{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30659574", "kind": "science-record", "revision": 8, "content_hash": "sha256:3b2e8b8e8fdd34f84b61c5569e4804572c734b0e907cd4bc1d0f31837a6806e2", "created_at": "2026-11-01T15:40:40Z", "updated_at": "2026-11-01T22:00:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Combined eight-long noncoding RNA signature: a new risk score predicting prognosis in elderly non-small cell lung cancer patients.", "doi": "10.18632/aging.101752", "pmid": "30659574", "authors": ["Runchen Miao", "Cuiyun Ge", "Xing Zhang", "Yang He", "Xiaohua Ma", "Xiaohong Xiang", "Jingxian Gu", "Yunong Fu", "Kai Qu", "Chang Liu", "Qifei Wu", "Ting Lin"], "journal": "Aging", "year": 2019, "abstract": "The elderly are the majority of patients with non-small cell lung cancer (NSCLC). Compared to the overall population's predictive guidance, an effective predictive guidance for elderly patients can better guide patients' postoperative treatment and improve overall survival (OS) and disease-free survival (DFS). Recently, the long non-coding RNAs (lncRNAs) have been found to play an important role in predicting tumor prognosis. To identify potential lncRNAs to predict survival in elderly patients with NSCLC, in the present study, we chose 456 elderly patients with NSCLC and analyzed differentially expressed lncRNAs from four Gene Expression Omnibus (GEO) datasets (GSE30219, GSE31546, GSE37745 and GSE50081). We then constructed an eight-lncRNA formula to predict elderly patients' prognosis in NSCLC. Furthermore, we validated the prognostic values of the new risk model in two independent datasets, TCGA (n=670) and GSE31210 (n=130). Our data suggested a significant association between risk model and patients' prognosis. Finally, stratification analysis further revealed the eight-lncRNA signature was an independent factor to predict OS and DFS in stage I elderly patients from both the discovery and validation groups. Functional prediction revealed that 8 lncRNAs have potential effects on tumor immune processes such as lymphocyte activation and TNF production in NSCLC. In summary, our data provides evidence that the eight-lncRNA signature could serve as an independent biomarker to predict prognosis in elderly patients with NSCLC especially in elderly stage I patients.", "claims": [{"id": "claim-method", "statement": "Cox proportional hazards regression was used to identify survival-related biomarkers. Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30659574", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "Cox proportional hazards regression was used to identify survival-related biomarkers."}, {"asset": "source:pmid:30659574", "locator": "sections[10] \"Patient information and study design\" paragraph 2", "quote": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30659574", "locator": "sections[10] \"Patient information and study design\" paragraph 2", "quote": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30659574"], "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:GSE30219"], "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:GSE30219"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30659574", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.101752", "sha256": "sha256:3f6fc015cfd1410819d7615ea28a943820acb14021226e3e56df10fc86daf2f0", "bytes": 