)", "11 (6.7)", "69 (12.1)"], ["Unknown", "33 (8.1)", "0 (0.0)", "33 (5.8)"], ["AJCC‐N"], ["N0", "235 (58.0)", "149 (90.3)", "384 (67.4)"], ["N1", "46 (11.4)", "8 (4.9)", "54 (9.5)"], ["N2", "75 (18.5)", "6 (3.6)", "81 (14.2)"], ["N3", "7 (1.7)", "1 (0.6)", "8 (1.4)"], ["Unknown", "42 (10.4)", "1 (0.6)", "43 (7.5)"], ["AJCC‐M"], ["M0", "195 (48.1)", "158 (95.8)", "353 (61.9)"], ["M1", "11 (2.7)", "7 (4.2)", "18 (3.2)"], ["Mx", "199 (49.2)", "NA", "NA"], ["Pathologic_stage"], ["I & II", "130 (32.1)", "NA", "NA"], ["III & IV", "273 (67.4)", "NA", "NA"], ["Unknown", "2 (0.5)", "NA", "NA"], ["Tumor_grade"], ["G1/G2", "20 (5.0)", "105 (63.6)", "125 (21.9)"], ["G3/G4", "382 ( 94.3)", "60 (36.4)", "442 (77.6)"], ["Unknown", "3 (0.7)", "NA", "NA"], ["MDGs risk score"], ["Low", "203 (50.1)", "82 (50.0)", "285 (50.0)"], ["High", "202 (49.9)", "83 (50.0)", "285 (50.0)"]], "row_count": 41, "column_count": 4, "numeric_cells": 77, "header_rows": 2, "locator": "section[3]/table-wrap[1]#cam42665-tbl-0001"}}, {"id": "asset:table:pmid:31794632:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7e28e086333e15e8094265c7af9d09dbfb472802a5477ed55f04ed41c6f68f9c", "bytes": 2557, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#cam42665-tbl-0002", "version": null, "note": "Functional analysis of MDGs based on ConsensusPathDB database", "structure": {"pmcid": "PMC6970050", "section_index": 13, "section_title": "Functional enriched pathways", "row_count": 41, "column_count": 3}, "table": {"label": "Table 2", "caption": "Functional analysis of MDGs based on ConsensusPathDB database", "rows": [["Enriched pathway", "P value", "source"], ["Signaling mediated by p38‐alpha and p38‐beta", ".024851855", "PID"], ["Wnt‐beta‐catenin Signaling Pathway in Leukemia", ".01023165", "Wikipathways"], ["WNT‐Core", ".037948147", "Signalink"], ["Glutathione metabolism", ".00704807", "KEGG"], ["Signaling events mediated by HDAC Class III", ".030398536", "PID"], ["B Cell Receptor Signaling Pathway", ".031370148", "Wikipathways"], ["Fas Ligand pathway and Stress induction of Heat Shock Proteins regulation", ".036385809", "Wikipathways"], ["Transcriptional cascade regulating adipogenesis", ".003598992", "Wikipathways"], ["Hydroxycarboxylic acid‐binding receptors", ".000144888", "Reactome"], ["Transcriptional misregulation in cancer", ".040866181", "KEGG"], ["Chemokine receptors bind chemokines", ".047839785", "Reactome"], ["FTO Obesity Variant Mechanism", ".001321732", "Wikipathways"], ["White fat cell differentiation", ".001423078", "Wikipathways"], ["Epithelial to mesenchymal transition in colorectal cancer", ".025906124", "Wikipathways"], ["TYROBP Causal Network", ".008528042", "Wikipathways"], ["Bopindolol Action Pathway", ".008924337", "SMPDB"], ["Timolol Action Pathway", ".008924337", "SMPDB"], ["Carteolol Action Pathway", ".008924337", "SMPDB"], ["Bevantolol Action Pathway", ".008924337", "SMPDB"], ["Practolol Action Pathway", ".008924337", "SMPDB"], ["Dobutamine Action Pathway", ".008924337", "SMPDB"], ["Isoprenaline Action Pathway", ".008924337", "SMPDB"], ["Arbutamine Action Pathway", ".008924337", "SMPDB"], ["Levobunolol Action Pathway", ".008924337", "SMPDB"], ["Metipranolol Action Pathway", ".008924337", "SMPDB"], ["Sotalol Action Pathway", ".008924337", "SMPDB"], ["Epinephrine Action