{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31190871", "kind": "science-record", "revision": 7, "content_hash": "sha256:14f82c2b158fe41382998a8447c36ce6a0a959b40e52486e0bc31d593f8d30a0", "created_at": "2026-11-01T15:40:46Z", "updated_at": "2026-11-01T22:00:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of an individualized autophagy-clinical prognostic index in bladder cancer patients.", "doi": "10.2147/OTT.S197676", "pmid": "31190871", "authors": ["Shi-Shuo Wang", "Gang Chen", "Sheng-Hua Li", "Jin-Shu Pang", "Kai-Teng Cai", "Hai-Biao Yan", "Zhi-Guang Huang", "Rong-Quan He"], "journal": "OncoTargets and therapy", "year": 2019, "abstract": "Purpose: Autophagy is a major catabolic system by which eukaryotic cells undergo self-degradation of damaged, defective, or unwanted intracellular components. An abnormal autophagic level is implicated in the pathogenesis of multiple diseases, including cancers. The aim of this study is to explore the prognostic value of autophagy in bladder cancer (BC), which is a major cause of cancer-related death globally. Patients and methods: First, 27 differentially expressed autophagy-related genes (ARGs) were identified in BC patients based on The Cancer Genome Atlas (TCGA) database. Functional enrichment analyses hinted that autophagy may act in a tumor-suppressive role in the initiation of BC. Then, the Cox proportional hazard regression model were employed to identify three key prognostic ARGs (JUN, MYC, and ITGA3), which were related with overall survival (OS) significantly in BC. The three genes represented important clinical significance and prognostic value in BC. Then a prognostic index (PI) was constructed. Results: The PI was constructed based on the three genes, and significantly stratified BC patients into high- and low-risk groups in terms of OS (HR=1.610, 95% CI=1.200-2.160, P=0.002). PI remained as an independent prognostic factor in multivariate analyses (HR=2.355, 95% CI=1.483-3.739, P<0.001). When integrated with clinical characteristics of age and stage, an autophagy-clinical prognostic index (ACPI) was finally validated, which had improved performance in predicting OS of BC patients (HR=2.669, 95% CI=1.986-3.587, P<0.001). The ACPI was confirmed in datasets of GSE13507 (HR=7.389, 95% CI=3.645-14.980, P<0.001) and GSE31684 (HR=1.665, 95% CI=0.872-3.179, P=0.122). Conclusion: This study provides a potential prognostic signature for predicting prognosis of BC patients and molecular insights of autophagy in BC.", "claims": [{"id": "claim-method", "statement": "The Multivariate Cox proportional hazards regression model was used to construct the PI and ACPI model based on the factor correlated with survival.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31190871", "locator": "sections[6] \"Statistical analysis\" paragraph 2", "quote": "The Multivariate Cox proportional hazards regression model was used to construct the PI and ACPI model based on the factor correlated with survival."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA-seq data and clinical information of BC analyzed in this study can be downloaded from The Cancer Genome Atlas (TCGA). The microarray data of GSE13507, GSE31684, GSE76211, GSE2109, GSE7476, GSE30522, GSE31189, GSE37815, GSE52519, GSE65635, GSE37817, GSE100926, GSE24152, GSE19915 (GPL3883 and GPL5186), and GSE40355 can be acquired from the Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31190871", "locator": "sections[17] \"Data sharing statement\" paragraph 2", "quote": "The RNA-seq data and clinical information of BC analyzed in this study can be downloaded from The Cancer Genome Atlas (TCGA). The microarray data of GSE13507, GSE31684, GSE76211, GSE2109, GSE7476, GSE30522, GSE31189, GSE37815, GSE52519, GSE65635, GSE37817, GSE100926, GSE24152, GSE19915 (GPL3883 and GPL5186), and GSE40355 can be acquired from the Gene Expression Omnibus (GEO) database."