26652, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.101752", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6366982", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30219", "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=GSE30219", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30219", "version": null, "note": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1465989", "GSM1465990", "GSM1465991", "GSM1465992", "GSM1465993", "GSM1465994", "GSM1465995", "GSM1465996", "GSM1465997", "GSM1465998", "GSM1465999", "GSM748053", "GSM748054", "GSM748055", "GSM748056", "GSM748057", "GSM748058", "GSM748059", "GSM748060", "GSM748061", "GSM748062", "GSM748063", "GSM748064", "GSM748065", "GSM748066", "GSM748067", "GSM748068", "GSM748069", "GSM748070", "GSM748071", "GSM748072", "GSM748073", "GSM748074", "GSM748075", "GSM748076", "GSM748077", "GSM748078", "GSM748079", "GSM748080", "GSM748081", "GSM748083", "GSM748084", "GSM748085", "GSM748086", "GSM748087", "GSM748088", "GSM748089", "GSM748090", "GSM748091", "GSM748092", "GSM748093", "GSM748094", "GSM748095", "GSM748096", "GSM748097", "GSM748098", "GSM748099", "GSM748100", "GSM748101", "GSM748102", "GSM748103", "GSM748104", "GSM748105", "GSM748106", "GSM748107", "GSM748108", "GSM748109", "GSM748110", "GSM748111", "GSM748112", "GSM748113", "GSM748115", "GSM748116", "GSM748117", "GSM748118", "GSM748119", "GSM748120", "GSM748121", "GSM748122", "GSM748123", "GSM748124", "GSM748125", "GSM748126", "GSM748127", "GSM748128", "GSM748129", "GSM748130", "GSM748131", "GSM748132", "GSM748133", "GSM748134", "GSM748135", "GSM748136", "GSM748137", "GSM748138", "GSM748139", "GSM748140", "GSM748141", "GSM748142", "GSM748143", "GSM748144", "GSM748145", "GSM748146", "GSM748147", "GSM748148", "GSM748149", "GSM748150", "GSM748151", "GSM748152", "GSM748153", "GSM748154", "GSM748155", "GSM748156", "GSM748157", "GSM748158", "GSM748159", "GSM748160", "GSM748161", "GSM748162", "GSM748163", "GSM748164", "GSM748165", "GSM748166", "GSM748167", "GSM748168", "GSM748169", "GSM748170", "GSM748171", "GSM748172", "GSM748173", "GSM748174", "GSM748175", "GSM748176", "GSM748177", "GSM748178", "GSM748179", "GSM748180", "GSM748181", "GSM748182", "GSM748183", "GSM748184", "GSM748185", "GSM748186", "GSM748187", "GSM748188", "GSM748189", "GSM748191", "GSM748192", "GSM748193", "GSM748195", "GSM748196", "GSM748197", "GSM748198", "GSM748199", "GSM748200", "GSM748201", "GSM748202", "GSM748203", "GSM748206", "GSM748207", "GSM748209", "GSM748210", "GSM748211", "GSM748212", "GSM748213", "GSM748214", "GSM748215", "GSM748216", "GSM748217", "GSM748218", "GSM748219", "GSM748220", "GSM748221", "GSM748222", "GSM748223", "GSM748224", "GSM748225", "GSM748226", "GSM748227", "GSM748228", "GSM748229", "GSM748232", "GSM748233", "GSM748234", "GSM748235", "GSM748239", "GSM748240", "GSM748242", "GSM748243", "GSM748244", "GSM748245", "GSM748246", "GSM748247", "GSM748248", "GSM748249", "GSM748250", "GSM748251", "GSM748252", "GSM748253", "GSM748254", "GSM748255", "GSM748256", "GSM748257", "GSM748258", "GSM748259", "GSM748260", "GSM748261", "GSM748262", "GSM748263", "GSM748264", "GSM748265", "GSM748266", "GSM748267", "GSM748268", "GSM748269", "GSM748270", "GSM748271", "GSM748272", "GSM748273", "GSM748274", "GSM748275", "GSM748276", "GSM748277", "GSM748278", "GSM748279", "GSM748280", "GSM748281", "GSM748282", "GSM748283", "GSM748284", "GSM748285", "GSM748286", "GSM748287", "GSM748288", "GSM748291", "GSM748292", "GSM748294", "GSM748295", "GSM748296", "GSM748297", "GSM748298", "GSM748299", "GSM748300", "GSM748301", "GSM748302", "GSM748303", "GSM748304", "GSM748305", "GSM748306", "GSM748307", "GSM748308", "GSM748309", "GSM748310", "GSM748311", "GSM748312", "GSM748313", "GSM748314", "GSM748315", "GSM748316", "GSM748317", "GSM748318", "GSM748319", "GSM748320", "GSM748321", "GSM748323", "GSM748324", "GSM748325", "GSM748326", "GSM748327", "GSM748328", "GSM748329", "GSM748330", "GSM748331", "GSM748332", "GSM748333", "GSM748334", "GSM748335", "GSM748336", "GSM748337", "GSM748338", "GSM748339", "GSM748341", "GSM748342", "GSM748343", "GSM748344", "GSM748345", "GSM748346", "GSM748347", "GSM748348", "GSM748349", "GSM748350", "GSM748351", "GSM748352", "GSM748353", "GSM748354", "GSM748355", "GSM748356", "GSM748357", "GSM748358", "GSM748359", "GSM748360", "GSM748361", "GSM748362", "GSM748363", "GSM748364", "GSM748365", "GSM748366"], "sample_count": 307, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "\"Off-context\" gene expression in lung cancer identifies a group of metastatic-prone tumors", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31210", "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=GSE31210", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31210", "version": null, "note": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM773540", "GSM773541", "GSM773542", "GSM773543", "GSM773544", "GSM773545", "GSM773546", "GSM773547", "GSM773548", "GSM773549", "GSM773550", "GSM773551", "GSM773552", "GSM773553", "GSM773554", "GSM773555", "GSM773556", "GSM773557", "GSM773558", "GSM773559", "GSM773560", "GSM773561", "GSM773562", "GSM773563", "GSM773564", "GSM773565", "GSM773566", "GSM773567", "GSM773568", "GSM773569", "GSM773570", "GSM773571", "GSM773572", "GSM773573", "GSM773574", "GSM773575", "GSM773576", "GSM773577", "GSM773578", "GSM773579", "GSM773580", "GSM773581", "GSM773582", "GSM773583", "GSM773584", "GSM773585", "GSM773586", "GSM773587", "GSM773588", "GSM773589", "GSM773590", "GSM773591", "GSM773592", "GSM773593", "GSM773594", "GSM773595", "GSM773596", "GSM773597", "GSM773598", "GSM773599", "GSM773600", "GSM773601", "GSM773602", "GSM773603", "GSM773604", "GSM773605", "GSM773606", "GSM773607", "GSM773608", "GSM773609", "GSM773610", "GSM773611", "GSM773612", "GSM773613", "GSM773614", "GSM773615", "GSM773616", "GSM773617", "GSM773618", "GSM773619", "GSM773620", "GSM773621", "GSM773622", "GSM773623", "GSM773624", "GSM773625", "GSM773626", "GSM773627", "GSM773628", "GSM773629", "GSM773630", "GSM773631", "GSM773632", "GSM773633", "GSM773634", "GSM773635", "GSM773636", "GSM773637", "GSM773638", "GSM773639", "GSM773640", "GSM773641", "GSM773642", "GSM773643", "GSM773644", "GSM773645", "GSM773646", "GSM773647", "GSM773648", "GSM773649", "GSM773650", "GSM773651", "GSM773652", "GSM773653", "GSM773654", "GSM773655", "GSM773656", "GSM773657", "GSM773658", "GSM773659", "GSM773660", "GSM773661", "GSM773662", "GSM773663", "GSM773664", "GSM773665", "GSM773666", "GSM773667", "GSM773668", "GSM773669", "GSM773670", "GSM773671", "GSM773672", "GSM773673", "GSM773674", "GSM773675", "GSM773676", "GSM773677", "GSM773678", "GSM773679", "GSM773680", "GSM773681", "GSM773682", "GSM773683", "GSM773684", "GSM773685", "GSM773686", "GSM773687", "GSM773688", "GSM773689", "GSM773690", "GSM773691", "GSM773692", "GSM773693", "GSM773694", "GSM773695", "GSM773696", "GSM773697", "GSM773698", "GSM773699", "GSM773700", "GSM773701", "GSM773702", "GSM773703", "GSM773704", "GSM773705", "GSM773706", "GSM773707", "GSM773708", "GSM773709", "GSM773710", "GSM773711", "GSM773712", "GSM773713", "GSM773714", "GSM773715", "GSM773716", "GSM773717", "GSM773718", "GSM773719", "GSM773720", "GSM773721", "GSM773722", "GSM773723", "GSM773724", "GSM773725", "GSM773726", "GSM773727", "GSM773728", "GSM773729", "GSM773730", "GSM773731", "GSM773732", "GSM773733", "GSM773734", "GSM773735", "GSM773736", "GSM773737", "GSM773738", "GSM773739", "GSM773740", "GSM773741", "GSM773742", "GSM773743", "GSM773744", "GSM773745", "GSM773746", "GSM773747", "GSM773748", "GSM773749", "GSM773750", "GSM773751", "GSM773752", "GSM773753", "GSM773754", "GSM773755", "GSM773756", "GSM773757", "GSM773758", "GSM773759", "GSM773760", "GSM773761", "GSM773762", "GSM773763", "GSM773764", "GSM773765", "GSM773766", "GSM773767", "GSM773768", "GSM773769", "GSM773770", "GSM773771", "GSM773772", "GSM773773", "GSM773774", "GSM773775", "GSM773776", "GSM773777", "GSM773778", "GSM773779", "GSM773780", "GSM773781", "GSM773782", "GSM773783", "GSM773784", "GSM773785"], "sample_count": 246, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data for pathological stage I-II lung adenocarcinomas", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31546", "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=GSE31546", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31546", "version": null, "note": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM782960", "GSM782961", "GSM782962", "GSM782963", "GSM782964", "GSM782965", "GSM782966", "GSM782967", "GSM782968", "GSM782969", "GSM782970", "GSM782971", "GSM782972", "GSM782973", "GSM782974", "GSM782975", "GSM782976"], "sample_count": 17, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "UMCCC Primary Lung Cancer Specimens", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE37745", "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=GSE37745", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37745", "version": null, "note": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1019138", "GSM1019139", "GSM1019140", "GSM1019141", "GSM1019142", "GSM1019143", "GSM1019144", "GSM1019145", "GSM1019146", "GSM1019147", "GSM1019148", "GSM1019149", "GSM1019150", "GSM1019151", "GSM1019152", "GSM1019153", "GSM1019154", "GSM1019155", "GSM1019156", "GSM1019157", "GSM1019158", "GSM1019159", "GSM1019160", "GSM1019161", "GSM1019162", "GSM1019163", "GSM1019164", "GSM1019165", "GSM1019166", "GSM1019167", "GSM1019168", "GSM1019169", "GSM1019170", "GSM1019171", "GSM1019172", "GSM1019173", "GSM1019174", "GSM1019175", "GSM1019176", "GSM1019177", "GSM1019178", "GSM1019179", "GSM1019180", "GSM1019181", "GSM1019182", "GSM1019183", "GSM1019184", "GSM1019185", "GSM1019186", "GSM1019187", "GSM1019188", "GSM1019189", "GSM1019190", "GSM1019191", "GSM1019192", "GSM1019193", "GSM1019194", "GSM1019195", "GSM1019196", "GSM1019197", "GSM1019198", "GSM1019199", "GSM1019200", "GSM1019201", "GSM1019202", "GSM1019203", "GSM1019204", "GSM1019205", "GSM1019206", "GSM1019207", "GSM1019208", "GSM1019209", "GSM1019210", "GSM1019211", "GSM1019212", "GSM1019213", "GSM1019214", "GSM1019215", "GSM1019216", "GSM1019217", "GSM1019218", "GSM1019219", "GSM1019220", "GSM1019221", "GSM1019222", "GSM1019223", "GSM1019224", "GSM1019225", "GSM1019226", "GSM1019227", "GSM1019228", "GSM1019229", "GSM1019230", "GSM1019231", "GSM1019232", "GSM1019233", "GSM1019234", "GSM1019235", "GSM1019236", "GSM1019237", "GSM1019238", "GSM1019239", "GSM1019240", "GSM1019241", "GSM1019242", "GSM1019243", "GSM1019244", "GSM1019245", "GSM1019246", "GSM1019247", "GSM1019248", "GSM1019249", "GSM1019250", "GSM1019251", "GSM1019252", "GSM1019253", "GSM1019254", "GSM1019255", "GSM1019256", "GSM1019257", "GSM1019258", "GSM1019259", "GSM1019260", "GSM1019261", "GSM1019262", "GSM1019263", "GSM1019264", "GSM1019265", "GSM1019266", "GSM1019267", "GSM1019268", "GSM1019269", "GSM1019270", "GSM1019271", "GSM1019272", "GSM1019273", "GSM1019274", "GSM1019275", "GSM1019276", "GSM1019277", "GSM1019278", "GSM1019279", "GSM1019280", "GSM1019281", "GSM1019282", "GSM1019283", "GSM1019284", "GSM1019285", "GSM1019286", "GSM1019287", "GSM1019288", "GSM1019289", "GSM1019290", "GSM1019291", "GSM1019292", "GSM1019293", "GSM1019294", "GSM1019295", "GSM1019296", "GSM1019297", "GSM1019298", "GSM1019299", "GSM1019300", "GSM1019301", "GSM1019302", "GSM1019303", "GSM1019304", "GSM1019305", "GSM1019306", "GSM1019307", "GSM1019308", "GSM1019309", "GSM1019310", "GSM1019311", "GSM1019312", "GSM1019313", "GSM1019314", "GSM1019315", "GSM1019316", "GSM1019317", "GSM1019318", "GSM1019319", "GSM1019320", "GSM1019321", "GSM1019322", "GSM1019323", "GSM1019324", "GSM1019325", "GSM1019326", "GSM1019327", "GSM1019328", "GSM1019329", "GSM1019330", "GSM1019331", "GSM1019332", "GSM1019333"], "sample_count": 196, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis and tissue microarray validation", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE50081", "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=GSE50081", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE50081", "version": null, "note": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1213669", "GSM1213670", "GSM1213671", "GSM1213672", "GSM1213673", "GSM1213674", "GSM1213675", "GSM1213676", "GSM1213677", "GSM1213678", "GSM1213679", "GSM1213680", "GSM1213681", "GSM1213682", "GSM1213683", "GSM1213684", "GSM1213685", "GSM1213686", "GSM1213687", "GSM1213688", "GSM1213689", "GSM1213690", "GSM1213691", "GSM1213692", "GSM1213693", "GSM1213694", "GSM1213695", "GSM1213696", "GSM1213697", "GSM1213698", "GSM1213699", "GSM1213700", "GSM1213701", "GSM1213702", "GSM1213703", "GSM1213704", "GSM1213705", "GSM1213706", "GSM1213707", "GSM1213708", "GSM1213709", "GSM1213710", "GSM1213711", "GSM1213712", "GSM1213713", "GSM1213714", "GSM1213715", "GSM1213716", "GSM1213717", "GSM1213718", "GSM1213719", "GSM1213720", "GSM1213721", "GSM1213722", "GSM1213723", "GSM1213724", "GSM1213725", "GSM1213726", "GSM1213727", "GSM1213728", "GSM1213729", "GSM1213730", "GSM1213731", "GSM1213732", "GSM1213733", "GSM1213734", "GSM1213735", "GSM1213736", "GSM1213737", "GSM1213738", "GSM1213739", "GSM1213740", "GSM1213741", "GSM1213742", "GSM1213743", "GSM1213744", "GSM1213745", "GSM1213746", "GSM1213747", "GSM1213748", "GSM1213749", "GSM1213750", "GSM1213751", "GSM1213752", "GSM1213753", "GSM1213754", "GSM1213755", "GSM1213756", "GSM1213757", "GSM1213758", "GSM1213759", "GSM1213760", "GSM1213761", "GSM1213762", "GSM1213763", "GSM1213764", "GSM1213765", "GSM1213766", "GSM1213767", "GSM1213768", "GSM1213769", "GSM1213770", "GSM1213771", "GSM1213772", "GSM1213773", "GSM1213774", "GSM1213775", "GSM1213776", "GSM1213777", "GSM1213778", "GSM1213779", "GSM1213780", "GSM1213781", "GSM1213782", "GSM1213783", "GSM1213784", "GSM1213785", "GSM1213786", "GSM1213787", "GSM1213788", "GSM1213789", "GSM1213790", "GSM1213791", "GSM1213792", "GSM1213793", "GSM1213794", "GSM1213795", "GSM1213796", "GSM1213797", "GSM1213798", "GSM1213799", "GSM1213800", "GSM1213801", "GSM1213802", "GSM1213803", "GSM1213804", "GSM1213805", "GSM1213806", "GSM1213807", "GSM1213808", "GSM1213809", "GSM1213810", "GSM1213811", "GSM1213812", "GSM1213813", "GSM1213814", "GSM1213815", "GSM1213816", "GSM1213817", "GSM1213818", "GSM1213819", "GSM1213820", "GSM1213821", "GSM1213822", "GSM1213823", "GSM1213824", "GSM1213825", "GSM1213826", "GSM1213827", "GSM1213828", "GSM1213829", "GSM1213830", "GSM1213831", "GSM1213832", "GSM1213833", "GSM1213834", "GSM1213835", "GSM1213836", "GSM1213837", "GSM1213838", "GSM1213839", "GSM1213840", "GSM1213841", "GSM1213842", "GSM1213843", "GSM1213844", "GSM1213845", "GSM1213846", "GSM1213847", "GSM1213848", "GSM1213849"], "sample_count": 181, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Validation of a histology-independent prognostic gene signature for early stage, non-small cell lung cancer including stage IA patients", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30659574:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5c9258604615694225bdebbb58a9dcf2f703884e214aab933799b078cc5a576e", "bytes": 1007, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#t1", "version": null, "note": "Eight lncRNAs significantly associated with prognosis of NSCLC patients in the training group.", "structure": {"pmcid": "PMC6366982", "section_index": 3, "section_title": "Identification of eight lncRNAs for prognosis prediction in the training group", "row_count": 9, "column_count": 7}, "table": {"label": "Table 1", "caption": "Eight lncRNAs significantly associated with prognosis of NSCLC patients in the training group.", "rows": [["Gene