{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34035068", "kind": "science-record", "revision": 4, "content_hash": "sha256:bfbc2247e8c4641e2ba5e33ad4b6ebf4aeb6342a6cfcec60f3047eb18b96d75f", "created_at": "2026-11-01T17:35:20Z", "updated_at": "2026-11-01T22:03:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "OCaMIR-A Noninvasive, Diagnostic Signature for Early-Stage Ovarian Cancer: A Multi-cohort Retrospective and Prospective Study.", "doi": "10.1158/1078-0432.CCR-21-0267", "pmid": "34035068", "authors": ["Raju Kandimalla", "Wei Wang", "Fan Yu", "Nianxin Zhou", "Feng Gao", "Monique Spillman", "Lucie Moukova", "Ondrej Slaby", "Bodour Salhia", "Shengtao Zhou", "Xin Wang", "Ajay Goel"], "journal": "Clinical cancer research : an official journal of the American Association for Cancer Research", "year": 2021, "abstract": "PURPOSE: Due to the lack of effective screening approaches and early detection biomarkers, ovarian cancer has the highest mortality rates among gynecologic cancers. Herein, we undertook a systematic biomarker discovery and validation approach to identify microRNA (miRNA) biomarkers for the early detection of ovarian cancer.\nEXPERIMENTAL DESIGN: During the discovery phase, we performed small RNA sequencing in stage I high-grade serous ovarian cancer (n = 31), which was subsequently validated in multiple, independent data sets (TCGA, n = 543; GSE65819, n = 87). Subsequently, we performed multivariate logistic regression-based training in a serum data set (GSE106817, n = 640), followed by its independent validation in three retrospective data sets (GSE31568, n = 85; GSE113486, n = 140; Czech Republic cohort, n = 192) and one prospective serum cohort (n = 95). In addition, we evaluated the specificity of OCaMIR, by comparing its performance in several other cancers (GSE31568 cohort, n = 369).\nRESULTS: The OCaMIR demonstrated a robust diagnostic accuracy in the stage I high-grade serous ovarian cancer patients in the discovery cohort (AUC = 0.99), which was consistently reproducible in both stage I (AUC = 0.96) and all stage patients (AUC = 0.89) in the TCGA cohort. Logistic regression-based training and validation of OCaMIR achieved AUC values of 0.89 (GSE106817), 0.85 (GSE31568), 0.86 (GSE113486), and 0.82 (Czech Republic cohort) in the retrospective serum validation cohorts, as well as prospective validation cohort (AUC = 0.92). More importantly, OCaMIR demonstrated a significantly superior diagnostic performance compared with CA125 levels, even in stage I patients, and was more cost-effective, highlighting its potential role for screening and early detection of ovarian cancer.\nCONCLUSIONS: Small RNA sequencing identified a robust noninvasive miRNA signature for early-stage serous ovarian cancer detection.", "claims": [{"id": "claim-method", "statement": "Eight miRNAs significantly upregulated in OC tissues were employed to build a multivariate logistic regression model from the discovery cohort, and the scoring formula derived from the model was applied to TCGA and GSE65819 for independent tissue validation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34035068", "locator": "sections[6] \"Statistical analysis\" paragraph 2", "quote": "Eight miRNAs significantly upregulated in OC tissues were employed to build a multivariate logistic regression model from the discovery cohort, and the scoring formula derived from the model was applied to TCGA and GSE65819 for independent tissue validation."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw sequencing data is accessible in GEO database (accession number: GSE127873).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34035068", "locator": "sections[4] \"Tissue RNA isolation and small RNA sequencing\" paragraph 2", "quote": "The raw sequencing data is accessible in GEO database (accession number: GSE127873)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The OCaMIR signature demonstrated robust diagnostic accuracy across discovery, retrospective, and prospective cohorts and outperformed CA125, including in stage-I ovarian cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34035068", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The OCaMIR demonstrated a robust diagnostic accuracy in the stage-I high-grade serous OC patients in the discovery cohort (area under the curve [AUC)]value=0.99), which was consistently reproducible in both stage-I (AUC=0.96) and all stage patients (AUC=0.89) in the TCGA cohort."