}], "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:31190871"], "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:GSE100926"], "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:GSE100926"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31190871", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S197676", "sha256": "sha256:350118c4196f1e39974dfcc2a08c632a0bebed08671afe9abe49f401caceb215", "bytes": 40573, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S197676", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6526186", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100926", "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=GSE100926", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100926", "version": null, "note": "The RNA-seq data and clinical information of BC analyzed in this study can be downloaded from The Cancer Genome Atlas (TCGA). The microarray data of GSE13507, GSE31684, GSE76211, GSE2109, GSE7476, GSE30522, GSE31189, GSE37815, GSE52519, GSE65635, GSE37817, GSE100926, GSE24152, GSE19915 (GPL3883 and GPL5186), and GSE40355 can be acquired from the Gene Expression Omnibus (GEO) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq data and clinical information of BC analyzed in this study can be downloaded from The Cancer Genome Atlas (TCGA). 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"GSM138014", "GSM138015", "GSM138016", "GSM138017", "GSM138018", "GSM138019", "GSM138020", "GSM138021", "GSM138022", "GSM138023", "GSM138024", "GSM138025", "GSM138026", "GSM138027", "GSM138028", "GSM138029", "GSM138030", "GSM138031", "GSM138032", "GSM138033", "GSM138034", "GSM138035", "GSM138036", "GSM138037", "GSM138038", "GSM138039", "GSM138040", "GSM138041", "GSM138042", "GSM138043", "GSM138044", "GSM138045", "GSM138046", "GSM138047", "GSM138048", "GSM138049", "GSM138050", "GSM138051", "GSM138052", "GSM138053", "GSM138054", "GSM152564", "GSM152565", "GSM152566", "GSM152567", "GSM152568", "GSM152569", "GSM152570", "GSM152571", "GSM152572", "GSM152573", "GSM152574", "GSM152575", "GSM152576", "GSM152577", "GSM152578", "GSM152579", "GSM152580", "GSM152581", "GSM152582", "GSM152583", "GSM152584", "GSM152585", "GSM152586", "GSM152587", "GSM152588", "GSM152589", "GSM152590", "GSM152591", "GSM152592", "GSM152593", "GSM152594", "GSM152595", "GSM152596", "GSM152597", "GSM152598", "GSM152599", "GSM152600", "GSM152601", "GSM152602", "GSM152603", "GSM152604", "GSM152605", "GSM152606", "GSM152607", "GSM152608", "GSM152609", "GSM152610", "GSM152611", "GSM152612", "GSM152613", "GSM152614", "GSM152615", "GSM152616", "GSM152617", "GSM152618", "GSM152619", "GSM152620", "GSM152621", "GSM152622", "GSM152623", "GSM152624", "GSM152625", "GSM152626", "GSM152627", "GSM152628", "GSM152629", "GSM152630", "GSM152631", "GSM152632", "GSM152633", "GSM152634", "GSM152635", "GSM152636", "GSM152637", "GSM152638", "GSM152639", "GSM152640", "GSM152641", "GSM152642", "GSM152643", "GSM152644", "GSM152645", "GSM152646", "GSM152647", "GSM152648", "GSM152649", "GSM152650", "GSM152651", "GSM152652", "GSM152653", "GSM152654", "GSM152655", "GSM152656", "GSM152657", "GSM152658", "GSM152659", "GSM152660", "GSM152661", "GSM152662", "GSM152663", "GSM152664", "GSM152665", "GSM152666", "GSM152667", "GSM152668", "GSM152669", "GSM152670", "GSM152671", "GSM152672", "GSM152673", "GSM152674", "GSM152675", "GSM152676", 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"GSM179805", "GSM179806", "GSM179807", "GSM179808", "GSM179809", "GSM179810", "GSM179811", "GSM179812", "GSM179813", "GSM179814", "GSM179815", "GSM179816", "GSM179817", "GSM179818", "GSM179819", "GSM179820", "GSM179821", "GSM179822", "GSM179823", "GSM179824", "GSM179825", "GSM179826", "GSM179827", "GSM179828", "GSM179829", "GSM179830", "GSM179831", "GSM179832", "GSM179833", "GSM179834", "GSM179835", "GSM179836", "GSM179837", "GSM179838", "GSM179839", "GSM179840", "GSM179841", "GSM179842", "GSM179843", "GSM179844", "GSM179845", "GSM179846", "GSM179847", "GSM179848", "GSM179849", "GSM179850", "GSM179851", "GSM179852", "GSM179853", "GSM179854", "GSM179855", "GSM179856", "GSM179857", "GSM179858", "GSM179859", "GSM179860", "GSM179861", "GSM179862", "GSM179863", "GSM179864", "GSM179865", "GSM179866", "GSM179867", "GSM179868", "GSM179869", "GSM179870", "GSM179871", "GSM179872", "GSM179873", "GSM179874", "GSM179875", "GSM179876", "GSM179877", "GSM179878", "GSM179879", "GSM179880", "GSM179881", "GSM179882", "GSM179883", "GSM179884", "GSM179885", "GSM179886", "GSM179887", "GSM179888", "GSM179889", "GSM179890", "GSM179891", "GSM179892", "GSM179893", "GSM179894", "