name", "Ensemble ID", "Chr.", "Coordinate", "Coefficient", "Hazard ratio", "P value"], ["LOC284632", "ENSG00000230023", "1", "24,200,240-24,211,690", "0.690", "1.993", "0.085"], ["LINC00869", "ENSG00000277147", "1", "149,607,012-149,679,523", "0.272", "1.313", "0.083"], ["LINC00703", "ENSG00000224382", "10", "4,384,246-4,410,612", "0.829", "2.291", "0.064"], ["LINC00662", "ENSG00000261824", "19", "27,790,493-27,793,940", "0.076", "1.079", "0.473"], ["LINC00324", "ENSG00000178977", "17", "8,220,630-8,224,043", "-0.646", "0.524", "<0.0001"], ["ITGA9-AS1", "ENSG00000235257", "3", "37,753,689-37,861,780", "-0.445", "0.641", "0.174"], ["HOXA11-AS", "ENSG00000240990", "7", "27,185,408-27,189,293", "0.020", "1.020", "0.909"], ["DHRS4-AS1", "ENSG00000215256", "14", "23,938,731-23,955,112", "-0.204", "0.815", "0.106"]], "row_count": 9, "column_count": 7, "numeric_cells": 54, "header_rows": 0, "locator": "section[3]/table-wrap[1]#t1"}}, {"id": "asset:table:pmid:30659574:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c6771b8120236a2f091fe172c5728a9774b979b69c700a30c8f0d6e4e70bd270", "bytes": 1988, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#t2", "version": null, "note": "The association between eight-lncRNA signature and OS of NSCLC patients in discovery and validating groups.", "structure": {"pmcid": "PMC6366982", "section_index": 6, "section_title": "The eight lncRNAs signature was associated with prognosis in stage I patients", "row_count": 18, "column_count": 10}, "table": {"label": "Table 2", "caption": "The association between eight-lncRNA signature and OS of NSCLC patients in discovery and validating groups.", "rows": [["Variable", "Discovery Group", "Validation Group-1", "Validation Group-2"], ["Number(High/Low)", "HR (95%CI)", "P value", "Number(High/Low)", "HR (95%CI)", "P value", "Number(High/Low)", "HR (95%CI)", "P value"], ["Total", "228/228", "2.08 (1.66-2.62)", "<0.001", "335/335", "1.48 (1.17-1.86)", "0.001", "65/65", "2.96 (1.28-6.83)", "0.017"], ["Gender", "", "", "", "", "", "", "", "", ""], ["Male", "171/142", "1.89(1.46-2.45)", "<0.001", "209/212", "1.46 (1.10-1.94)", "0.008", "35/25", "5.68 (1.41-11.47)", "0.010"], ["Female", "57/86", "2.34 (1.53-3.96)", "<0.001", "126/123", "1.55 (1.03-2.34)", "0.036", "30/40", "1.23 (0.31-4.96)", "0.772"], ["Smoking history", "", "", "", "", "", "", "", "", ""], ["Never smoker", "1/16", "4.60 (0.49-1458)", "0.117", "22/29", "1.74(0.72-4.17)", "0.189", "24/42", "1.75(0.43-7.65)", "0.420"], ["Ever smoker", "10/61", "0.96 (0.34-2.70)", "0.934", "217/237", "1.382(1.03-1.85)", "0.029", "41/22", "3.889(0.98-8.38)", "0.055"], ["Current smoker", "8/40", "1.11 (0.45-3.10)", "0.786", "84/59", "1.52(0.97-2.36)", "0.060", "0/0", "NA", "NA"], ["Histology", "", "", "", "", "", "", "", "", ""], ["Squamous Carcinoma", "141/95", "2.04 (1.30-2.86)", "0.001", "219/196", "1.27 (0.96-1.70)", "0.099", "0/0", "NA", "NA"], ["Adenocarcinoma", "68/152", "2.11 (1.60-3.54)", "<0.001", "116/139", "1.97 (1.32-2.95)", "<0.001", "0/0", "NA", "NA"], ["AJCC stage", "", "", "", "", "", "", "", "", ""], ["Stage I", "144/166", "2.12 (1.63-2.88)", "< 0.001", "180/174", "1.68 (1.19-2.38)", "0.003", "41/56", "4.39 (1.32-13.25)", "0.015"], ["Stage II", "39/50", "1.49 (0.88-2.57)", "0.138", "97/86", "1.44 (0.91-2.28)", "0.118", "24/9", "1.29 (0.37-4.37)", "0.703"], ["Stage III", "37/9", "1.84 (0.94-3.31)", "0.087", "54/57", "1.25 (0.76-2.06)", "0.382", "0/0", "NA", "NA"], ["Stage IV", "5/3", "1.08 (0.22-5.44)", "0.925", "3/13", "6.02 (0.52-70.04)", "0.003", "0/0", "NA", "NA"]], "row_count": 18, "column_count": 10, "numeric_cells": 103, "header_rows": 0, "locator": "section[6]/table-wrap[1]#t2"}}, {"id": "asset:table:pmid:30659574:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e628cfc8a4c73271a44688981ad58b101dbfeec59ff0a805b5887ca59b737ad5", "bytes": 