}, {"asset": "source:pmid:34035068", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "More importantly, OCaMIR demonstrated a significantly superior diagnostic performance compared to CA125 levels, even in stage-I patients, and was more cost effective: highlighting its potential role for screening and early detection of ovarian cancer."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The OCaMIR signature demonstrated robust diagnostic accuracy across discovery, retrospective, and prospective cohorts and outperformed CA125, including in stage-I ovarian cancer.", "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:34035068"], "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:GSE106817"], "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:GSE106817"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34035068", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1158/1078-0432.CCR-21-0267", "sha256": "sha256:a77cfa28df9cb339ffb5c9e35e165591d6c5a0d971c853fd97c93b9bc184f17e", "bytes": 30137, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1158/1078-0432.CCR-21-0267", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10327469", "source": "ncbi_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE106817", "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=GSE106817", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE106817", "version": null, "note": "The raw sequencing data is accessible in GEO database (accession number: GSE127873).", "structure": 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"GSM2851543", "GSM2851544", "GSM2851545", "GSM2851546", "GSM2851547", "GSM2851548", "GSM2851549", "GSM2851550", "GSM2851551", "GSM2851552", "GSM2851553", "GSM2851554", "GSM2851555", "GSM2851556", "GSM2851557", "GSM2851558", "GSM2851559", "GSM2851560", "GSM2851561", "GSM2851562", "GSM2851563", "GSM2851564", "GSM2851565", "GSM2851566", "GSM2851567", "GSM2851568", "GSM2851569", "GSM2851570", "GSM2851571", "GSM2851572", "GSM2851573", "GSM2851574", "GSM2851575", "GSM2851576", "GSM2851577", "GSM2851578", "GSM2851579", "GSM2851580", "GSM2851581", "GSM2851582", "GSM2851583", "GSM2851584", "GSM2851585", "GSM2851586", "GSM2851587", "GSM2851588", "GSM2851589", "GSM2851590", "GSM2851591", "GSM2851592", "GSM2851593", "GSM2851594", "GSM2851595", "GSM2851596", "GSM2851597", "GSM2851598", "GSM2851599", "GSM2851600", "GSM2851601", "GSM2851602", "GSM2851603", "GSM2851604", "GSM2851605", "GSM2851606", "GSM2851607", "GSM2851608", "GSM2851609", "GSM2851610", "GSM2851611", "GSM2851612", "GSM2851613", 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"GSM2851827", "GSM2851828", "GSM2851829", "GSM2851830", "GSM2851831", "GSM2851832", "GSM2851833", "GSM2851834", "GSM2851835", "GSM2851836", "GSM2851837", "GSM2851838", "GSM2851839", "GSM2851840", "GSM2851841", "GSM2851842", "GSM2851843", "GSM2851844", "GSM2851845", "GSM2851846", "GSM2851847", "GSM2851848", "GSM2851849", "GSM2851850", "GSM2851851", "GSM2851852", "GSM2851853", "GSM2851854", "GSM2851855", "GSM2851856", "GSM2851857", "GSM2851858", "GSM2851859", "GSM2851860", "GSM2851861", "GSM2851862", "GSM2851863", "GSM2851864", "GSM2851865", "GSM2851866", "GSM2851867", "GSM2851868", "GSM2851869", "GSM2851870", "GSM2851871", "GSM2851872", "GSM2851873", "GSM2851874", "GSM2851875", "GSM2851876", "GSM2851877", "GSM2851878", "GSM2851879", "GSM2851880", "GSM2851881", "GSM2851882", "GSM2851883", "GSM2851884", "GSM2851885", "GSM2851886", "GSM2851887", "GSM2851888", "GSM2851889", "GSM2851890", "GSM2851891", "GSM2851892", "GSM2851893", "GSM2851894", "GSM2851895", "GSM2851896", "GSM2851897", "GSM2851898", "GSM2851899", "GSM2851900", "GSM2851901", "GSM2851902", "GSM2851903", "GSM2851904", "GSM2851905", "GSM2851906", "GSM2851907", "GSM2851908", "GSM2851909", "GSM2851910", "GSM2851911", "GSM2851912", "GSM2851913", "GSM2851914", "GSM2851915", "GSM2851916", "GSM2851917", "GSM2851918", "GSM2851919", "GSM2851920", "GSM2851921", "GSM2851922", "GSM2851923", "GSM2851924", "GSM2851925", "GSM2851926", "GSM2851927", "GSM2851928", "GSM2851929", "GSM2851930", "GSM2851931", "GSM2851932", "GSM2851933", "GSM2851934", "GSM2851935", "GSM2851936", "GSM2851937", "GSM2851938", "GSM2851939", "GSM2851940", "GSM2851941", "GSM2851942", "GSM2851943", "GSM2851944", "GSM2851945", "GSM2851946", "GSM2851947", "GSM2851948", "GSM2851949", "GSM2851950", "GSM2851951", "GSM2851952", "GSM2851953", "GSM2851954", "GSM2851955", "GSM2851956", "GSM2851957", "GSM2851958", "GSM2851959", "GSM2851960", "GSM2851961", "GSM2851962", "GSM2851963", "GSM2851964", "GSM2851965", "GSM2851966", "GSM2851967", "GSM2851968", "GSM2851969", "GSM2851970", "GSM2851971", "GSM2851972", "GSM2851973", "GSM2851974", "GSM2851975", "GSM2851976", "GSM2851977", "GSM2851978", "GSM2851979", "GSM2851980", "GSM2851981", "GSM2851982", "GSM2851983", "GSM2851984", "GSM2851985", "GSM2851986", "GSM2851987", "GSM2851988", "GSM2851989", "GSM2851990", "GSM2851991", "GSM2851992", "GSM2851993", "GSM2851994", "GSM2851995", "GSM2851996", "GSM2851997", "GSM2851998", "GSM2851999", "GSM2852000", "GSM2852001", "GSM2852002", "GSM2852003", "GSM2852004", "GSM2852005", "GSM2852006", "GSM2852007", "GSM2852008", "GSM2852009", "GSM2852010", "GSM2852011", "GSM2852012", "GSM2852013", "GSM2852014", "GSM2852015", "GSM2852016", "GSM2852017", "GSM2852018", "GSM2852019", "GSM2852020", "GSM2852021", "GSM2852022", "GSM2852023", "GSM2852024", "GSM2852025", "GSM2852026", "GSM2852027", "GSM2852028", "GSM2852029", "GSM2852030", "GSM2852031", "GSM2852032", "GSM2852033", "GSM2852034", "GSM2852035", "GSM2852036", "GSM2852037", "GSM2852038", "GSM2852039", "GSM2852040", "GSM2852041", "GSM2852042", "GSM2852043", "GSM2852044", "GSM2852045", "GSM2852046", "GSM2852047", "GSM2852048", "GSM2852049", "GSM2852050", "GSM2852051", "GSM2852052", "GSM2852053", "GSM2852054", "GSM2852055", "GSM2852056", "GSM2852057", "GSM2852058", "GSM2852059", "GSM2852060", "GSM2852061", "GSM2852062", "GSM2852063", "GSM2852064", "GSM2852065", "GSM2852066", "GSM2852067", "GSM2852068", "GSM2852069", "GSM2852070", "GSM2852071", "GSM2852072", "GSM2852073", "GSM2852074", "GSM2852075", "GSM2852076", "GSM2852077", "GSM2852078", "GSM2852079", "GSM2852080", "GSM2852081", "GSM2852082", "GSM2852083", "GSM2852084", "GSM2852085", "GSM2852086", "GSM2852087", "GSM2852088", "GSM2852089", "GSM2852090", "GSM2852091", "GSM2852092", "GSM2852093", "GSM2852094", "GSM2852095", "GSM2852096", "GSM2852097", "GSM2852098", "GSM2852099", "GSM2852100", "GSM2852101", "GSM2852102", "GSM2852103", "GSM2852104", "GSM2852105", "GSM2852106", "GSM2852107", "GSM2852108", "GSM2852109", "GSM2852110", "GSM2852111", "GSM2852112", "GSM2852113", "GSM2852114", "GSM2852115", "GSM2852116", "GSM2852117", "GSM2852118", "GSM2852119", "GSM2852120", "GSM2852121", "GSM2852122", "GSM2852123", "GSM2852124", "GSM2852125", "GSM2852126", "GSM2852127", "GSM2852128", "GSM2852129", "GSM2852130", "GSM2852131", "GSM2852132", "GSM2852133", "GSM2852134", "GSM2852135", "GSM2852136", "GSM2852137", "GSM2852138", "GSM2852139", "GSM2852140", "GSM2852141", "GSM2852142", "GSM2852143", "GSM2852144", "GSM2852145", "GSM2852146", "GSM2852147", "GSM2852148", "GSM2852149", "GSM2852150", "GSM2852151", "GSM2852152", "GSM2852153", "GSM2852154", "GSM2852155", "GSM2852156", "GSM2852157", "GSM2852158", "GSM2852159", "GSM2852160", "GSM2852161", "GSM2852162", "GSM2852163", "GSM2852164", "GSM2852165", "GSM2852166", "GSM2852167", "GSM2852168", "GSM2852169", "GSM2852170", "GSM2852171", "GSM2852172", "GSM2852173", "GSM2852174", "GSM2852175", "GSM2852176", "GSM2852177", "GSM2852178", "GSM2852179", "GSM2852180", "GSM2852181", "GSM2852182", "GSM2852183", "GSM2852184", "GSM2852185", "GSM2852186", "GSM2852187", "GSM2852188", "GSM2852189", "GSM2852190", "GSM2852191", "GSM2852192", "GSM2852193", "GSM2852194", "GSM2852195", "GSM2852196", "GSM2852197", "GSM2852198", "GSM2852199", "GSM2852200", "GSM2852201", "GSM2852202", "GSM2852203", "GSM2852204", "GSM2852205", "GSM2852206", "GSM2852207", "GSM2852208", "GSM2852209", "GSM2852210", "GSM2852211", "GSM2852212", "GSM2852213", "GSM2852214", "GSM2852215", "GSM2852216", "GSM2852217", "GSM2852218", "GSM2852219", "GSM2852220", "GSM2852221", "GSM2852222", "GSM2852223", "GSM2852224", "GSM2852225", "GSM2852226", "GSM2852227", "GSM2852228", "GSM2852229", "GSM2852230", "GSM2852231", "GSM2852232", "GSM2852233", "GSM2852234", "GSM2852235", "GSM2852236", "GSM2852237", "GSM2852238", "GSM2852239", "GSM2852240", "GSM2852241", "GSM2852242", "GSM2852243", "GSM2852244", "GSM2852245", "GSM2852246", "GSM2852247", "GSM2852248", "GSM2852249", "GSM2852250", "GSM2852251", "GSM2852252", "GSM2852253", "GSM2852254", "GSM2852255", "GSM2852256", "GSM2852257", "GSM2852258", "GSM2852259", "GSM2852260", "GSM2852261", "GSM2852262", "GSM2852263", "GSM2852264", "GSM2852265", "GSM2852266", "GSM2852267", "GSM2852268", "GSM2852269", "GSM2852270", "GSM2852271", "GSM2852272", "GSM2852273", "GSM2852274", "GSM2852275", "GSM2