GSM179895", "GSM179896", "GSM179897", "GSM179898", "GSM179899", "GSM179900", "GSM179901", "GSM179902", "GSM179903", "GSM179904", "GSM179905", "GSM179906", "GSM179907", "GSM179908", "GSM179909", "GSM179910", "GSM179911", "GSM179912", "GSM179913", "GSM179914", "GSM179915", "GSM179916", "GSM179917", "GSM179918", "GSM179919", "GSM179920", "GSM179921", "GSM179922", "GSM179923", "GSM179924", "GSM179925", "GSM179926", "GSM179927", "GSM179928", "GSM179929", "GSM179930", "GSM179931", "GSM179932", "GSM179933", "GSM179934", "GSM179935", "GSM179936", "GSM179937", "GSM179938", "GSM179939", "GSM179940", "GSM179941", "GSM179942", "GSM179943", "GSM179944", "GSM179945", "GSM179946", "GSM179947", "GSM179948", "GSM179949", "GSM179950", "GSM179951", "GSM179952", "GSM179953", "GSM179954", "GSM179955", "GSM179956", "GSM179957", "GSM203622", 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"GSM203777", "GSM203778", "GSM203779", "GSM203780", "GSM203781", "GSM203782", "GSM203783", "GSM203784", "GSM203785", "GSM203786", "GSM203787", "GSM203788", "GSM203789", "GSM203790", "GSM203791", "GSM203792", "GSM203793", "GSM203794", "GSM203795", "GSM203796", "GSM203797", "GSM203798", "GSM203799", "GSM203800", "GSM203801", "GSM231868", "GSM231869", "GSM231870", "GSM231871", "GSM231872", "GSM231873", "GSM231874", "GSM231875", "GSM231876", "GSM231877", "GSM231878", "GSM231879", "GSM231880", "GSM231881", "GSM231882", "GSM231883", "GSM231884", "GSM231885", "GSM231886", "GSM231887", "GSM231888", "GSM231889", "GSM231890", "GSM231891", "GSM231892", "GSM231893", "GSM231894", "GSM231895", "GSM231896", "GSM231897", "GSM231898", "GSM231899", "GSM231900", "GSM231901", "GSM231902", "GSM231903", "GSM231904", "GSM231905", "GSM231906", "GSM231907", "GSM231908", "GSM231909", "GSM231910", "GSM231911", "GSM231912", "GSM231913", "GSM231914", "GSM231915", "GSM231916", "GSM231917", "GSM231918", "GSM231919", "GSM231920", "GSM231921", "GSM231922", "GSM231923", "GSM231924", "GSM231925", "GSM231926", "GSM231927", "GSM231928", "GSM231929", "GSM231930", "GSM231931", "GSM231932", "GSM231933", "GSM231934", "GSM231935", "GSM231936", "GSM231937", "GSM231938", "GSM231939", "GSM231940", "GSM231941", "GSM231942", "GSM231943", "GSM231944", "GSM231945", "GSM231946", "GSM231947", "GSM231948", "GSM231949", "GSM231950", "GSM231951", "GSM231952", "GSM231953", "GSM231954", "GSM231955", "GSM231956", "GSM231957", "GSM231958", "GSM231959", "GSM231960", "GSM231961", "GSM231962", "GSM231963", "GSM231964", "GSM231965", "GSM231966", "GSM231967", "GSM231968", "GSM231969", "GSM231970", "GSM231971", "GSM231972", "GSM231973", "GSM231974", "GSM231975", "GSM231976", "GSM231977", "GSM231978", "GSM231979", "GSM231980", "GSM231981", "GSM231982", "GSM231983", "GSM231984", "GSM231985", "GSM231986", "GSM231987", "GSM231988", "GSM231989", "GSM231990", "GSM231991", "GSM231992", "GSM277677", "GSM277678", "GSM277679", "GSM277680", "GSM277681", "GSM277682", "GSM277683", "GSM277684", "GSM277685", "GSM277686", "GSM277687", "GSM277688", "GSM277689", "GSM277690", "GSM277691", "GSM277692", "GSM277693", "GSM277694", "GSM277695", "GSM277696", "GSM277697", "GSM277698", "GSM277699", "GSM277700", "GSM277701", "GSM277702", "GSM277703", "GSM277704", "GSM277705", "GSM277706", "GSM277707", "GSM277708", "GSM277709", "GSM277710", "GSM277711", "GSM277712", "GSM277713", "GSM277714", "GSM277715", "GSM277716", "GSM277717", "GSM277718", "GSM277719", "GSM277720", "GSM277721", "GSM277722", "GSM277723", "GSM277724", "GSM277725", "GSM277726", "GSM277727", "GSM277728", "GSM277729", "GSM277730", "GSM277731", "GSM277732", "GSM277733", "GSM277734", "GSM277735", "GSM277736", "GSM277737", "GSM277738", "GSM301651", "GSM301652", "GSM301653", "GSM301654", "GSM301655", "GSM301656", "GSM301657", "GSM301658", "GSM301659", "GSM301660", "GSM301661", "GSM301662", "GSM301663", "GSM301664", "GSM301665", "GSM301666", "GSM301667", "GSM301668", "GSM301669", 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The microarray data of GSE13507, GSE31684, GSE76211, GSE2109, GSE7476, GSE30522, GSE31189, GSE37815, GSE52519, GSE65635, GSE37817, GSE100926, GSE24152, GSE19915 (GPL3883 and GPL5186), and GSE40355 can be acquired from the Gene Expression Omnibus (GEO) database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1976573", "GSM1976574", "GSM1976575", "GSM1976577", "GSM1976579", "GSM1976580"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "17586", "taxon": "Homo sapiens", "title": "mRNA Expression data from bladder cancer and normal bladder tissue", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31190871:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e960820ce9a6f3142fbdb0dec88b5b81ffd43104040007f915439492b3b6088b", "bytes": 4950, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T0001", "version": null, "note": "GO and KEGG analysis of differentially expressed autophagy-related genes", "structure": {"pmcid": "PMC6526186", "section_index": 9, "section_title": "Functional annotation of the differentially expressed ARGs", "row_count": 41, "column_count": 5}, "table": {"label": "Table 1", "caption": "GO and KEGG analysis of differentially expressed autophagy-related genes", "rows": [["Category", "ID", "Term", "P-value", "Genes"], ["Biological Process", "GO:0042493", "Response to drug", "4.44E−06", "FOS, CDKN1A, JUN, BCL2, ITGA3, MYC, TP73"], ["Biological Process", "GO:0010332", "Response to gamma radiation", "1.27E−05", "CCL2, BCL2, MYC, TP73"], ["Biological Process", "GO:0006915", "Apoptotic process", "1.36E−05", "DLC1, EVA1A, CDKN2A, CXCR4, BCL2, BIRC5, PPP1R15A, TP73"], ["Biological Process", "GO:0007346", "Regulation of mitotic cell cycle", "2.78E−05", "CDKN1A, BIRC5, MYC, TP73"], ["Biological Process", "GO:0043524", "Negative regulation of neuron apoptotic process", "4.06E−05", "CCL2, JUN, BCL2, BIRC5, TP73"], ["Biological Process", "GO:0007050", "Cell cycle arrest", "5.25E−05", "CDKN1A, CDKN2A, PPP1R15A, MYC, TP73"], ["Biological Process", "GO:0006974", "Cellular response to DNA damage stimulus", "2.36E−04", "CDKN1A, BCL2, PPP1R15A, MYC, TP73"], ["Biological Process", "GO:0001836", "Release of cytochrome c from mitochondria", "5.28E−04", "BID, JUN, BCL2"], ["Biological Process", "GO:0045893", "Positive regulation of transcription, DNA-templated", "8.50E−04", "FOS, CDKN2A, JUN, MYC, TP53INP2, TP73"], ["Biological Process", "GO:1900740", "Positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway", "9.02E−04", "BID, BCL2, TP73"], ["Cellular Component", "GO:0005829", "Cytosol", "3.94E−06", "BID, DLC1, NAMPT, GABARAPL1, BIRC5, TP73, FOS, CDKN1A, EIF4EBP1, CDKN2A, JUN, BCL2, BAG3, MYC, PPP1R15A, TP53INP2"], ["Cellular Component", "GO:0043234", "Protein complex", "0.002235", "EIF4EBP1, CDKN1A, CDKN2A, MYC, ITPR1"], ["Cellular Component", "GO:0005739", "Mitochondrion", "0.007959", "BID, GABARAPL1, CDKN2A, BCL2, PPP1R15A, MYC, TP73"], ["Cellular Component", "GO:0005654", "Nucleoplasm", "0.008942", "NAMPT, FOS, EIF4EBP1, CDKN1A, CDKN2A, JUN, HSPB8, BIRC5, MYC, TP73"], ["Cellular Component", "GO:0005741", "Mitochondrial outer membrane", "0.017612", "BID, BCL2, PPP1R15A"], ["Cellular Component", "GO:0030054", "Cell junction", "0.024203", "NAMPT, CXCR4, ITGB4, TP73"], ["Cellular Component", "GO:0005783", "Endoplasmic reticulum", "0.025005", "FOS, GABARAPL1, BCL2, PPP1R15A, ITPR1"], ["Cellular Component", "GO:0005667", "Transcription factor complex", "0.028532", "FOS, JUN, TP73"], ["Cellular Component", "GO:0005794", "Golgi apparatus", "0.028578", "GABARAPL1, HSPB8, RGS19, PPP1R15A"], ["Cellular Component", "GO:0008305", "Integrin complex", "0.036412", "ITGB4, ITGA3"], ["Cellular Component", "GO:0005515", "Protein binding", "3.97E−05", "BID, DLC1, NAMPT, GABARAPL1, ITGB4, RGS19, BIRC5, ITGA3, CX3CL1, TP73, ITPR1, FOS, CDKN1A, EIF4EBP1, CDKN2A, CXCR4, JUN, HSPB8, BCL2, BAG3, MYC, PPP1R15A, TP53INP2"], ["Molecular Function", "GO:0008134", "Transcription factor binding", "4.25E−05", "FOS, CDKN2A, JUN, BCL2, MYC, TP73"], ["Molecular Function", "GO:0031625", "Ubiquitin protein ligase binding", "6.65E−04", "BID, GABARAPL1, CDKN1A, CXCR4, BCL2"], ["Molecular Function", "GO:0046982", "Protein heterodimerization activity", "0.003898", "FOS, JUN, BCL2, BIRC5, ITGA3"], ["Molecular Function", "GO:0001077", "Transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding", "0.004395", "FOS, JUN, MYC, TP73"], ["Molecular Function", "GO:0043565", "Sequence-specific DNA binding", "0.005716", "FOS, JUN, BCL2, MYC, TP73"], ["Molecular Function", "GO:0000978", "RNA polymerase II core promoter proximal