Pathway", ".008924337", "SMPDB"], ["Betaxolol Action Pathway", ".008924337", "SMPDB"], ["Atenolol Action Pathway", ".008924337", "SMPDB"], ["Alprenolol Action Pathway", ".008924337", "SMPDB"], ["Acebutolol Action Pathway", ".008924337", "SMPDB"], ["Propranolol Action Pathway", ".008924337", "SMPDB"], ["Pindolol Action Pathway", ".008924337", "SMPDB"], ["Penbutolol Action Pathway", ".008924337", "SMPDB"], ["Oxprenolol Action Pathway", ".008924337", "SMPDB"], ["Metoprolol Action Pathway", ".008924337", "SMPDB"], ["Esmolol Action Pathway", ".008924337", "SMPDB"], ["Bisoprolol Action Pathway", ".008924337", "SMPDB"], ["Bupranolol Action Pathway", ".008924337", "SMPDB"], ["Nebivolol Action Pathway", ".008924337", "SMPDB"]], "row_count": 41, "column_count": 3, "numeric_cells": 41, "header_rows": 1, "locator": "section[13]/table-wrap[1]#cam42665-tbl-0002"}}, {"id": "asset:table:pmid:31794632:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f55c5052933b987f5f9d6a84d6bb8897639e650de05748e2535b833d8a1da6bf", "bytes": 2752, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#cam42665-tbl-0003", "version": null, "note": "Screening of 38 prognostic risk loci associated with hub MDGs in Bca", "structure": {"pmcid": "PMC6970050", "section_index": 16, "section_title": "Screening of risk methylation loci with survival analysis, joint survival analysis", "row_count": 39, "column_count": 5}, "table": {"label": "Table 3", "caption": "Screening of 38 prognostic risk loci associated with hub MDGs in Bca", "rows": [["Risk methtylated locus", "Related genes", "Hazard ratio", "z", "P value"], ["cg18414381", "EHF", "3.9737182", "3.347493733", ".000815458"], ["cg05503887", "EHF", "3.296494314", "3.334039828", ".000855944"], ["cg00543460", "TPM1", "0.313566503", "−3.040593266", ".002361126"], ["cg11065015", "NRSN2", "0.171047292", "−3.031903254", ".002430171"], ["cg13836318", "TPM1", "0.000319606", "−3.014958919", ".002570141"], ["cg24504361", "KRT8", "6.742218982", "2.907971041", ".00363782"], ["cg14506696", "DAPP1", "3.366923308", "2.895197969", ".003789195"], ["cg21614638", "DAPP1", "2.982090283", "2.81620796", ".00485942"], ["cg24097814", "KRT8", "3.116236706", "2.791702503", ".005243154"], ["cg08198488", "TPM1", "0.293122612", "−2.782702312", ".005390824"], ["cg10397389", "DAPP1", "2.804089164", "2.770618241", ".005594998"], ["cg01902605", "BHMT2", "0.156581583", "−2.672356579", ".007532056"], ["cg12494355", "TPM2", "0.095012775", "−2.660337122", ".007806247"], ["cg10843343", "KRT8", "5.522987956", "2.648437613", ".008086477"], ["cg22235258", "EHF", "2.970907821", "2.633435641", ".008452585"], ["cg00520135", "TPM1", "0.199663869", "−2.632332676", ".008480078"], ["cg19460095", "EHF", "2.88706523", "2.62182459", ".008746043"], ["cg17147440", "TPM1", "0.38112838", "−2.608256727", ".009100467"], ["cg26357344", "KRT8", "2.626134721", "2.58341772", ".00978268"], ["cg13107144", "TPM1", "0.080325594", "−2.567638984", ".010239373"], ["cg06398236", "DAPP1", "3.783262029", "2.507009355", ".012175749"], ["cg06997997", "MFAP4", "0.058274726", "−2.502867154", ".012319178"], ["cg03790745", "RCOR2", "0.002665687", "−2.480754698", ".013110456"], ["cg07814567", "DAPP1", "2.30196051", "2.478978727", ".013175916"], ["cg10403394", "TPM1", "0.231823345", "−2.390524206", ".01682434"], ["cg21083175", "RCOR2", "0.188494833