852276", "GSM2852277", "GSM2852278", "GSM2852279", "GSM2852280", "GSM2852281", "GSM2852282", "GSM2852283", "GSM2852284", "GSM2852285", "GSM2852286", "GSM2852287", "GSM2852288", "GSM2852289", "GSM2852290", "GSM2852291", "GSM2852292", "GSM2852293", "GSM2852294", "GSM2852295", "GSM2852296", "GSM2852297", "GSM2852298", "GSM2852299", "GSM2852300", "GSM2852301", "GSM2852302", "GSM2852303", "GSM2852304", "GSM2852305", "GSM2852306", "GSM2852307", "GSM2852308", "GSM2852309", "GSM2852310", "GSM2852311", "GSM2852312", "GSM2852313", "GSM2852314", "GSM2852315", "GSM2852316", "GSM2852317", "GSM2852318", "GSM2852319", "GSM2852320", "GSM2852321", "GSM2852322", "GSM2852323", "GSM2852324", "GSM2852325", "GSM2852326", "GSM2852327", "GSM2852328", "GSM2852329", "GSM2852330", "GSM2852331", "GSM2852332", "GSM2852333", "GSM2852334", "GSM2852335", "GSM2852336", "GSM2852337", "GSM2852338", "GSM2852339", "GSM2852340", "GSM2852341", "GSM2852342", "GSM2852343", "GSM2852344", "GSM2852345", "GSM2852346", "GSM2852347", "GSM2852348", "GSM2852349", "GSM2852350", "GSM2852351", "GSM2852352", "GSM2852353", "GSM2852354", "GSM2852355", "GSM2852356", "GSM2852357", "GSM2852358", "GSM2852359", "GSM2852360", "GSM2852361", "GSM2852362", "GSM2852363", "GSM2852364", "GSM2852365", "GSM2852366", "GSM2852367", "GSM2852368", "GSM2852369", "GSM2852370", "GSM2852371", "GSM2852372", "GSM2852373", "GSM2852374", "GSM2852375", "GSM2852376", "GSM2852377", "GSM2852378", "GSM2852379", "GSM2852380", "GSM2852381", "GSM2852382", "GSM2852383", "GSM2852384", "GSM2852385", "GSM2852386", "GSM2852387", "GSM2852388", "GSM2852389", "GSM2852390", "GSM2852391", "GSM2852392", "GSM2852393", "GSM2852394", "GSM2852395", "GSM2852396", "GSM2852397", "GSM2852398", "GSM2852399", "GSM2852400", "GSM2852401", "GSM2852402", "GSM2852403", "GSM2852404", "GSM2852405", "GSM2852406", "GSM2852407", "GSM2852408", "GSM2852409", "GSM2852410", "GSM2852411", "GSM2852412", "GSM2852413", "GSM2852414", "GSM2852415", "GSM2852416", "GSM2852417", "GSM2852418", "GSM2852419", "GSM2852420", "GSM2852421", "GSM2852422", "GSM2852423", "GSM2852424", "GSM2852425", "GSM2852426", "GSM2852427", "GSM2852428", "GSM2852429", "GSM2852430", "GSM2852431", "GSM2852432", "GSM2852433", "GSM2852434", "GSM2852435", "GSM2852436", "GSM2852437", "GSM2852438", "GSM2852439", "GSM2852440", "GSM2852441", "GSM2852442", "GSM2852443", "GSM2852444", "GSM2852445", "GSM2852446", "GSM2852447", "GSM2852448", "GSM2852449", "GSM2852450", "GSM2852451", "GSM2852452", "GSM2852453", "GSM2852454", "GSM2852455", "GSM2852456", "GSM2852457", "GSM2852458", "GSM2852459", "GSM2852460", "GSM2852461", "GSM2852462", "GSM2852463", "GSM2852464", "GSM2852465", "GSM2852466", "GSM2852467", "GSM2852468", "GSM2852469", "GSM2852470", "GSM2852471", "GSM2852472", "GSM2852473", "GSM2852474", "GSM2852475", "GSM2852476", "GSM2852477", "GSM2852478", "GSM2852479", "GSM2852480", "GSM2852481", "GSM2852482", "GSM2852483", "GSM2852484", "GSM2852485", "GSM2852486", "GSM2852487", "GSM2852488", "GSM2852489", "GSM2852490", "GSM2852491", "GSM2852492", "GSM2852493", "GSM2852494", "GSM2852495", "GSM2852496", "GSM2852497", "GSM2852498", "GSM2852499", "GSM2852500", "GSM2852501", "GSM2852502", "GSM2852503", "GSM2852504", "GSM2852505", "GSM2852506", "GSM2852507", "GSM2852508", "GSM2852509", "GSM2852510", "GSM2852511", "GSM2852512", "GSM2852513", "GSM2852514", "GSM2852515", "GSM2852516", "GSM2852517", "GSM2852518", "GSM2852519", "GSM2852520", "GSM2852521", "GSM2852522", "GSM2852523", "GSM2852524", "GSM2852525", "GSM2852526", "GSM2852527", "GSM2852528", "GSM2852529", "GSM2852530", "GSM2852531", "GSM2852532", "GSM2852533", "GSM2852534", "GSM2852535", "GSM2852536", "GSM2852537", "GSM2852538", "GSM2852539", "GSM2852540", "GSM2852541", "GSM2852542", "GSM2852543", "GSM2852544", "GSM2852545", "GSM2852546", "GSM2852547", "GSM2852548", "GSM2852549", "GSM2852550", "GSM2852551", "GSM2852552", "GSM2852553", "GSM2852554", "GSM2852555", "GSM2852556", "GSM2852557", "GSM2852558", "GSM2852559", "GSM2852560", "GSM2852561", "GSM2852562", "GSM2852563", "GSM2852564", "GSM2852565", "GSM2852566", "GSM2852567", "GSM2852568", "GSM2852569", "GSM2852570", "GSM2852571", "GSM2852572", "GSM2852573", "GSM2852574", "GSM2852575", "GSM2852576", "GSM2852577", "GSM2852578", "GSM2852579", "GSM2852580", "GSM2852581", "GSM2852582", "GSM2852583", "GSM2852584", "GSM2852585", "GSM2852586", "GSM2852587", "GSM2852588", "GSM2852589", "GSM2852590", "GSM2852591", "GSM2852592", "GSM2852593", "GSM2852594