region sequence-specific DNA binding", "0.013453", "FOS, JUN, MYC, TP73"], ["Molecular Function", "GO:0004861", "Cyclin-dependent protein serine/threonine kinase inhibitor activity", "0.015533", "CDKN1A, CDKN2A"], ["Molecular Function", "GO:0019901", "Protein kinase binding", "0.015684", "CDKN2A, RGS19, PPP1R15A, TP73"], ["Molecular Function", "GO:0042802", "Identical protein binding", "0.020127", "JUN, HSPB8, BCL2, BIRC5, TP73"], ["KEGG PATHWAY", "hsa05200", "Pathways in cancer", "3.16E−07", "BID, FOS, CDKN1A, CDKN2A, CXCR4, JUN, BCL2, BIRC5, ITGA3, MYC"], ["KEGG PATHWAY", "hsa05210", "Colorectal cancer", "2.06E−05", "FOS, JUN, BCL2, BIRC5, MYC"], ["KEGG PATHWAY", "hsa05161", "Hepatitis B", "3.48E−05", "FOS, CDKN1A, JUN, BCL2, BIRC5, MYC"], ["KEGG PATHWAY", "hsa04012", "ErbB signaling pathway", "7.87E−05", "EIF4EBP1, CDKN1A, JUN, NRG2, MYC"], ["KEGG PATHWAY", "hsa04115", "p53 signaling pathway", "7.56E−04", "BID, CDKN1A, CDKN2A, TP73"], ["KEGG PATHWAY", "hsa04151", "PI3K-Akt signaling pathway", "0.001961", "EIF4EBP1, CDKN1A, BCL2, ITGB4, ITGA3, MYC"], ["KEGG PATHWAY", "hsa04668", "TNF signaling pathway", "0.002843", "FOS, CCL2, JUN, CX3CL1"], ["KEGG PATHWAY", "hsa05166", "HTLV-I infection", "0.004594", "FOS, CDKN1A, CDKN2A, JUN, MYC"], ["KEGG PATHWAY", "hsa05219", "Bladder cancer", "0.00551", "CDKN1A, CDKN2A, MYC"], ["KEGG PATHWAY", "hsa04921", "Oxytocin signaling pathway", "0.008685", "FOS, CDKN1A, JUN, ITPR1"]], "row_count": 41, "column_count": 5, "numeric_cells": 106, "header_rows": 1, "locator": "section[9]/table-wrap[1]#T0001"}}, {"id": "asset:table:pmid:31190871:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:85290b1004f06323d417f99574c28833ca5b20ce382eb206080b666856c474f4", "bytes": 4540, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T0002", "version": null, "note": "Expression and Cox regression analysis data of the prognosis-related ARGs in bladder cancer by TCGA", "structure": {"pmcid": "PMC6526186", "section_index": 10, "section_title": "Identification of prognostic ARGs", "row_count": 56, "column_count": 10}, "table": {"label": "Table 2", "caption": "Expression and Cox regression analysis data of the prognosis-related ARGs in bladder cancer by TCGA", "rows": [["Gene", "Expression", "Univariate Cox", "Multivariate Cox"], ["mean±SD", "P-value", "HR", "z", "P-value", "HR", "z", "P-value"], ["JUN", "Tumor", "13.002773±1.164031", "<0.0001", "1.198762", "2.651598", "0.008011", "1.1786", "2.38", "0.017"], ["", "Non-tumor", "15.027896±1.185059", "", "", "", "", "", "", ""], ["MYC", "Tumor", "11.541411±1.554496", "<0.0001", "1.14059", "2.606545", "0.009146", "1.1682", "2.97", "0.003"], ["", "Non-tumor", "13.287664±1.265550", "", "", "", "", "", "", ""], ["ITGA3", "Tumor", "13.822128±1.515658", "<0.0001", "0.907077", "−2.0139", "0.04402", "−0.1505", "−2.97", "0.003"], ["", "Non-tumor", "12.975430±1.091134", "", "", "", "", "", "", ""], ["NAMPT", "Tumor", "12.330813±1.009040", "<0.0001", "1.172207", "2.001379", "0.045352", "", "", "0.340"], ["", "Non-tumor", "13.308780±1.459465", "", "", "", "", "", "", ""], ["FOS", "Tumor", "13.343147±1.608937", "<0.0001", "1.063323", "1.267733", "0.204893", "", "", ""], ["", "Non-tumor", "16.672991±1.404332", "", "", "", "", "", "", ""], ["HSPB8", "Tumor", "10.106659±2.154647", "<0.0001", "1.068919", "1.911278", "0.055969", "", "", ""], ["", "Non-tumor", "13.749171±1.702493", "", "", "", "", "", "", ""], ["CDKN1A", "Tumor", "13.124746±1.128535", "<0.0001", "1.01594", "0.22579", "0.821364", "", "", ""], ["", "Non-tumor", "14.389922±1.347070", "", "", "", "", "", "", ""], ["ITPR1", "Tumor", "9.5318665±1.169013", "<0.0001", "0.997873", "−0.03415", "0.972754", "", "", ""], ["", "Non-tumor", "11.929274±1.585768", "", "", "", "", "", "", ""], ["TP53INP2", "Tumor", "10.462387±0.976958", "<0.0001", "1.119264", "1.518161", "0.128974", "", "", ""], ["", "Non-tumor", "12.653637±1.109542", "", "", "", "", "", "", ""], ["BIRC5", "Tumor", "11.387251±1.094559", "<0.0001", "1.06901", "0.897696", "0.369347", "", "", ""], ["", "Non-tumor", "7.9468232±2.565110", "", "", "", "", "", "", ""], ["PPP1R15A", "Tumor", "12.441886±0.891543", "<0.0001", "0.940067", "−0.71379", "0.475356", "", "", ""], ["", "Non-tumor", "13.738993±1.001618", "", "", "", "", "", "", ""], ["DLC1", "Tumor", "9.5131164±1.257221", "<0.0001", "1.021996", "0.347978", "0.727857", "", "", ""], ["", "Non-tumor", "11.242183±0.995269", "", "", "", "", "", "", ""], ["BAG3", "Tumor", "11.719572±0.731981", "<0.0001", "1.192655", "1.702932", "0.088581", "", "", ""], ["", "Non-tumor", "12.704785±1.108736", "", "", "", "", "", "", ""], ["GABARAPL1", "Tumor", "11.058632±0.792235", "<0.0001", "1.051224", "0.525272", "0.599394", "", "", ""], ["", "Non-tumor", "12.255963±0.614109", "", "", "", "", "", "", ""], ["BCL2", "Tumor", "8.3027604±1.178505", "<0.0001", "1.051513", "0.768008", "0.442482", "", "", ""], ["", "Non-tumor", "10.256868±0.425816", "", "", "", "", "", "", ""], ["CDKN2A", "Tumor", "8.9951212±3.453185", "<0.0001", "0.990449", "−0.44257", "0.658076", "", "", ""], ["", "Non-tumor", "6.6235955±1.685343", "", "", "", "", "", "", ""], ["CCL2", "Tumor", "9.0438964±1.821760", "<0.0001", "1.053817", "1.273601", "0.202805", "", "", ""], ["", "Non-tumor", "11.704824±2.040782", "", "", "", "", "", "", ""], ["PRKN", "Tumor", "5.2978598±1.521700", "<0.0001", "1.009973", "0.201647", "0.840193", "", "", ""], ["", "Non-tumor", "8.1483213±1.213423", "", "", "", "", "", "", ""], ["BID", "Tumor", "11.340986±0.737984", "<0.0001", "0.839371", "−1.70367", "0.088442", "", "", ""], ["", "Non-tumor", "10.105586±0.651137", "", "", "", "", "", "", ""], ["EVA1A", "Tumor", "6.5437907±2.147278", "<0.0001", "1.057202", "1.528728", "0.126332", "", "", ""], ["", "Non-tumor", "3.8921911±1.267249", "", "", "", "", "", "", ""], ["CXCR4", "Tumor", "10.259886±1.380760", "<0.0001", "1.013263", "0.261675", "0.793572", "", "", ""], ["", "Non-tumor", "11.447608±1.958345", "", "", "", "", "", "", ""], ["NRG2", "Tumor", "4.7761532±2.145474", "<0.0001", "0.985697", "−0.43265", "0.665266", "", "", ""], ["", "Non-tumor", "7.9643803±1.000720", "", "", "", "", "", "", ""], ["TP73", "Tumor", "7.9164301±2.009466", "<0.0001", "0.984879", "−0.3943", "0.69336", "", "", ""], ["", "Non-tumor", "5.9146373±2.363484", "", "", "", "", "", "", ""], ["RGS19", "Tumor", "9.9259644±0.729683", "<0.0001", "1.143028", "1.313883", "0.188886", "", "", ""], ["", "Non-tumor", "8.6949825±0.978522", "", "", "", "", "", "", ""], ["EIF4EBP1", "Tumor", "11.427944±1.081142", "<0.0001", "1.046433", "0.666103", "0.505345", "", "", ""], ["", "Non-tumor", "9.8783883±0.927159", "", "", "", "", "", "", ""], ["CX3CL1", "Tumor", "9.7520038±1.782426", "<0.0001", "1.034169", "0.77976", "0.435532", "", "", ""], ["", "Non-tumor", "12.084799±0.955857", "", "", "", "", "", "", ""], ["ITGB4", "Tumor", "14.253622±1.551662", "<0.0001", "0.936675", "−1.33788", "0.180934", "", "", ""], ["", "Non-tumor", "13.188612±1.541228", "", "", "", "", "", "", ""]], "row_count": 56, "column_count": 10, "numeric_cells": 176, "header_rows": 2, "locator": "section[10]/table-wrap[1]#T0002"}}, {"id": "asset:table:pmid:31190871:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8455598ce6b03c89b05ae2856fd379ace37272ce14d02e4cbd6e5e3718499832", "bytes": 2514, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#T0003", "version": null, "note": "Relationships between three key prognostic genes expression and clinical parameters in bladder cancer by TCGA", "structure": {"pmcid": "PMC6526186", "section_index": 10, "section_title": "Identification of prognostic ARGs", "row_count": 22, "column_count": 12}, "table": {"label": "Table 3", "caption": "Relationships between three key prognostic genes expression and clinical parameters in bladder cancer by TCGA", "rows": [["Parameters", "N", "JUN expression value", "MYC expression value", "ITGA3 expression value"], ["M±SD", "t value", "P-value", "M±SD", "t value", "P-value", "M±SD", "t value", "P-value"], ["Tissues", "Tumor", "414", "13.0028±1.1640", "−7.410", "<0.001", "11.5414±1.5545", "−4.822", "<0.001", "13.8221±1.5157", "2.405", "0.017"], ["Non-tumor", "19", "15.0279±1.1851", "13.2877±1.2655", "12.9754±1.0911"], ["Age", "≥60", "321", "13.0359±1.1327", "1.076", "0.150", "11.6119±1.5304", "1.571", "0.117", "13.7787±1.5272", "−1.665", "0.097"], ["<60", "87", "12.8852±1.2530", "11.3177±1.6171", "14.0830±1.4561"], ["Gender", "Male", "301", "12.9868±1.1674", "−0.495", "0.621", "11.4625±1.5666", "−1.898", "0.058", "13.7850±1.5661", "−1.311", "0.191"], ["Female", "107", "13.0515±1.1410", "11.7930±1.4901", "14.0084±1.3574"], ["Subtype", "Non-papillary", "271", "13.1979±1.0811", "4.903", "<0.001", "11.7343±1.5708", "3.405", "0.001", "13.7762±1.5897", "−1.492", "0.136"], ["Papillary", "132", "12.6091±1.2284", "11.1787±1.4654", "14.0137±1.2921"], ["Tumor