Identification and Characterization of a ceRNA Regulatory Network Involving LINC00482 and PRRC2B in Peripheral Blood Mononuclear Cells: Implications for COPD Pathogenesis and Diagnosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38348310", "kind": "science-record", "revision": 4, "content_hash": "sha256:f00da25a6d09790da2d230e44886919a8a8ca7fdc4a76b31222c845cb15252aa", "created_at": "2026-11-01T19:20:17Z", "updated_at": "2026-11-01T22:53:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Characterization of a ceRNA Regulatory Network Involving LINC00482 and PRRC2B in Peripheral Blood Mononuclear Cells: Implications for COPD Pathogenesis and Diagnosis.", "doi": "10.2147/COPD.S437046", "pmid": "38348310", "authors": ["Wenjie Huang", "Ting Luo", "Mengqiu Lan", "Wenting Zhou", "Ming Zhang", "Lihong Wu", "Zhenni Lu", "Li Fan"], "journal": "International journal of chronic obstructive pulmonary disease", "year": 2024, "abstract": "Purpose: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide, characterized by intense lung infiltrations of immune cells (macrophages and monocytes). While existing studies have highlighted the crucial role of the competitive endogenous RNA (ceRNA) regulatory network in COPD development, the complexity and characteristics of the ceRNA network in monocytes remain unexplored.\nMethods: We downloaded messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) microarray data from GSE146560, GSE102915, and GSE71220 in the Gene Expression Omnibus (GEO) database. This data was used to identify differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), and lncRNAs (DElncRNAs). Predicted miRNAs that bind to DElncRNAs were intersected with DEmiRNAs, forming a set of intersecting miRNAs. This set was then used to predict potential binding mRNAs, intersected with DEmRNAs, and underwent functional enrichment analysis using R software and the STRING database. The resulting triple regulatory network and hub genes were constructed using Cytoscape. Comparative Toxicomics Database (CTD) was utilized for disease correlation predictions, and ROC curve analysis assessed diagnostic accuracy.\nResults: Our study identified 5 lncRNAs, 4 miRNAs, and 149 mRNAs as differentially expressed. A lncRNA-miRNA-mRNA regulatory network was constructed, and hub genes were selected through hub analysis. Enrichment analysis highlighted terms related to cell movement and gene expression regulation. We established a LINC00482-has-miR-6088-PRRC2B ceRNA network with diagnostic relevance for COPD. ROC analysis demonstrated the diagnostic value of these genes. Moreover, a positive correlation between LINC00482 and PRRC2B expression was observed in COPD PBMCs. The CTD database indicated their involvement in inflammatory responses.\nConclusion: In summary, our study not only identified pivotal hub genes in peripheral blood mononuclear cells (PBMCs) of COPD but also constructed a ceRNA regulatory network. This contributes to understanding the pathophysiological processes of COPD through bioinformatics analysis, expanding our knowledge of COPD, and providing a foundation for potential diagnostic and therapeutic targets for COPD.", "claims": [{"id": "claim-method", "statement": "To evaluate the diagnostic value of hub genes, ROC curve analysis was performed using the R package pROC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38348310", "locator": "sections[7] \"The Receiver Operating Characteristic (ROC) Curves of Hub Genes\" paragraph 2", "quote": "To evaluate the diagnostic value of hub genes, ROC curve analysis was performed using the R package pROC."