", "GSM2852595", "GSM2852596", "GSM2852597", "GSM2852598", "GSM2852599", "GSM2852600", "GSM2852601", "GSM2852602", "GSM2852603", "GSM2852604", "GSM2852605", "GSM2852606", "GSM2852607", "GSM2852608", "GSM2852609", "GSM2852610", "GSM2852611", "GSM2852612", "GSM2852613", "GSM2852614", "GSM2852615", "GSM2852616", "GSM2852617", "GSM2852618", "GSM2852619", "GSM2852620", "GSM2852621", "GSM2852622", "GSM2852623", "GSM2852624", "GSM2852625", "GSM2852626", "GSM2852627", "GSM2852628", "GSM2852629", "GSM2852630", "GSM2852631", "GSM2852632", "GSM2852633", "GSM2852634", "GSM2852635", "GSM2852636", "GSM2852637", "GSM2852638", "GSM2852639", "GSM2852640", "GSM2852641", "GSM2852642", "GSM2852643", "GSM2852644", "GSM2852645", "GSM2852646", "GSM2852647", "GSM2852648", "GSM2852649", "GSM2852650", "GSM2852651", "GSM2852652", "GSM2852653", "GSM2852654", "GSM2852655", "GSM2852656", "GSM2852657", "GSM2852658", "GSM2852659", "GSM2852660", "GSM2852661", "GSM2852662", "GSM2852663", "GSM2852664", "GSM2852665", "GSM2852666", "GSM2852667", "GSM2852668", "GSM2852669", "GSM2852670", "GSM2852671", "GSM2852672", "GSM2852673", "GSM2852674", "GSM2852675", "GSM2852676", "GSM2852677", "GSM2852678", "GSM2852679", "GSM2852680", "GSM2852681", "GSM2852682", "GSM2852683", "GSM2852684", "GSM2852685", "GSM2852686", "GSM2852687", "GSM2852688", "GSM2852689", "GSM2852690", "GSM2852691", "GSM2852692", "GSM2852693", "GSM2852694", "GSM2852695", "GSM2852696", "GSM2852697", "GSM2852698", "GSM2852699", "GSM2852700", "GSM2852701", "GSM2852702", "GSM2852703", "GSM2852704", "GSM2852705", "GSM2852706", "GSM2852707", "GSM2852708", "GSM2852709", "GSM2852710", "GSM2852711", "GSM2852712", "GSM2852713", "GSM2852714", "GSM2852715", "GSM2852716", "GSM2852717", "GSM2852718", "GSM2852719", "GSM2852720", "GSM2852721", "GSM2852722", "GSM2852723", "GSM2852724", "GSM2852725", "GSM2852726", "GSM2852727", "GSM2852728", "GSM2852729", "GSM2852730", "GSM2852731", "GSM2852732", "GSM2852733", "GSM2852734", "GSM2852735", "GSM2852736", "GSM2852737", "GSM2852738", "GSM2852739", "GSM2852740", "GSM2852741", "GSM2852742", "GSM2852743", "GSM2852744", "GSM2852745", "GSM2852746", "GSM2852747", "GSM2852748", "GSM2852749", "GSM2852750", "GSM2852751", "GSM2852752", "GSM2852753", "GSM2852754", "GSM2852755", "GSM2852756", "GSM2852757", "GSM2852758", "GSM2852759", "GSM2852760", "GSM2852761", "GSM2852762", "GSM2852763", "GSM2852764", "GSM2852765", "GSM2852766", "GSM2852767", "GSM2852768", "GSM2852769", "GSM2852770", "GSM2852771", "GSM2852772", "GSM2852773", "GSM2852774", "GSM2852775", "GSM2852776", "GSM2852777", "GSM2852778", "GSM2852779", "GSM2852780", "GSM2852781", "GSM2852782", "GSM2852783", "GSM2852784", "GSM2852785", "GSM2852786", "GSM2852787", "GSM2852788", "GSM2852789", "GSM2852790", "GSM2852791", "GSM2852792", "GSM2852793", "GSM2852794", "GSM2852795", "GSM2852796", "GSM2852797", "GSM2852798", "GSM2852799", "GSM2852800", "GSM2852801", "GSM2852802", "GSM2852803", "GSM2852804", "GSM2852805", "GSM2852806", "GSM2852807", "GSM2852808", "GSM2852809", "GSM2852810", "GSM2852811", "GSM2852812", "GSM2852813", "GSM2852814", "GSM2852815", "GSM2852816", "GSM2852817", "GSM2852818", "GSM2852819", "GSM2852820", "GSM2852821", "GSM2852822", "GSM2852823", "GSM2852824", "GSM2852825", "GSM2852826", "GSM2852827", "GSM2852828", "GSM2852829", "GSM2852830", "GSM2852831", "GSM2852832", "GSM2852833", "GSM2852834", "GSM2852835", "GSM2852836", "GSM2852837", "GSM2852838", "GSM2852839", "GSM2852840", "GSM2852841", "GSM2852842", "GSM2852843", "GSM2852844", "GSM2852845", "GSM2852846", "GSM2852847", "GSM2852848", "GSM2852849", "GSM2852850", "GSM2852851", "GSM2852852", "GSM2852853", "GSM2852854", "GSM2852855", "GSM2852856", "GSM2852857", "GSM2852858", "GSM2852859", "GSM2852860", "GSM2852861", "GSM2852862", "GSM2852863", "GSM2852864", "GSM2852865", "GSM2852866", "GSM2852867", "GSM2852868", "GSM2852869", "GSM2852870", "GSM2852871", "GSM2852872", "GSM2852873", "GSM2852874", "GSM2852875", "GSM2852876", "GSM2852877", "GSM2852878", "GSM2852879", "GSM2852880", "GSM2852881", "GSM2852882", "GSM2852883", "GSM2852884", "GSM2852885", "GSM2852886", "GSM2852887", "GSM2852888", "GSM2852889", "GSM2852890", "GSM2852891", "GSM2852892", "GSM2852893", "GSM2852894", "GSM2852895", "GSM2852896", "GSM2852897", "GSM2852898", "GSM2852899", "GSM2852900", "GSM2852901", "GSM2852902", "GSM2852903", "GSM2852904", "GSM2852905", "GSM2852906", "GSM2852907", "GSM2852908", "GSM2852909", "GSM2852910", "GSM2852911", "GSM2852912", "