status", "With tumor", "151", "13.0248±1.0119", "0.459", "0.647", "11.6697±1.5948", "1.351", "0.177", "13.7276±1.5787", "1.763", "0.079"], ["Tumor free", "201", "12.9720±1.2459", "11.4571±1.4702", "13.9996±1.4314"], ["Histological grade", "High grade", "384", "13.0359±1.1529", "2.143", "0.033", "11.5759±1.5844", "3.002", "0.005", "13.7990±1.5338", "−6.996", "<0.001"], ["Low grade", "21", "12.4819±1.1653", "11.0637±0.6886", "14.8231±0.5669"], ["Pathologic stage", "Ⅲ～Ⅳ", "274", "13.1826±1.0448", "4.206", "<0.001", "11.6576±1.4617", "1.944", "0.053", "13.7353±1.5386", "−2.136", "0.033"], ["I~II", "132", "12.6367±1.3030", "11.3387±1.7148", "14.0770±1.4496"], ["T stage", "T3–T4", "252", "13.1958±1.0249", "3.064", "0.002", "11.6811±1.4423", "1.643", "0.101", "13.7290±1.5227", "−2.684", "0.008"], ["T1–T2", "123", "12.8322±1.1819", "11.4088±1.6306", "14.1726±1.4599"], ["N stage", "N1–3", "129", "13.1086±0.9329", "1.265", "0.207", "11.4309±1.4607", "−1.517", "0.130", "13.6208±1.4944", "−2.427", "0.016"], ["N0", "237", "12.9643±1.2176", "11.6798±1.5195", "14.0205±1.5112"], ["M stage", "M1", "11", "12.8009±1.0016", "−0.191", "0.849", "11.9098±1.8601", "1.245", "0.215", "13.5755±1.3148", "−0.792", "0.429"], ["M0", "196", "12.8728±1.2223", "11.3199±1.5104", "13.9395±1.4919"]], "row_count": 22, "column_count": 12, "numeric_cells": 143, "header_rows": 2, "locator": "section[10]/table-wrap[2]#T0003"}}, {"id": "asset:table:pmid:31190871:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c2ff2bc776f8eab5d91fa372e4b3e687cf08c78e055b8ea7f2cf95531fabe6bc", "bytes": 842, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T0004", "version": null, "note": "Univariate and multivariate analyses of OS in bladder cancer patients of TCGA", "structure": {"pmcid": "PMC6526186", "section_index": 11, "section_title": "Construction and definition of the PI", "row_count": 8, "column_count": 5}, "table": {"label": "Table 4", "caption": "Univariate and multivariate analyses of OS in bladder cancer patients of TCGA", "rows": [["Variables", "Univariate analysis", "Multivariate analysis"], ["Hazard ratio (95%CI)", "P-value", "Hazard ratio (95% CI)", "P-value"], ["Age", "1.033 (1.017–1.049)", "<0.001", "1.029 (1.014–1.045)", "<0.001"], ["Gender", "0.872 (0.631–1.203)", "0.404", "0.818 (0.588–1.139)", "0.235"], ["Subtype", "1.458 (1.030–2.065)", "0.033", "1.084 (0.756–1.553)", "0.661"], ["Pathologic stage", "1.707 (1.412–2.065)", "<0.001", "1.617 (1.321–1.978)", "<0.001"], ["Histologic grade", "2.968 (0.734–11.995)", "0.127", "0.931 (0.221–3.918)", "0.922"], ["Prognostic index", "2.717 (1.764–4.184)", "<0.001", "2.355 (1.483–3.739)", "<0.001"]], "row_count": 8, "column_count": 5, "numeric_cells": 26, "header_rows": 2, "locator": "section[11]/table-wrap[1]#T0004"}}], "gaps": ["asset:data:geo:GSE100926 not downloaded", "asset:data:geo:GSE100926 licence not read", "asset:data:geo:GSE13507 not downloaded", "asset:data:geo:GSE13507 licence not read", "asset:data:geo:GSE2109 not downloaded", "asset:data:geo:GSE2109 licence not read", "asset:data:geo:GSE24152 not downloaded", "asset:data:geo:GSE24152 licence not read", "asset:data:geo:GSE30522 not downloaded", "asset:data:geo:GSE30522 licence not read", "asset:data:geo:GSE31189 not downloaded", "asset:data:geo:GSE31189 licence not read", "asset:data:geo:GSE31684 not downloaded", "asset:data:geo:GSE31684 licence not read", "asset:data:geo:GSE37815 not downloaded", "asset:data:geo:GSE37815 licence not read", "asset:data:geo:GSE37817 not downloaded", "asset:data:geo:GSE37817 licence not read", "asset:data:geo:GSE40355 not downloaded", "asset:data:geo:GSE40355 licence not read", "asset:data:geo:GSE52519 not downloaded", "asset:data:geo:GSE52519 licence not read", "asset:data:geo:GSE65635 not downloaded", "asset:data:geo:GSE65635 licence not read", "asset:data:geo:GSE7476 not downloaded", "asset:data:geo:GSE7476 licence not read", "asset:data:geo:GSE76211 not downloaded", "asset:data:geo:GSE76211 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": "The Multivariate Cox proportional hazards regression model was used to construct the PI and ACPI model based on the factor correlated with survival."