", "−2.368506257", ".017860078"], ["cg03400060", "BHMT2", "0.228984691", "−2.360536791", ".018248508"], ["cg14260530", "AKNA", "0.162252883", "−2.333684214", ".019612263"], ["cg18560551", "EHF", "2.009472208", "2.329803583", ".019816535"], ["cg21867345", "ZKSCAN7", "2.078224581", "2.182145936", ".029098764"], ["cg13969788", "TPM2", "0.400926556", "−2.158779228", ".030867299"], ["cg14022090", "EHF", "2.242798579", "2.148000039", ".031713752"], ["cg08162426", "CPNE8", "2.345731899", "2.132073638", ".033000793"], ["cg22619810", "RCOR2", "0.015622716", "−2.130825555", ".033103516"], ["cg20324165", "KRT8", "2.762704434", "2.109031651", ".03494185"], ["cg13999433", "AKNA", "0.137520251", "−2.017220181", ".043672541"], ["cg02619205", "AKNA", "0.36559657", "−1.976424603", ".048106707"], ["cg01835489", "KRT8", "2.264564818", "1.964142113", ".049513614"]], "row_count": 39, "column_count": 5, "numeric_cells": 152, "header_rows": 1, "locator": "section[16]/table-wrap[1]#cam42665-tbl-0003"}}], "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": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We conducted the univariate Cox regression analysis to select prognostic MDGs with P < .05 as the threshold."}}, {"id": "method-2", "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"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["We obtained RNA‐seq data of transcriptome profiles of BCA from TCGA database (https://portal.gdc.cancer.gov/), including 414 tumor tissues and 10 normal tissues. We used edgeR package19 to normalize the raw data. Moreover, we utilized the tool of TCGA‐Assembler to download the DNA methylation data (419 BCA and corresponding 21 normal samples) based on the Illumina Infinium Human Methylation 450 platform, which detecting over 480 K human genome methylated sites. Limma package was applied to do the normalization.20"], "basis": "The paper names GSE13507 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": ["cox_ph"], "assets": ["source:pmid:31794632", "data:geo:GSE13507", "asset:table:pmid:31794632:1", "asset:table:pmid:31794632:2", "asset:table:pmid:31794632:3"], "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": "2026-10-31T18:17:16Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 21626, "completion_tokens": 3201, "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:31794632", "type": "paper", "label": "pmid:31794632"}, {"id": "source:pmid:31794632", "type": "manuscript", "label": "PMID 31794632 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31794632", "type": "paper", "label": "pmid:31794632"}, {"id": "source:pmid:31794632", "type": "manuscript", "label": "PMID 31794632 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31794632", "type": "extraction", "used": ["source:pmid:31794632"], "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:31794632", "parent_hash": "sha256:73b6700beca5f77826242a9a270fbd6bb68d618ed15518faa7021d4389ded41f", "fork_of": null, "generation": 7}, "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": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We conducted the univariate Cox regression analysis to select prognostic MDGs with P < .05 as the threshold."], "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":"2026-11-04T02:48:38+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}}}