GSM2852913", "GSM2852914", "GSM2852915", "GSM2852916", "GSM2852917", "GSM2852918", "GSM2852919", "GSM2852920", "GSM2852921", "GSM2852922", "GSM2852923", "GSM2852924", "GSM2852925", "GSM2852926", "GSM2852927", "GSM2852928", "GSM2852929", "GSM2852930", "GSM2852931", "GSM2852932", "GSM2852933", "GSM2852934", "GSM2852935", "GSM2852936", "GSM2852937", "GSM2852938", "GSM2852939", "GSM2852940", "GSM2852941", "GSM2852942", "GSM2852943", "GSM2852944", "GSM2852945", "GSM2852946", "GSM2852947", "GSM2852948", "GSM2852949", "GSM2852950", "GSM2852951", "GSM2852952", "GSM2852953", "GSM2852954", "GSM2852955", "GSM2852956", "GSM2852957", "GSM2852958", "GSM2852959", "GSM2852960", "GSM2852961", "GSM2852962", "GSM2852963", "GSM2852964", "GSM2852965", "GSM2852966", "GSM2852967", "GSM2852968", "GSM2852969", "GSM2852970", "GSM2852971", "GSM2852972", "GSM2852973", "GSM2852974", "GSM2852975", "GSM2852976", "GSM2852977", "GSM2852978", "GSM2852979", "GSM2852980", "GSM2852981", "GSM2852982", "GSM2852983", "GSM2852984", "GSM2852985", "GSM2852986", "GSM2852987", "GSM2852988", "GSM2852989", "GSM2852990", "GSM2852991", "GSM2852992", "GSM2852993", "GSM2852994", "GSM2852995", "GSM2852996", "GSM2852997", "GSM2852998", "GSM2852999", "GSM2853000", "GSM2853001", "GSM2853002", "GSM2853003", "GSM2853004", "GSM2853005", "GSM2853006", "GSM2853007", "GSM2853008", "GSM2853009", "GSM2853010", "GSM2853011", "GSM2853012", "GSM2853013", "GSM2853014", "GSM2853015", "GSM2853016", "GSM2853017", "GSM2853018", "GSM2853019", "GSM2853020", "GSM2853021", "GSM2853022", "GSM2853023", "GSM2853024", "GSM2853025", "GSM2853026", "GSM2853027", "GSM2853028", "GSM2853029", "GSM2853030", "GSM2853031", "GSM2853032", "GSM2853033", "GSM2853034", "GSM2853035", "GSM2853036", "GSM2853037", "GSM2853038", "GSM2853039", "GSM2853040", "GSM2853041", "GSM2853042", "GSM2853043", "GSM2853044", "GSM2853045", "GSM2853046", "GSM2853047", "GSM2853048", "GSM2853049", "GSM2853050", "GSM2853051", "GSM2853052", "GSM2853053", "GSM2853054", "GSM2853055", "GSM2853056", "GSM2853057", "GSM2853058", "GSM2853059", "GSM2853060", "GSM2853061", "GSM2853062", "GSM2853063", "GSM2853064", "GSM2853065", "GSM2853066", "GSM2853067", "GSM2853068", "GSM2853069", "GSM2853070", "GSM2853071", "GSM2853072", "GSM2853073", "GSM2853074", "GSM2853075", "GSM2853076", "GSM2853077", "GSM2853078", "GSM2853079", "GSM2853080", "GSM2853081", "GSM2853082", "GSM2853083", "GSM2853084", "GSM2853085", "GSM2853086", "GSM2853087", "GSM2853088", "GSM2853089", "GSM2853090", "GSM2853091", "GSM2853092", "GSM2853093", "GSM2853094", "GSM2853095", "GSM2853096", "GSM2853097", "GSM2853098", "GSM2853099", "GSM2853100", "GSM2853101", "GSM2853102", "GSM2853103", "GSM2853104", "GSM2853105", "GSM2853106", "GSM2853107", "GSM2853108", "GSM2853109", "GSM2853110", "GSM2853111", "GSM2853112", "GSM2853113", "GSM2853114", "GSM2853115", "GSM2853116", "GSM2853117", "GSM2853118", "GSM2853119", "GSM2853120", "GSM2853121", "GSM2853122", "GSM2853123", "GSM2853124", "GSM2853125", "GSM2853126", "GSM2853127", "GSM2853128", "GSM2853129", "GSM2853130", "GSM2853131", "GSM2853132", "GSM2853133", "GSM2853134", "GSM2853135", "GSM2853136", "GSM2853137", "GSM2853138", "GSM2853139", "GSM2853140", "GSM2853141", "GSM2853142", "GSM2853143", "GSM2853144", "GSM2853145", "GSM2853146", "GSM2853147", "GSM2853148", "GSM2853149", "GSM2853150", "GSM2853151", "GSM2853152", "GSM2853153", "GSM2853154", "GSM2853155", "GSM2853156", "GSM2853157", "GSM2853158", "GSM2853159", "GSM2853160", "GSM2853161", "GSM2853162", "GSM2853163", "GSM2853164", "GSM2853165", "GSM2853166", "GSM2853167", "GSM2853168", "GSM2853169", "GSM2853170", "GSM2853171", "GSM2853172", "GSM2853173", "GSM2853174", "GSM2853175", "GSM2853176", "GSM2853177", "GSM2853178", "GSM2853179", "GSM2853180", "GSM2853181", "GSM2853182", "GSM2853183", "GSM2853184", "GSM2853185", "GSM2853186", "GSM2853187", "GSM2853188", "GSM2853189", "GSM2853190", "GSM2853191", "GSM2853192", "GSM2853193", "GSM2853194", "GSM2853195", "GSM2853196", "GSM2853197", "GSM2853198", "GSM2853199", "GSM2853200", "GSM2853201", "GSM2853202", "GSM2853203", "GSM2853204", "GSM2853205", "GSM2853206", "GSM2853207", "GSM2853208", "GSM2853209", "GSM2853210", "GSM2853211", "GSM2853212", "GSM2853213", "GSM2853214", "GSM2853215", "GSM2853216", "GSM2853217", "GSM2853218", "GSM2853219", "GSM2853220", "GSM2853221", "GSM2853222", "GSM2853223", "GSM2853224", "GSM2853225", "GSM2853226", "GSM2853227", "GSM2853228", "GSM2853229", "GSM2853230", "GSM2853