{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34734491", "kind": "science-record", "revision": 3, "content_hash": "sha256:86bcc4a43fa1317fb90ed44f39bd0c722b383023bdba299e98fab64d32f461aa", "created_at": "2026-11-01T17:36:25Z", "updated_at": "2026-11-01T21:26:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Nonnegative matrix factorization-based bioinformatics analysis reveals that TPX2 and SELENBP1 are two predictors of the inner sub-consensuses of lung adenocarcinoma.", "doi": "10.1002/cam4.4386", "pmid": "34734491", "authors": ["Haiwei Wang", "Xinrui Wang", "Liangpu Xu", "Hua Cao", "Ji Zhang"], "journal": "Cancer medicine", "year": 2021, "abstract": "BACKGROUND: Lung adenocarcinoma (LUAD) is a heterogeneous disease. However the inner sub-groups of LUAD have not been fully studied. Markers predicted the sub-groups and prognosis of LUAD are badly needed.\nAIMS: To identify biomarkers associated with the sub-groups and prognosis of LUAD.\nMATERIALS AND METHODS: Using nonnegative matrix factorization (NMF) clustering, LUAD patients from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) datasets and LUAD cell lines from Genomics of Drug Sensitivity in Cancer (GDSC) dataset were divided into different sub-consensuses based on the gene expression profiling. The overall survival of LUAD patients in each sub-consensus was determined by Kaplan-Meier survival analysis. The common genes which were differentially expressed in each sub-consensus of LUAD patients and LUAD cell lines were identified using TBtools. The predictive accuracy of TPX2 and SELENBP1 for theinner sub-consensuses of LUAD was determined by Receiver operator characteristic (ROC) analysis. The Kaplan-Meier survival analysis was also used to test the prognostic significance of TPX2 and SELENBP1 in LUAD patients.\nRESULTS: Using nonnegative matrix factorization clustering, LUAD patients in The Cancer Genome Atlas (TCGA), GSE30219, GSE42127, GSE50081, GSE68465, and GSE72094 datasets were divided into three sub-consensuses. Sub-consensus3 LUAD patients were with low overall survival and were with high TP53 mutations. Similarly, LUAD cell lines were also divided into three sub-consensuses by NMF method, and sub-consensus2 cell lines were resistant to EGFR inhibitors. Identification of the common genes which were differentially expressed in different sub-consensuses of LUAD patients and LUAD cell lines revealed that TPX2 was highly expressed in sub-consensus3 LUAD patients and sub-consensus2 LUAD cell lines. On the contrary, SELENBP1 was highly expressed in sub-consensus1 LUAD patients and sub-consensus1 LUAD cell lines. The expression levels of TPX2 and SELENBP1 could distinguish sub-consensus3 LUAD patients or sub-consensus2 LUAD cell lines from other sub-consensuses of LUAD patients or cell lines. Moreover, compared with normal lung tissues, TPX2 was highly expressed, while, SELENBP1 was lowly expressed in LUAD tissues. Furthermore, the higher expression levels of TPX2 were associated with the lower relapse-free survival and the lower overall survival of LUAD patients. While, the higher expression levels of SELENBP1 were associated with the higher relapse-free survival and higher overall survival. At last, we showed that TP53 mutant LUAD patients were with higher TPX2 and lower SELENBP1 expressions.\nDISCUSSION: Both iCluster and NMF method are proved to be robust LUAD classification systems. However, the LUAD patients in different iclusters had no significant clinical overall survival, while, sub-consensus3 LUAD patients from NMF classification were with lower overall survival than other sub-consensuses.\nCONCLUSIONS: By integrated analysis of 1765 LUAD patients and 64 LUAD cell lines, we showed that NMF was a robust inner sub-consensuses classification method of LUAD. TPX2 and SELENBP1 were differentially expressed in different LUAD sub- consensuses, and predicted the inner sub-consensuses of LUAD with high accuracy. TPX2 was an unfavorable prognostic biomarker of LUAD which was up-regulated in LUAD tissues and associated with the low overall survival of LUAD. SELENBP1 was a favorable prognostic biomarker of LUAD which was down-regulated in LUAD tissues and associated with the prolonged overall survival of LUAD.", "claims": [{"id": "claim-method", "statement": "The overall survival of LUAD patients in each sub‐consensus