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38348310", "locator": "sections[17] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 5 lncRNAs, 4 miRNAs, and 149 mRNAs as differentially expressed and established a LINC00482-has-miR-6088-PRRC2B ceRNA network with diagnostic relevance for COPD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38348310", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Our study identified 5 lncRNAs, 4 miRNAs, and 149 mRNAs as differentially expressed."}, {"asset": "source:pmid:38348310", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We established a LINC00482-has-miR-6088-PRRC2B ceRNA network with diagnostic relevance for COPD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 5 lncRNAs, 4 miRNAs, and 149 mRNAs as differentially expressed and established a LINC00482-has-miR-6088-PRRC2B ceRNA network with diagnostic relevance for COPD.", "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:38348310"], "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:GSE102915"], "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:GSE102915"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38348310", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/COPD.S437046", "sha256": "sha256:ee4fedf7820bddf9f8f83880ce6163e985432f7794f00c0921b703532e8f4efb", "bytes": 28347, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/COPD.S437046", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10860591", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102915", "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=GSE102915", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102915", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2748233", "GSM2748234", "GSM2748235", "GSM2748236", "GSM2748237", "GSM2748238", "GSM2748239", "GSM2748240", "GSM2748241", "GSM2748242", "GSM2748243", "GSM2748244"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "20712", "taxon": "Homo sapiens", "title": "MiRNAs expression in peripheral blood monouclear cells from stable COPD and healthy adults", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE146560", "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=GSE146560", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE146560", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4395416", "GSM4395418", "GSM4395419", "GSM4395421", "GSM4395422", "GSM4395424", "GSM4395425", "GSM4395426", "GSM4395428", "GSM4395430", "GSM4395431", "GSM4395433", "GSM4395434", "GSM4395436", "GSM4395437", "GSM4395439"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Homo sapiens whole genome expression microarray of peripheral blood monocytes obtained from Control Smokers, Control Never Smokers, COPD Smokers and COPD ExSmokers.", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE71220", "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=GSE71220", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71220", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1830157", "GSM1830158", "GSM1830159", "GSM1830160", "GSM1830161", "GSM1830162", "GSM1830163", "GSM1830164", "GSM1830165", "GSM1830166", "GSM1830167", "GSM1830168", "GSM1830169", "GSM1830170", "GSM1830171", "GSM1830172", "GSM1830173", "GSM1830174", "GSM1830175", "GSM1830176", "GSM1830177", "GSM1830178", "GSM1830179", "GSM1830180", "GSM1830181", "GSM1830182", "GSM1830183", "GSM1830184", "GSM1830185", "GSM1830186", "GSM1830187", "GSM1830188", "GSM1830189", "GSM1830190", "GSM1830191", "GSM1830192", "GSM1830193", "GSM1830194", "GSM1830195", "GSM1830196", "GSM1830197", "GSM1830198", "GSM1830199", "GSM1830200", "GSM1830201", "GSM1830202", "GSM1830203", "GSM1830204", "GSM1830205", "GSM1830206", "GSM1830207", "GSM1830208", "GSM1830209", "GSM1830210", "GSM1830