1976, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[2]#t3", "version": null, "note": "The association between eight-lncRNA signature and DFS of NSCLC patients in discovery and validating groups.", "structure": {"pmcid": "PMC6366982", "section_index": 6, "section_title": "The eight lncRNAs signature was associated with prognosis in stage I patients", "row_count": 18, "column_count": 10}, "table": {"label": "Table 3", "caption": "The association between eight-lncRNA signature and DFS of NSCLC patients in discovery and validating groups.", "rows": [["Variable", "Discovery Group", "Validation Group-1", "Validation Group-2"], ["Number(High/Low)", "HR (95%CI)", "Pvalue", "Number(High/Low)", "HR (95%CI)", "P value", "Number(High/Low)", "HR (95%CI)", "Pvalue"], ["Total", "228/228", "2.61 (1.91-3.67)", "<0.001", "335/335", "1.45 (1.11-1.91)", "0.006", "65/65", "3.05 (1.58-5.26)", "<0.001"], ["Gender", "", "", "", "", "", "", "", "", ""], ["Male", "196/160", "2.64 (1.74-3.63)", "<0.001", "209/212", "1.31 (0.93-1.86)", "0.120", "34/26", "7.45 (2.16-10.36)", "<0.001"], ["Female", "63/107", "2.25 (1.23-5.41)", "0.013", "126/123", "1.70 (1.10-2.63)", "0.018", "31/39", "1.28 (0.50-3.25)", "0.603"], ["Smoking history", "", "", "", "", "", "", "", "", ""], ["Never smoker", "2/15", "3.89 (0.92-157.30)", "0.065", "22/29", "0.65(0.27-1.60)", "0.366", "24/43", "1.26(0.47-3.42)", "0.638"], ["Ever smoker", "20/53", "3.26 (1.57-12.45)", "0.005", "217/237", "1.43(1.01-2.02)", "0.040", "41/22", "8.17(1.80-8.60)", "0.001"], ["Current smoker", "10/39", "1.33 (0.33-5.54)", "0.665", "84/59", "1.62(0.93-2.82)", "0.093", "0/0", "NA", "NA"], ["Histology", "", "", "", "", "", "", "", "", ""], ["Squamous Carcinoma", "107/69", "3.08 (1.40-4.67)", "0.002", "219/196", "1.46 (1.00-2.12)", "0.048", "0/0", "NA", "NA"], ["Adenocarcinoma", "86/165", "2.50 (1.73-5.48)", "<0.001", "116/139", "1.57 (1.05-2.35)", "0.021", "0/0", "NA", "NA"], ["AJCC stage", "", "", "", "", "", "", "", "", ""], ["Stage I", "165/193", "2.40 (1.61-3.81)", "< 0.001", "180/174", "1.61 (1.06-2.44)", "0.021", "43/54", "2.52 (1.15-5.64)", "0.022"], ["Stage II", "46/54", "2.20 (1.14-4.66)", "0.021", "97/86", "1.25 (0.76-2.06)", "0.382", "22/11", "2.67 (0.85-5.92)", "0.104"], ["Stage III", "35/6", "3.68 (1.30-6.70)", "0.015", "54/57", "1.21 (0.65-2.25)", "0.552", "0/0", "NA", "NA"], ["Stage IV", "5/4", "0.31 (0.00-2.29)", "0.221", "3/13", "NA", "0.635", "0/0", "NA", "NA"]], "row_count": 18, "column_count": 10, "numeric_cells": 102, "header_rows": 0, "locator": "section[6]/table-wrap[2]#t3"}}, {"id": "asset:table:pmid:30659574:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cd232c61925320338ce7e827fbb3466e0dc5d30bd73e1229d76d9909c2d41aee", "bytes": 1080, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t4", "version": null, "note": "Clinical features of elderly patients (age>=60 years) with NSCLC in the training and validating groups.", "structure": {"pmcid": "PMC6366982", "section_index": 10, "section_title": "Patient information and study design", "row_count": 19, "column_count": 4}, "table": {"label": "Table 4", "caption": "Clinical features of elderly patients (age>=60 years) with NSCLC in the training and validating groups.", "rows": [["Features", "Training group(n=456)", "Validation group-1(n=670)", "Validation group-2(n=130)"], ["Age, no (%)", "", "", ""], ["<75 years", "353", "486", "123"], [">=75 years", "103", "184", "7"], ["Gender, no (%)", "", "", ""], ["Male", "313 (68.6)", "421 (62.8)", "60 (46.2)"], ["Female", "143 (31.4)", "249 (37.2)", "70 (53.8)"], ["Smoking status, no (%)", "", "", ""], ["Never smoker", "17 (12.5)", "51 (7.9)", "67 (51.5)"], ["Ever smoker", "71 (52.2)", "454 (70.1)", "63 (48.5)"], ["Current smoker", "48 (35.3)", "143 (22.0)", ""], ["Pathological grade, no (%)", "", "", ""], ["Squamous Carcinoma", "236 (39.9)", "415 (61.9)", "NA"], ["Adenocarcinoma", "220 (60.1)", "255 (38.1)", "NA"], ["AJCC stage, no (%)", "", "", ""], ["I", "313 (68.4)", "356 (53.3)", "97 (74.6)"], ["II", "89 (19.6)", "185 (27.6)", "33 (25.4)"], ["III", "46 (10.2)", "112 (16.7)", "NA"], ["IV", "8 (1.8)", "17 (2.4)", "NA"]], "row_count": 19, "column_count": 4, "numeric_cells": 39, "header_rows": 0, "locator": "section[10]/table-wrap[1]#t4"}}], "gaps": ["asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE31210 not downloaded", "asset:data:geo:GSE31210 licence not read", "asset:data:geo:GSE31546 not downloaded", "asset:data:geo:GSE31546 licence not read", "asset:data:geo:GSE37745 not downloaded", "asset:data:geo:GSE37745 licence not read", "asset:data:geo:GSE50081 not downloaded", "asset:data:geo:GSE50081 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "reordered", "quote": "Cox proportional hazards regression was used to identify survival-related biomarkers. Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE30219", "GSE31546", "GSE37745", "GSE50081", "GSE31210"], "resolved_accessions": ["GSE30219", "GSE31546", "GSE37745", "GSE50081", "GSE31210"], "statements": ["Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites. Among them, four GEO datasets (GSE30219, GSE31546, GSE37745 and GSE50081) were integrated as a training group via data normalization, including 456 patients."], "basis": "The paper names GSE30219, GSE31546, GSE37745, GSE50081, GSE31210 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:30659574", "data:geo:GSE30219", "asset:table:pmid:30659574:1", "asset:table:pmid:30659574:2", "asset:table:pmid:30659574:3", "asset:table:pmid:30659574:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE30219"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:33Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 19360, "completion_tokens": 1831, "cached_tokens": 528}}, "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:30659574", "type": "paper", "label": "pmid:30659574"}, {"id": "source:pmid:30659574", "type": "manuscript", "label": "PMID 30659574 full text"}, {"id": "data:geo:GSE30219", "type": "dataset", "label": "GEO GSE30219"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30659574", "type": "paper", "label": "pmid:30659574"}, {"id": "source:pmid:30659574", "type": "manuscript", "label": "PMID 30659574 full text"}, {"id": "data:geo:GSE30219", "type": "dataset", "label": "GEO GSE30219"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30659574", "type": "extraction", "used": ["source:pmid:30659574"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE30219", "type": "accession_resolution", "used": ["data:geo:GSE30219"], "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:30659574", "parent_hash": "sha256:eec5580aca513c47adabce341f0a042ddbf221d9161f516ad62c19e282d7d453", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE31210 licence not read", "asset:data:geo:GSE31210 not downloaded", "asset:data:geo:GSE31546 licence not read", "asset:data:geo:GSE31546 not downloaded", "asset:data:geo:GSE37745 licence not read", "asset:data:geo:GSE37745 not downloaded", "asset:data:geo:GSE50081 licence not read", "asset:data:geo:GSE50081 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Cox proportional hazards regression was used to identify survival-related biomarkers. Five of them (GSE30219, GSE31546, GSE37745, GSE50081 and GSE31210) were downloaded from the Gene Expression Omnibus (GEO) and two (TCGA-LUSC and TCGA-LUAD) from The Cancer Genome Atlas (TCGA) websites."], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:36:21+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}}}