{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40263537", "kind": "science-record", "revision": 3, "content_hash": "sha256:ffc63d2cbd0eb37100a51a20a33012f54f2c53262bb3703b30e9cf2e86606245", "created_at": "2026-11-01T20:30:25Z", "updated_at": "2026-11-01T22:13:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "To establish and validate autophagy related biomarkers for the diagnosis of IgA nephropathy.", "doi": "10.1038/s41598-025-98591-y", "pmid": "40263537", "authors": ["Sijia Ma", "Chao Wang", "Jing Liu", "Hangyu Duan", "Xiaoxin Tian", "Shijie Xu", "Yu Zhang"], "journal": "Scientific reports", "year": 2025, "abstract": "IgA nephropathy (IgAN) is one of the most common immune-related primary glomerular diseases. The pathological mechanism of this disease is complex, and the specific pathogenesis is still unclear. To obtain a comprehensive understanding of its molecular mechanism and to provide new perspectives regarding the detection and treatment of the disease, this study investigated the role of immune cells in IgAN, as well as the role of autophagy-related biomarkers in IgAN development. The original datasets GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857 were downloaded from Gene Expression Omnibus (GEO) and were further integrated and analyzed. The differentially expressed genes (DEGs) between IgAN and healthy control (HC) group were identified by the \"limma\" R package. The gene ontology (GO) function, Kyoto Encyclopedia of Genes and Genome (KEGG) pathway, GeneSet Enrichment Analysis (GSEA) and DisGeNet enrichment were adopted to analyze the genes from the intersection of DEGs. The hub genes were screened by the square least absolute shrinkage and selection operator (LASSO) and cross validation. Immune cell infiltration was analyzed using CIBERSORT. The correlation between hub genes and infiltrating immune cells was calculated by R software. For the purpose of exploring the value of hub genes for diagnosing IgAN, a receiver operating characteristic (ROC) curve was constructed. Finally, Real-time quantitative polymerase chain reaction (qRT-PCR) was used to verify the relative mRNA level of the AT-DEGs. 12 DEGs were screened out. Enrichment analysis revealed that autophagy-related DEGs (AT-DEGs) were mainly related to intrinsic apoptotic signaling pathway, cellular response to external stimulus, transcription repressor complex and other cellular functions, KEGG pathways enriched by AT-DEGs mainly included biological metabolic pathways related to autophagy, while DisGeNET analysis showed that these AT-DEGs were mainly related to immunological diseases. The optimal six hub genes were obtained by lasso analysis as potential biomarkers for IgAN. ROC curve analysis showed that 4 of the 6 HUB genes had great diagnostic value. Immune infiltration results showed B cells memory, macrophages M2, NK cells activated, T cells CD4+ memory resting, and monocytes are the predominant immune cells with the development of IgAN. The qRT-PCR results showed that, compared to the NC group, SIRT1 mRNA expression in PBMCs from IgAN patients was significantly reduced, while BAG3, CDKN1A, and FOS mRNA levels were markedly elevated. SIRT1, BAG3, COKN1A and FOS can be considered as effective biomarkers related to autophagy for the diagnosis of IgAN. These findings suggest some potential new serum biomarkers for IgAN diagnosis.", "claims": [{"id": "claim-method", "statement": "The hub genes were screened by the square least absolute shrinkage and selection operator (LASSO) and cross validation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40263537", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The hub genes were screened by the square least absolute shrinkage and selection operator (LASSO) and cross validation."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40263537", "locator": "sections[27] \"notes\" paragraph 1", "quote": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The AT-DEGs diagnostic risk-score model achieved an AUC of 0.994 in the training dataset and 0.856 in the validation dataset.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40263537", "locator": "sections[17] \"Evaluation and validation of AT-DEGs related diagnostic model\" paragraph 2", "quote": "The area under the AUC curve of the riskscore of the training dataset was 0.994, indicating that the model had a high accuracy rate (Fig. 6A)."