211", "GSM1830212", "GSM1830213", "GSM1830214", "GSM1830215", "GSM1830216", "GSM1830217", "GSM1830218", "GSM1830219", "GSM1830220", "GSM1830221", "GSM1830222", "GSM1830223", "GSM1830224", "GSM1830225", "GSM1830226", "GSM1830227", "GSM1830228", "GSM1830229", "GSM1830230", "GSM1830231", "GSM1830232", "GSM1830233", "GSM1830234", "GSM1830235", "GSM1830236", "GSM1830237", "GSM1830238", "GSM1830239", "GSM1830240", "GSM1830241", "GSM1830242", "GSM1830243", "GSM1830244", "GSM1830245", "GSM1830246", "GSM1830247", "GSM1830248", "GSM1830249", "GSM1830250", "GSM1830251", "GSM1830252", "GSM1830253", "GSM1830254", "GSM1830255", "GSM1830256", "GSM1830257", "GSM1830258", "GSM1830259", "GSM1830260", "GSM1830261", "GSM1830262", "GSM1830263", "GSM1830264", "GSM1830265", "GSM1830266", "GSM1830267", "GSM1830268", "GSM1830269", "GSM1830270", "GSM1830271", "GSM1830272", "GSM1830273", "GSM1830274", "GSM1830275", "GSM1830276", "GSM1830277", "GSM1830278", "GSM1830279", "GSM1830280", "GSM1830281", "GSM1830282", "GSM1830283", "GSM1830284", "GSM1830285", "GSM1830286", "GSM1830287", "GSM1830288", "GSM1830289", "GSM1830290", "GSM1830291", "GSM1830292", "GSM1830293", "GSM1830294", "GSM1830295", "GSM1830296", "GSM1830297", "GSM1830298", "GSM1830299", "GSM1830300", "GSM1830301", "GSM1830302", "GSM1830303", "GSM1830304", "GSM1830305", "GSM1830306", "GSM1830307", "GSM1830308", "GSM1830309", "GSM1830310", "GSM1830311", "GSM1830312", "GSM1830313", "GSM1830314", "GSM1830315", "GSM1830316", "GSM1830317", "GSM1830318", "GSM1830319", "GSM1830320", "GSM1830321", "GSM1830322", "GSM1830323", "GSM1830324", "GSM1830325", "GSM1830326", "GSM1830327", "GSM1830328", "GSM1830329", "GSM1830330", "GSM1830331", "GSM1830332", "GSM1830333", "GSM1830334", "GSM1830335", "GSM1830336", "GSM1830337", "GSM1830338", "GSM1830339", "GSM1830340", "GSM1830341", "GSM1830342", "GSM1830343", "GSM1830344", "GSM1830345", "GSM1830346", "GSM1830347", "GSM1830348", "GSM1830349", "GSM1830350", "GSM1830351", "GSM1830352", "GSM1830353", "GSM1830354", "GSM1830355", "GSM1830356", "GSM1830357", "GSM1830358", "GSM1830359", "GSM1830360", "GSM1830361", "GSM1830362", "GSM1830363", "GSM1830364", "GSM1830365", "GSM1830366", "GSM1830367", "GSM1830368", "GSM1830369", "GSM1830370", "GSM1830371", "GSM1830372", "GSM1830373", "GSM1830374", "GSM1830375", "GSM1830376", "GSM1830377", "GSM1830378", "GSM1830379", "GSM1830380", "GSM1830381", "GSM1830382", "GSM1830383", "GSM1830384", "GSM1830385", "GSM1830386", "GSM1830387", "GSM1830388", "GSM1830389", "GSM1830390", "GSM1830391", "GSM1830392", "GSM1830393", "GSM1830394", "GSM1830395", "GSM1830396", "GSM1830397", "GSM1830398", "GSM1830399", "GSM1830400", "GSM1830401", "GSM1830402", "GSM1830403", "GSM1830404", "GSM1830405", "GSM1830406", "GSM1830407", "GSM1830408", "GSM1830409", "GSM1830410", "GSM1830411", "GSM1830412", "GSM1830413", "GSM1830414", "GSM1830415", "GSM1830416", "GSM1830417", "GSM1830418", "GSM1830419", "GSM1830420", "GSM1830421", "GSM1830422", "GSM1830423", "GSM1830424", "GSM1830425", "GSM1830426", "GSM1830427", "GSM1830428", "GSM1830429", "GSM1830430", "GSM1830431", "GSM1830432", "GSM1830433", "GSM1830434", "GSM1830435", "GSM1830436", "GSM1830437", "GSM1830438", "GSM1830439", "GSM1830440", "GSM1830441", "GSM1830442", "GSM1830443", "GSM1830444", "GSM1830445", "GSM1830446", "GSM1830447", "GSM1830448", "GSM1830449", "GSM1830450", "GSM1830451", "GSM1830452", "GSM1830453", "GSM1830454", "GSM1830455", "GSM1830456", "GSM1830457", "GSM1830458", "GSM1830459", "GSM1830460", "GSM1830461", "GSM1830462", "GSM1830463", "GSM1830464", "GSM1830465", "GSM1830466", "GSM1830467", "GSM1830468", "GSM1830469", "GSM1830470", "GSM1830471", "GSM1830472", "GSM1830473", "GSM1830474", "GSM1830475", "GSM1830476", "GSM1830477", "GSM1830478", "GSM1830479", "GSM1830480", "GSM1830481", "GSM1830482", "GSM1830483", "GSM1830484", "GSM1830485", "GSM1830486", "GSM1830487", "GSM1830488", "GSM1830489", "GSM1830490", "GSM1830491", "GSM1830492", "GSM1830493", "GSM1830494", "GSM1830495", "GSM1830496", "GSM1830497", "GSM1830498", "GSM1830499", "GSM1830500", "GSM1830501", "GSM1830502", "GSM1830503", "GSM1830504", "GSM1830505", "GSM1830506", "GSM1830507", "GSM1830508", "GSM1830509", "GSM1830510", "GSM1830511", "GSM1830512", "GSM1830513", "GSM1830514", "GSM1830515", "GSM1830516", "GSM1830517", "GSM1830518", "GSM1830519", "GSM1830520", "GSM1830521", "GSM1830522", "GSM1830523", "GSM1830524", "GSM1830525", "GSM1830526", "GSM1830527", "GSM1830528", "GSM1830529", "GSM1830530", "GSM1830531", "GSM1830532", "GSM1830533", "GSM1830534", "GSM1830535", "GSM1830536", "GSM1830537", "GSM1830538", "GSM1830539", "GSM1830540", "GSM1830541", "GSM1830542", "GSM1830543", "GSM1830544", "GSM1830545", "GSM1830546", "GSM1830547", "GSM1830548", "GSM1830549", "GSM1830550", "GSM1830551", "GSM1830552", "GSM1830553", "GSM1830554", "GSM1830555", "GSM1830556", "GSM1830557", "GSM1830558", "GSM1830559", "GSM1830560", "GSM1830561", "GSM1830562", "GSM1830563", "GSM1830564", "GSM1830565", "GSM1830566", "GSM1830567", "GSM1830568", "GSM1830569", "GSM1830570", "GSM1830571", "GSM1830572", "GSM1830573", "GSM1830574", "GSM1830575", "GSM1830576", "GSM1830577", "GSM1830578", "GSM1830579", "GSM1830580", "GSM1830581", "GSM1830582", "GSM1830583", "GSM1830584", "GSM1830585", "GSM1830586", "GSM1830587", "GSM1830588", "GSM1830589", "GSM1830590", "GSM1830591", "GSM1830592", "GSM1830593", "GSM1830594", "GSM1830595", "GSM1830596", "GSM1830597", "GSM1830598", "GSM1830599", "GSM1830600", "GSM1830601", "GSM1830602", "GSM1830603", "GSM1830604", "GSM1830605", "GSM1830606", "GSM1830607", "GSM1830608", "GSM1830609", "GSM1830610", "GSM1830611", "GSM1830612", "GSM1830613", "GSM1830614", "GSM1830615", "GSM1830616", "GSM1830617", "GSM1830618", "GSM1830619", "GSM1830620", "GSM1830621", "GSM1830622", "GSM1830623", "GSM1830624", "GSM1830625", "GSM1830626", "GSM1830627", "GSM1830628", "GSM1830629", "GSM1830630", "GSM1830631", "GSM1830632", "GSM1830633", "GSM1830634", "GSM1830635", "GSM1830636", "GSM1830637", "GSM1830638", "GSM1830639", "GSM1830640", "GSM1830641", "GSM1830642", "GSM1830643", "GSM1830644", "GSM1830645", "GSM1830646", "GSM1830647", "GSM1830648", "GSM1830649", "GSM1830650", "GSM1830651", "GSM1830652", "GSM1830653", "GSM1830654", "GSM1830655", "GSM1830656", "GSM1830657", "GSM1830658", "GSM1830659", "GSM1830660", "GSM1830661", "GSM1830662", "GSM1830663", "GSM1830664", "GSM1830665", "GSM1830666", "GSM1830667", "GSM1830668", "GSM1830669", "GSM1830670", "GSM1830671", "GSM1830672", "GSM1830673", "GSM1830674", "GSM1830675", "GSM1830676", "GSM1830677", "GSM1830678", "GSM1830679", "GSM1830680", "GSM1830681", "GSM1830682", "GSM1830683", "GSM1830684", "GSM1830685", "GSM1830686", "GSM1830687", "GSM1830688", "GSM1830689", "GSM1830690", "GSM1830691", "GSM1830692", "GSM1830693", "GSM1830694", "GSM1830695", "GSM1830696", "GSM1830697", "GSM1830698", "GSM1830699", "GSM1830700", "GSM1830701", "GSM1830702", "GSM1830703", "GSM1830704", "GSM1830705", "GSM1830706", "GSM1830707", "GSM1830708", "GSM1830709", "GSM1830710", "GSM1830711", "GSM1830712", "GSM1830713", "GSM1830714", "GSM1830715", "GSM1830716", "GSM1830717", "GSM1830718", "GSM1830719", "GSM1830720", "GSM1830721", "GSM1830722", "GSM1830723", "GSM1830724", "GSM1830725", "GSM1830726", "GSM1830727", "GSM1830728", "GSM1830729", "GSM1830730", "GSM1830731", "GSM1830732", "GSM1830733", "GSM1830734", "GSM1830735", "GSM1830736", "GSM1830737", "GSM1830738", "GSM1830739", "GSM1830740", "GSM1830741", "GSM1830742", "GSM1830743", "GSM1830744", "GSM1830745", "GSM1830746", "GSM1830747", "GSM1830748", "GSM1830749", "GSM1830750", "GSM1830751", "GSM1830752", "GSM1830753", "GSM1830754", "GSM1830755", "GSM1830756", "GSM1830757", "GSM1830758", "GSM1830759", "GSM1830760", "GSM1830761", "GSM1830762", "GSM1830763", "GSM1830764", "GSM1830765", "GSM1830766", "GSM1830767", "GSM1830768", "GSM1830769", "GSM1830770", "GSM1830771", "GSM1830772", "GSM1830773"], "sample_count": 