231", "GSM2853232", "GSM2853233", "GSM2853234", "GSM2853235", "GSM2853236", "GSM2853237", "GSM2853238", "GSM2853239", "GSM2853240", "GSM2853241", "GSM2853242", "GSM2853243", "GSM2853244", "GSM2853245", "GSM2853246", "GSM2853247", "GSM2853248", "GSM2853249", "GSM2853250", "GSM2853251", "GSM2853252", "GSM2853253", "GSM2853254", "GSM2853255", "GSM2853256", "GSM2853257", "GSM2853258", "GSM2853259", "GSM2853260", "GSM2853261", "GSM2853262", "GSM2853263", "GSM2853264", "GSM2853265", "GSM2853266", "GSM2853267", "GSM2853268", "GSM2853269", "GSM2853270", "GSM2853271", "GSM2853272", "GSM2853273", "GSM2853274", "GSM2853275", "GSM2853276", "GSM2853277", "GSM2853278", "GSM2853279", "GSM2853280", "GSM2853281", "GSM2853282", "GSM2853283", "GSM2853284", "GSM2853285", "GSM2853286", "GSM2853287", "GSM2853288", "GSM2853289", "GSM2853290", "GSM2853291", "GSM2853292", "GSM2853293", "GSM2853294", "GSM2853295", "GSM2853296", "GSM2853297", "GSM2853298", "GSM2853299", "GSM2853300", "GSM2853301", "GSM2853302", "GSM2853303", "GSM2853304", "GSM2853305", "GSM2853306", "GSM2853307", "GSM2853308", "GSM2853309", "GSM2853310", "GSM2853311", "GSM2853312", "GSM2853313", "GSM2853314", "GSM2853315", "GSM2853316", "GSM2853317", "GSM2853318", "GSM2853319", "GSM2853320", "GSM2853321", "GSM2853322", "GSM2853323", "GSM2853324", "GSM2853325", "GSM2853326", "GSM2853327", "GSM2853328", "GSM2853329", "GSM2853330", "GSM2853331", "GSM2853332", "GSM2853333", "GSM2853334", "GSM2853335", "GSM2853336", "GSM2853337", "GSM2853338", "GSM2853339", "GSM2853340", "GSM2853341", "GSM2853342", "GSM2853343", "GSM2853344", "GSM2853345", "GSM2853346", "GSM2853347", "GSM2853348", "GSM2853349", "GSM2853350", "GSM2853351", "GSM2853352", "GSM2853353", "GSM2853354", "GSM2853355", "GSM2853356", "GSM2853357", "GSM2853358", "GSM2853359", "GSM2853360", "GSM2853361", "GSM2853362", "GSM2853363", "GSM2853364", "GSM2853365", "GSM2853366", "GSM2853367", "GSM2853368", "GSM2853369", "GSM2853370", "GSM2853371", "GSM2853372", "GSM2853373", "GSM2853374", "GSM2853375", "GSM2853376", "GSM2853377", "GSM2853378", "GSM2853379", "GSM2853380", "GSM2853381", "GSM2853382", "GSM2853383", "GSM2853384", "GSM2853385", "GSM2853386", "GSM2853387", "GSM2853388", "GSM2853389", "GSM2853390", "GSM2853391", "GSM2853392", "GSM2853393", "GSM2853394", "GSM2853395", "GSM2853396", "GSM2853397", "GSM2853398", "GSM2853399", "GSM2853400", "GSM2853401", "GSM2853402", "GSM2853403", "GSM2853404", "GSM2853405", "GSM2853406", "GSM2853407", "GSM2853408", "GSM2853409", "GSM2853410", "GSM2853411", "GSM2853412", "GSM2853413", "GSM2853414", "GSM2853415", "GSM2853416", "GSM2853417", "GSM2853418", "GSM2853419", "GSM2853420", "GSM2853421", "GSM2853422", "GSM2853423", "GSM2853424", "GSM2853425", "GSM2853426", "GSM2853427", "GSM2853428", "GSM2853429", "GSM2853430", "GSM2853431", "GSM2853432", "GSM2853433", "GSM2853434", "GSM2853435", "GSM2853436", "GSM2853437", "GSM2853438", "GSM2853439", "GSM2853440", "GSM2853441", "GSM2853442", "GSM2853443", "GSM2853444", "GSM2853445", "GSM2853446", "GSM2853447", "GSM2853448", "GSM2853449", "GSM2853450", "GSM2853451", "GSM2853452", "GSM2853453", "GSM2853454", "GSM2853455", "GSM2853456", "GSM2853457", "GSM2853458", "GSM2853459", "GSM2853460", "GSM2853461", "GSM2853462", "GSM2853463", "GSM2853464", "GSM2853465", "GSM2853466", "GSM2853467", "GSM2853468", "GSM2853469", "GSM2853470", "GSM2853471", "GSM2853472", "GSM2853473", "GSM2853474", "GSM2853475", "GSM2853476", "GSM2853477", "GSM2853478", "GSM2853479", "GSM2853480", "GSM2853481", "GSM2853482", "GSM2853483", "GSM2853484", "GSM2853485", "GSM2853486", "GSM2853487", "GSM2853488", "GSM2853489", "GSM2853490", "GSM2853491", "GSM2853492", "GSM2853493", "GSM2853494", "GSM2853495", "GSM2853496", "GSM2853497", "GSM2853498", "GSM2853499", "GSM2853500", "GSM2853501", "GSM2853502", "GSM2853503", "GSM2853504", "GSM2853505", "GSM2853506", "GSM2853507", "GSM2853508", "GSM2853509", "GSM2853510", "GSM2853511", "GSM2853512", "GSM2853513", "GSM2853514", "GSM2853515", "GSM2853516", "GSM2853517", "GSM2853518", "GSM2853519", "GSM2853520", "GSM2853521", "GSM2853522", "GSM2853523", "GSM2853524", "GSM2853525", "GSM2853526", "GSM2853527", "GSM2853528", "GSM2853529", "GSM2853530", 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"GSM1606828", "GSM1606829", "GSM1606830", "GSM1606831", "GSM1606832", "GSM1606833", "GSM1606834", "GSM1606835", "GSM1606836", "GSM1606837", "GSM1606838", "GSM1606839", "GSM1606840", "GSM1606841", "GSM1606842", "GSM1606843", "GSM1606844", "GSM1606845", "GSM1606846", "GSM1606847", "GSM1606848", "GSM1606849", "GSM1606850", "GSM1606851", "GSM1606852", "GSM1606853", "GSM1606854"], "sample_count": 