was determined by the Kaplan–Meier survival analysis which was performed using “survival” package (version 3.1‐8) in R statistics software. The prognostic values of TPX2 and SELENBP1 on the relapse‐free survival or overall survival were also determined using “survival” package. P values were calculated by the log‐rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34734491", "locator": "sections[5] \"Survival analysis\" paragraph 2", "quote": "The overall survival of LUAD patients in each sub‐consensus was determined by the Kaplan–Meier survival analysis which was performed using “survival” package (version 3.1‐8) in R statistics software. The prognostic values of TPX2 and SELENBP1 on the relapse‐free survival or overall survival were also determined using “survival” package. P values were calculated by the log‐rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34734491", "locator": "sections[28] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Integrated NMF analysis of 1765 LUAD patients and 64 LUAD cell lines identified robust LUAD sub-consensuses and identified TPX2 and SELENBP1 as sub-consensus predictors and prognostic biomarkers.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34734491", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "By integrated analysis of 1765 LUAD patients and 64 LUAD cell lines, we showed that NMF was a robust inner sub‐consensuses classification method of LUAD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Integrated NMF analysis of 1765 LUAD patients and 64 LUAD cell lines identified robust LUAD sub-consensuses and identified TPX2 and SELENBP1 as sub-consensus predictors and prognostic biomarkers.", "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:34734491"], "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:GSE10072"], "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:GSE10072"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34734491", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/cam4.4386", "sha256": "sha256:c30dc350b0691df446045ab95bb112057a8367b46b662058faa5819fd7fbd906", "bytes": 38636, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/cam4.4386", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8683537", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10072", "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=GSE10072", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10072", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM254625", "GSM254626", "GSM254627", "GSM254628", "GSM254629", "GSM254630", "GSM254631", "GSM254632", "GSM254633", "GSM254634", "GSM254635", "GSM254636", "GSM254637", "GSM254638", "GSM254639", "GSM254640", "GSM254641", "GSM254642", "GSM254643", "GSM254644", "GSM254645", "GSM254646", "GSM254647", "GSM254648", "GSM254649", "GSM254650", "GSM254651", "GSM254652", "GSM254653", "GSM254654", "GSM254655", "GSM254656", "GSM254657", "GSM254658", "GSM254659", "GSM254660", "GSM254661", "GSM254662", "GSM254663", "GSM254664", "GSM254665", "GSM254666", "GSM254667", "GSM254668", "GSM254669", "GSM254670", "GSM254671", "GSM254672", "GSM254673", "GSM254674", "GSM254675", "GSM254676", "GSM254677", "GSM254678", "GSM254679", "GSM254680", "GSM254681", "GSM254682", "GSM254683", "GSM254684", "GSM254685", "GSM254686", "GSM254687", "GSM254688", "GSM254689", "GSM254690", "GSM254691", "GSM254692", "GSM254693", "GSM254694", "GSM254695", "GSM254696", "GSM254697", "GSM254698", "GSM254699", "GSM254700", "GSM254701", "GSM254702", "GSM254703", "GSM254704", "GSM254705", "GSM254706", "GSM254707", "GSM254708", "GSM254709", "GSM254710", "GSM254711", "GSM254712", "GSM254713", "GSM254714", "GSM254715", "GSM254716", "GSM254717", "GSM254718", "GSM254719", "GSM254720", "GSM254721", "GSM254722", "GSM254723", "GSM254724", "GSM254725", "GSM254726", "GSM254727", "GSM254728", "GSM254729", "GSM254730", "GSM254731"], "sample_count": 107, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival", "resolution_checked_at": "2026-11-01T15:30:21Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE18842", "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=GSE18842", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18842", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM466947", "GSM466948", "GSM466949", "GSM466950", "GSM466951", "GSM466952", "GSM466953", "GSM466954", "GSM466955", "GSM466956", "GSM466957", "GSM466958", "GSM466959", "GSM466960", "GSM466961", "GSM466962", "GSM466963", "GSM466964", "GSM466965", "GSM466966", "GSM466967", "GSM466968", "GSM466969", "GSM466970", "GSM466971", "GSM466972", "GSM466973", "GSM466974", "GSM466975", "GSM466976", "GSM466977", "GSM466978", "GSM466979", "GSM466980", "GSM466981", "GSM466982", "GSM466983", "GSM466984", "GSM466985", "GSM466986", "GSM466987", "GSM466988", "GSM466989", "GSM466990", "GSM466991", "GSM466992", "GSM466993", "GSM466994", "GSM466995", "GSM466996", "GSM466997", "GSM466998", "GSM466999", "GSM467000", "GSM467001", "GSM467002", "GSM467003", "GSM467004", "GSM467005", "GSM467006", "GSM467007", "GSM467008", "GSM467009", "GSM467010", "GSM467011", "GSM467012", "GSM467013", "GSM467014", "GSM467015", "GSM467016", "GSM467017", "GSM467018", "GSM467019", "GSM467020", "GSM467021", "GSM467022", "GSM467023", "GSM467024", "GSM467025", "GSM467026", "GSM467027", "GSM467028", "GSM467029", "GSM467030", "GSM467031", "GSM467032", "GSM467033", "GSM467034", "GSM467035", "GSM467036", "GSM467037"], "sample_count": 91, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression analysis of human lung cancer and control samples", "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:GSE27262", "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=GSE27262", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27262", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM673870", "GSM673871", "GSM673872", "GSM673873", "GSM673874", "GSM673875", "GSM673876", "GSM673877", "GSM673878", "GSM673879", "GSM673880", "GSM673881", "GSM673882", "GSM673883", "GSM673884", "GSM673885", "GSM673886", "GSM673887", "GSM673888", "GSM673889", "GSM673890", "GSM673891", "GSM673892", "GSM673893", "GSM673894", "GSM673895", "GSM673896", "GSM673897", "GSM673898", "GSM673899", "GSM673900", "GSM673901", "GSM673902", "GSM673903", "GSM673904", "GSM673905", "GSM673906", "GSM673907", "GSM673908", "GSM673909", "GSM673910", "GSM673911", "GSM673912", "GSM673913", "GSM673914", "GSM673915", "GSM673916", "GSM673917", "GSM673918", "GSM673919"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling of Non-small cell lung cancer in Taiwan", "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: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": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_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:GSE32863", "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=GSE32863", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32863", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM813411", "GSM813412", "GSM813413", "GSM813414", "GSM813415", "GSM813416", "GSM813417", "GSM813418", "GSM813419", "GSM813420", "GSM813421", "GSM813422", "GSM813423", "GSM813424", "GSM813425", "GSM813426", "GSM813427", "GSM813428", "GSM813429", "GSM813430", "GSM813431", "GSM813432", "GSM813433", "GSM813434", "GSM813435", "GSM813436", "GSM813437", "GSM813438", "GSM813439", "GSM813440", "GSM813441", "GSM813442", "GSM813443", "GSM813444", "GSM813445", "GSM813446", "GSM813447", "GSM813448", "GSM813449", "GSM813450", "GSM813451", "GSM813452", "GSM813453", "GSM813454", "GSM813455", "GSM813456", "GSM813457", "GSM813458", "GSM813459", "GSM813460", "GSM813461", "GSM813462", "GSM813463", "GSM813464", "GSM813465", "GSM813466", "GSM813467", "GSM813468", "GSM813469", "GSM813470", "GSM813471", "GSM813472", "GSM813473", "GSM813474", "GSM813475", "GSM813476", "GSM813477", "GSM813478", "GSM813479", "GSM813480", "GSM813481", "GSM813482", "GSM813483", "GSM813484", "GSM813485", "GSM813486", "GSM813487", "GSM813488", "GSM813489", "GSM813490", "GSM813491", "GSM813492", "GSM813493", "GSM813494", "GSM813495", "GSM813496", "GSM813497", "GSM813498", "GSM813499", "GSM813500", "GSM813501", "GSM813502", "GSM813503", "GSM813504", "GSM813505", "GSM813506", "GSM813507", "GSM813508", "GSM813509", "GSM813510", "GSM813511", "GSM813512", "GSM813513", "GSM813514", "GSM813515", "GSM813516", "GSM813517", "GSM813518", "GSM813519", "GSM813520", "GSM813521", "GSM813522", "GSM813523", "GSM813524", "GSM813525", "GSM813526"], "sample_count": 116, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Gene expression analysis of lung adenocarcinoma and matched adjacent non-tumor lung