}}, {"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": 0.8, "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": ["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", "GSE31684", "GSE76211", "GSE2109", "GSE7476", "GSE30522", "GSE31189", "GSE37815", "GSE52519", "GSE65635", "GSE37817", "GSE100926", "GSE24152", "GSE19915 (GPL3883 and GPL5186)", "GSE40355"], "resolved_accessions": ["GSE13507", "GSE31684", "GSE76211", "GSE2109", "GSE7476", "GSE30522", "GSE31189", "GSE37815", "GSE52519", "GSE65635", "GSE37817", "GSE100926", "GSE24152", "GSE40355"], "statements": ["The RNA-seq data and clinical information of BC analyzed in this study can be downloaded from The Cancer Genome Atlas (TCGA). The microarray data of GSE13507, GSE31684, GSE76211, GSE2109, GSE7476, GSE30522, GSE31189, GSE37815, GSE52519, GSE65635, GSE37817, GSE100926, GSE24152, GSE19915 (GPL3883 and GPL5186), and GSE40355 can be acquired from the Gene Expression Omnibus (GEO) database."], "basis": "The paper names GSE13507, GSE31684, GSE76211, GSE2109, GSE7476, GSE30522, GSE31189, GSE37815, GSE52519, GSE65635, GSE37817, GSE100926, GSE24152, GSE40355 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:31190871", "data:geo:GSE100926", "asset:table:pmid:31190871:1", "asset:table:pmid:31190871:2", "asset:table:pmid:31190871:3", "asset:table:pmid:31190871:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100926"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34891, "completion_tokens": 3754, "cached_tokens": 648}}, "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:31190871", "type": "paper", "label": "pmid:31190871"}, {"id": "source:pmid:31190871", "type": "manuscript", "label": "PMID 31190871 full text"}, {"id": "data:geo:GSE100926", "type": "dataset", "label": "GEO GSE100926"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31190871", "type": "paper", "label": "pmid:31190871"}, {"id": "source:pmid:31190871", "type": "manuscript", "label": "PMID 31190871 full text"}, {"id": "data:geo:GSE100926", "type": "dataset", "label": "GEO GSE100926"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31190871", "type": "extraction", "used": ["source:pmid:31190871"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100926", "type": "accession_resolution", "used": ["data:geo:GSE100926"], "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:31190871", "parent_hash": "sha256:dfe5813d55e32f2ac36170f078df49a10e3d0c53dc7c2fbb07481797dc3500de", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE100926 licence not read", "asset:data:geo:GSE100926 not downloaded", "asset:data:geo:GSE13507 licence not read", "asset:data:geo:GSE13507 not downloaded", "asset:data:geo:GSE2109 licence not read", "asset:data:geo:GSE2109 not downloaded", "asset:data:geo:GSE24152 licence not read", "asset:data:geo:GSE24152 not downloaded", "asset:data:geo:GSE30522 licence not read", "asset:data:geo:GSE30522 not downloaded", "asset:data:geo:GSE31189 licence not read", "asset:data:geo:GSE31189 not downloaded", "asset:data:geo:GSE31684 licence not read", "asset:data:geo:GSE31684 not downloaded", "asset:data:geo:GSE37815 licence not read", "asset:data:geo:GSE37815 not downloaded", "asset:data:geo:GSE37817 licence not read", "asset:data:geo:GSE37817 not downloaded", "asset:data:geo:GSE40355 licence not read", "asset:data:geo:GSE40355 not downloaded", "asset:data:geo:GSE52519 licence not read", "asset:data:geo:GSE52519 not downloaded", "asset:data:geo:GSE65635 licence not read", "asset:data:geo:GSE65635 not downloaded", "asset:data:geo:GSE7476 licence not read", "asset:data:geo:GSE7476 not downloaded", "asset:data:geo:GSE76211 licence not read", "asset:data:geo:GSE76211 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": ["The Multivariate Cox proportional hazards regression model was used to construct the PI and ACPI model based on the factor correlated with survival."], "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":"2026-11-04T02:54:59+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}}}