121, "group_sizes": null, "group_sizes_basis": null, "platform": "19765", "taxon": "Homo sapiens", "title": "Whole genome characterisation of chemoresistant ovarian cancer [NanoString miRNA]", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE106817 not downloaded", "asset:data:geo:GSE106817 licence not read", "asset:data:geo:GSE113486 not downloaded", "asset:data:geo:GSE113486 licence not read", "asset:data:geo:GSE127873 not downloaded", "asset:data:geo:GSE127873 licence not read", "asset:data:geo:GSE31568 not downloaded", "asset:data:geo:GSE31568 licence not read", "asset:data:geo:GSE65819 not downloaded", "asset:data:geo:GSE65819 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Eight miRNAs significantly upregulated in OC tissues were employed to build a multivariate logistic regression model from the discovery cohort, and the scoring formula derived from the model was applied to TCGA and GSE65819 for independent tissue validation."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "Principal components analysis"}}, {"id": "method-3", "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": 0.8, "band": "high", "quote": "limma"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["glm_logit_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: logistic."}, "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": ["GSE65819", "GSE106817", "GSE113486", "GSE31568", "GSE127873"], "resolved_accessions": ["GSE65819", "GSE106817", "GSE113486", "GSE31568", "GSE127873"], "statements": ["The raw sequencing data is accessible in GEO database (accession number: GSE127873)."], "basis": "The paper names GSE65819, GSE106817, GSE113486, GSE31568, GSE127873 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": ["glm_logit_fit"], "assets": ["source:pmid:34035068", "data:geo:GSE106817"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE106817"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:02:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8656, "completion_tokens": 2132, "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:34035068", "type": "paper", "label": "pmid:34035068"}, {"id": "source:pmid:34035068", "type": "manuscript", "label": "PMID 34035068 full text"}, {"id": "data:geo:GSE106817", "type": "dataset", "label": "GEO GSE106817"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34035068", "type": "paper", "label": "pmid:34035068"}, {"id": "source:pmid:34035068", "type": "manuscript", "label": "PMID 34035068 full text"}, {"id": "data:geo:GSE106817", "type": "dataset", "label": "GEO GSE106817"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34035068", "type": "extraction", "used": ["source:pmid:34035068"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE106817", "type": "accession_resolution", "used": ["data:geo:GSE106817"], "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:34035068", "parent_hash": "sha256:6bd47dda0d9a9bdea8f0a5f1474b429ad0bfda397f9bfbed85abfd89b20bce56", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE106817 licence not read", "asset:data:geo:GSE106817 not downloaded", "asset:data:geo:GSE113486 licence not read", "asset:data:geo:GSE113486 not downloaded", "asset:data:geo:GSE127873 licence not read", "asset:data:geo:GSE127873 not downloaded", "asset:data:geo:GSE31568 licence not read", "asset:data:geo:GSE31568 not downloaded", "asset:data:geo:GSE65819 licence not read", "asset:data:geo:GSE65819 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ring the discovery phase, we performed small RNA sequencing in stage I high-grade serous ovarian cancer", "ection of ovarian cancer. CONCLUSIONS: Small RNA sequencing identified a robust noninvasive miRNA signat", "een cancer and normal tissues from the small RNA sequencing data using limma (32). Differential miRNAs w"], "order_basis": "paper_text_order:476", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Eight miRNAs significantly upregulated in OC tissues were employed to build a multivariate logistic regression model from the discovery cohort, and the scoring formula derived from the model was applied to TCGA and GSE65819 for independent tissue validation."], "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":"2026-11-04T02:25:29+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}}}