}, {"asset": "source:pmid:40263537", "locator": "sections[17] \"Evaluation and validation of AT-DEGs related diagnostic model\" paragraph 2", "quote": "Then the ROC curve of the validation dataset was made, and the AUC area of riskscore was 0.856, which confirmed that the diagnostic model of AT-DEGs had a high degree of prediction accuracy (Fig. 6B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The AT-DEGs diagnostic risk-score model achieved an AUC of 0.994 in the training dataset and 0.856 in the validation dataset.", "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:40263537"], "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:GSE115857"], "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:GSE115857"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40263537", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-98591-y", "sha256": "sha256:365e7daebdf2705da626b5682306b24392905a1c4c70b3f5929899a4dc8bb770", "bytes": 35969, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-98591-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12015508", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE115857", "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=GSE115857", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE115857", "version": null, "note": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3191893", "GSM3191894", "GSM3191895", "GSM3191896", "GSM3191897", "GSM3191898", "GSM3191899", "GSM3191900", "GSM3191901", "GSM3191902", "GSM3191903", "GSM3191904", "GSM3191905", "GSM3191906", "GSM3191907", "GSM3191908", "GSM3191909", "GSM3191910", "GSM3191911", "GSM3191912", "GSM3191913", "GSM3191914", "GSM3191915", "GSM3191916", "GSM3191917", "GSM3191918", "GSM3191919", "GSM3191920", "GSM3191921", "GSM3191922", "GSM3191923", "GSM3191924", "GSM3191925", "GSM3191926", "GSM3191927", "GSM3191928", "GSM3191929", "GSM3191930", "GSM3191931", "GSM3191932", "GSM3191933", "GSM3191934", "GSM3191935", "GSM3191936", "GSM3191937", "GSM3191938", "GSM3191939", "GSM3191940", "GSM3191941", "GSM3191942", "GSM3191943", "GSM3191944", "GSM3191945", "GSM3191946", "GSM3191947", "GSM3191948", "GSM3191949", "GSM3191950", "GSM3191951", "GSM3191952", "GSM3191953", "GSM3191954", "GSM3191955", "GSM3191956", "GSM3191957", "GSM3191958", "GSM3191959", "GSM3191960", "GSM3191961", "GSM3191962", "GSM3191963", "GSM3191964", "GSM3191965", "GSM3191966", "GSM3191967", "GSM3191968", "GSM3191969", "GSM3191970", "GSM3191971", "GSM3191972", "GSM3191973", "GSM3191974", "GSM3191975", "GSM3191976", "GSM3191977", "GSM3191978"], "sample_count": 86, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "SPECIFIC BIOMARKERS ASSOCIATED WITH CHRONIC RENAL LESIONS IN IGA NEPHROPATHY PATIENTS. A MULTICENTER STUDY", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE116626", "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=GSE116626", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116626", "version": null, "note": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3244301", "GSM3244302", "GSM3244303", "GSM3244304", "GSM3244305", "GSM3244306", "GSM3244307", "GSM3244308", "GSM3244309", "GSM3244310", "GSM3244311", "GSM3244312", "GSM3244313", "GSM3244314", "GSM3244315", "GSM3244316", "GSM3244317", "GSM3244318", "GSM3244319", "GSM3244320", "GSM3244321", "GSM3244322", "GSM3244323", "GSM3244324", "GSM3244325", "GSM3244326", "GSM3244327", "GSM3244328", "GSM3244329", "GSM3244330", "GSM3244331", "GSM3244332", "GSM3244333", "GSM3244334", "GSM3244335", "GSM3244336", "GSM3244337", "GSM3244338", "GSM3244339", "GSM3244340", "GSM3244341", "GSM3244342", "GSM3244343", "GSM3244344", "GSM3244345", "GSM3244346", "GSM3244347", "GSM3244348", "GSM3244349", "GSM3244350", "GSM3244351", "GSM3244352", "GSM3244353", "GSM3244354", "GSM3244355", "GSM3244356", "GSM3244357", "GSM3244358", "GSM3244359", "GSM3244360", "GSM3244361", "GSM3244362", "GSM3244363", "GSM3244364", "GSM3244365", "GSM3244366", "GSM3244367", "GSM3244368", "GSM3244369", "GSM3244370", "GSM3244371", "GSM3244372", "GSM3244373", "GSM3244374", "GSM3244375", "GSM3244376", "GSM3244377", "GSM3244378", "GSM3244379", "GSM3244380", "GSM3244381"], "sample_count": 81, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "Specific biomarkers Associated with Active and Chronic Renal Lesions in IgA Nephropathy. A Multicenter Study", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE35487", "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=GSE35487", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE35487", "version": null, "note": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM869311", "GSM869315", "GSM869316", "GSM869317", "GSM869318", "GSM869319", "GSM869320", "GSM869321", "GSM869322", "GSM869323", "GSM869324", "GSM869325", "GSM869326", "GSM869327", "GSM869328", "GSM869329", "GSM869330", "GSM869331", "GSM869332", "GSM869333", "GSM869334", "GSM869335", "GSM869336", "GSM869337", "GSM869338", "GSM869339", "GSM869340", "GSM869341", "GSM869342", "GSM869343", "GSM869344"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from human with IgA nephropathy (IgAN) [HG-U133A]", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE58539", "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=GSE58539", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58539", "version": null, "note": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1413151", "GSM1413152", "GSM1413153", "GSM1413154", "GSM1413155", "GSM1413156", "GSM1413157", "GSM1413158", "GSM1413159", "GSM1413160", "GSM1413161", "GSM1413162", "GSM1413163", "GSM1413164", "GSM1413165", "GSM1413166", "GSM1413167"], "sample_count": 17, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "ALTERED MONOCYTE GENE EXPRESSION AND EXPANSION OF  CD14+CD16+ SUBSET IN IgA NEPHROPATHY PATIENTS", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE93798", "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=GSE93798", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE93798", "version": null, "note": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2462533", "GSM2462534", "GSM2462535", "GSM2462536", "GSM2462537", "GSM2462538", "GSM2462539", "GSM2462540", "GSM2462541", "GSM2462542", "GSM2462543", "GSM2462544", "GSM2462545", "GSM2462546", "GSM2462547", "GSM2462548", "GSM2462549", "GSM2462550", "GSM2462551", "GSM2462552", "GSM2462553", "GSM2462554", "GSM2462555", "GSM2462556", "GSM2462557", "GSM2462558", "GSM2462559", "GSM2462560", "GSM2462561", "GSM2462562", "GSM2462563", "GSM2462564", "GSM2462565", "GSM2462566", "GSM2462567", "GSM2462568", "GSM2462569", "GSM2462570", "GSM2462571", "GSM2462572", "GSM2462573", "GSM2462574"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "22945", "taxon": "Homo sapiens", "title": "Transcriptomic and proteomic profiling reveal insights of mesangial cell function in patients with IgA Nephropathy", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE115857 not downloaded", "asset:data:geo:GSE115857 licence not read", "asset:data:geo:GSE116626 not downloaded", "asset:data:geo:GSE116626 licence not read", "asset:data:geo:GSE35487 not downloaded", "asset:data:geo:GSE35487 licence not read", "asset:data:geo:GSE58539 not downloaded", "asset:data:geo:GSE58539 licence not read", "asset:data:geo:GSE93798 not downloaded", "asset:data:geo:GSE93798 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}, {"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"}}, {"id": "method-3", "family": null, "specific": null, "label": "square least absolute shrinkage and selection operator (LASSO) and cross validation", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The hub genes were screened by the square least absolute shrinkage and selection operator (LASSO) and cross validation."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE93798", "GSE35487", "GSE58539", "GSE116626", "GSE115857"], "resolved_accessions": ["GSE93798", "GSE35487", "GSE58539", "GSE116626", "GSE115857"], "statements": ["The datasets used and analysed during the current study available from the corresponding author on reasonable request. Furthermore, the datasets (GSE93798, GSE35487, GSE58539, GSE116626 and GSE115857) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/geo."], "basis": "The paper names GSE93798, GSE35487, GSE58539, GSE116626, GSE115857 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40263537", "data:geo:GSE115857"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE115857"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:50:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10166, "completion_tokens": 2752, "cached_tokens": 256}}, "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:40263537", "type": "paper", "label": "pmid:40263537"}, {"id": "source:pmid:40263537", "type": "manuscript", "label": "PMID 40263537 full text"}, {"id": "data:geo:GSE115857", "type": "dataset", "label": "GEO GSE115857"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40263537", "type": "paper", "label": "pmid:40263537"}, {"id": "source:pmid:40263537", "type": "manuscript", "label": "PMID 40263537 full text"}, {"id": "data:geo:GSE115857", "type": "dataset", "label": "GEO GSE115857"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40263537", "type": "extraction", "used": ["source:pmid:40263537"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE115857", "type": "accession_resolution", "used": ["data:geo:GSE115857"], "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:40263537", "parent_hash": "sha256:182a0e32eacd95a9f94e001556df05383228e52fee52acfb4d53fe1ef8a6b26b", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE115857 licence not read", "asset:data:geo:GSE115857 not downloaded", "asset:data:geo:GSE116626 licence not read", "asset:data:geo:GSE116626 not downloaded", "asset:data:geo:GSE35487 licence not read", "asset:data:geo:GSE35487 not downloaded", "asset:data:geo:GSE58539 licence not read", "asset:data:geo:GSE58539 not downloaded", "asset:data:geo:GSE93798 licence not read", "asset:data:geo:GSE93798 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["utophagy, such as lipid and atherosclerosis, apoptosis, cellular senescence and cell cycle and immu"], "order_basis": "paper_text_order:6170", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["limma"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:51:04+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}}}