617, "group_sizes": null, "group_sizes_basis": null, "platform": "11532", "taxon": "Homo sapiens", "title": "The effect of statins on blood gene expression in COPD", "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:GSE102915 not downloaded", "asset:data:geo:GSE102915 licence not read", "asset:data:geo:GSE146560 not downloaded", "asset:data:geo:GSE146560 licence not read", "asset:data:geo:GSE71220 not downloaded", "asset:data:geo:GSE71220 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "To evaluate the diagnostic value of hub genes, ROC curve analysis was performed using the R package pROC."}}], "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": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: roc."}, "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": ["GSE146560", "GSE102915", "GSE71220"], "resolved_accessions": ["GSE146560", "GSE102915", "GSE71220"], "statements": ["The datasets generated and/or analyzed during the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE146560, GSE102915, GSE71220 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": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "assets": ["source:pmid:38348310", "data:geo:GSE102915"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102915"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:08:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8417, "completion_tokens": 1384, "cached_tokens": 264}}, "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:38348310", "type": "paper", "label": "pmid:38348310"}, {"id": "source:pmid:38348310", "type": "manuscript", "label": "PMID 38348310 full text"}, {"id": "data:geo:GSE102915", "type": "dataset", "label": "GEO GSE102915"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38348310", "type": "paper", "label": "pmid:38348310"}, {"id": "source:pmid:38348310", "type": "manuscript", "label": "PMID 38348310 full text"}, {"id": "data:geo:GSE102915", "type": "dataset", "label": "GEO GSE102915"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38348310", "type": "extraction", "used": ["source:pmid:38348310"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102915", "type": "accession_resolution", "used": ["data:geo:GSE102915"], "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:38348310", "parent_hash": "sha256:4fd10c12c566f58d0e9e2df4922efe17fbecdc200e8817d211998070cc276bc4", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE102915 licence not read", "asset:data:geo:GSE102915 not downloaded", "asset:data:geo:GSE146560 licence not read", "asset:data:geo:GSE146560 not downloaded", "asset:data:geo:GSE71220 licence not read", "asset:data:geo:GSE71220 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["RNA (miRNA), and long noncoding RNA (lncRNA) microarray data from GSE146560, GSE102915, and GSE71220"], "order_basis": "paper_text_order:653", "id": "assay:1"}, {"role": "analysis", "definition_id": "diagnostic_evaluation", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To evaluate the diagnostic value of hub genes, ROC curve analysis was performed using the R package pROC."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}