tissue", "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:GSE42127", "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=GSE42127", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42127", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1032881", "GSM1032882", "GSM1032883", "GSM1032884", "GSM1032885", "GSM1032886", "GSM1032887", "GSM1032888", "GSM1032889", "GSM1032890", "GSM1032891", "GSM1032892", "GSM1032893", "GSM1032894", "GSM1032895", "GSM1032896", "GSM1032897", "GSM1032898", "GSM1032899", "GSM1032900", "GSM1032901", "GSM1032902", "GSM1032903", "GSM1032904", "GSM1032905", "GSM1032906", "GSM1032907", "GSM1032908", "GSM1032909", "GSM1032910", "GSM1032911", "GSM1032912", "GSM1032913", "GSM1032914", "GSM1032915", "GSM1032916", "GSM1032917", "GSM1032918", "GSM1032919", "GSM1032920", "GSM1032921", "GSM1032922", "GSM1032923", "GSM1032924", "GSM1032925", "GSM1032926", "GSM1032927", "GSM1032928", "GSM1032929", "GSM1032930", "GSM1032931", "GSM1032932", "GSM1032933", "GSM1032934", "GSM1032935", "GSM1032936", "GSM1032937", "GSM1032938", "GSM1032939", "GSM1032940", "GSM1032941", "GSM1032942", "GSM1032943", "GSM1032944", "GSM1032945", "GSM1032946", "GSM1032947", "GSM1032948", "GSM1032949", "GSM1032950", "GSM1032951", "GSM1032952", "GSM1032953", "GSM1032954", "GSM1032955", "GSM1032956", "GSM1032957", "GSM1032958", "GSM1032959", "GSM1032960", "GSM1032961", "GSM1032962", "GSM1032963", "GSM1032964", "GSM1032965", "GSM1032966", "GSM1032967", "GSM1032968", "GSM1032969", "GSM1032970", "GSM1032971", "GSM1032972", "GSM1032973", "GSM1032974", "GSM1032975", "GSM1032976", "GSM1032977", "GSM1032978", "GSM1032979", "GSM1032980", "GSM1032981", "GSM1032982", "GSM1032983", "GSM1032984", "GSM1032985", "GSM1032986", "GSM1032987", "GSM1032988", "GSM1032989", "GSM1032990", "GSM1032991", "GSM1032992", "GSM1032993", "GSM1032994", "GSM1032995", "GSM1032996", "GSM1032997", "GSM1032998", "GSM1032999", "GSM1033000", "GSM1033001", "GSM1033002", "GSM1033003", "GSM1033004", "GSM1033005", "GSM1033006", "GSM1033007", "GSM1033008", "GSM1033009", "GSM1033010", "GSM1033011", "GSM1033012", "GSM1033013", "GSM1033014", "GSM1033015", "GSM1033016", "GSM1033017", "GSM1033018", "GSM1033019", "GSM1033020", "GSM1033021", "GSM1033022", "GSM1033023", "GSM1033024", "GSM1033025", "GSM1033026", "GSM1033027", "GSM1033028", "GSM1033029", "GSM1033030", "GSM1033031", "GSM1033032", "GSM1033033", "GSM1033034", "GSM1033035", "GSM1033036", "GSM1033037", "GSM1033038", "GSM1033039", "GSM1033040", "GSM1033041", "GSM1033042", "GSM1033043", "GSM1033044", "GSM1033045", "GSM1033046", "GSM1033047", "GSM1033048", "GSM1033049", "GSM1033050", "GSM1033051", "GSM1033052", "GSM1033053", "GSM1033054", "GSM1033055", "GSM1033056"], "sample_count": 176, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Expression data for non-small-cell lung cancer", "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": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_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": "data:geo:GSE68465", "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=GSE68465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68465", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1672281", "GSM1672282", "GSM1672283", "GSM1672284", "GSM1672285", "GSM1672286", "GSM1672287", "GSM1672288", "GSM1672289", "GSM1672290", "GSM1672291", "GSM1672292", "GSM1672293", "GSM1672294", "GSM1672295", "GSM1672296", "GSM1672297", "GSM1672298", "GSM1672299", "GSM1672300", "GSM1672301", "GSM1672302", "GSM1672303", "GSM1672304", "GSM1672305", "GSM1672306", "GSM1672307", "GSM1672308", "GSM1672309", "GSM1672310", "GSM1672311", "GSM1672312", "GSM1672313", "GSM1672314", "GSM1672315", "GSM1672316", "GSM1672317", "GSM1672318", "GSM1672319", "GSM1672320", "GSM1672321", "GSM1672322", "GSM1672323", "GSM1672324", "GSM1672325", "GSM1672326", "GSM1672327", "GSM1672328", "GSM1672329", "GSM1672330", "GSM1672331", "GSM1672332", "GSM1672333", "GSM1672334", "GSM1672335", "GSM1672336", "GSM1672337", "GSM1672338", "GSM1672339", "GSM1672340", "GSM1672341", "GSM1672342", "GSM1672343", "GSM1672344", "GSM1672345", "GSM1672346", "GSM1672347", "GSM1672348", "GSM1672349", "GSM1672350", "GSM1672351", "GSM1672352", "GSM1672353", "GSM1672354", "GSM1672355", "GSM1672356", "GSM1672357", "GSM1672358", "GSM1672359", "GSM1672360", "GSM1672361", "GSM1672362", "GSM1672363", "GSM1672364", "GSM1672365", "GSM1672366", "GSM1672367", "GSM1672368", "GSM1672369", "GSM1672370", "GSM1672371", "GSM1672372", "GSM1672373", "GSM1672374", "GSM1672375", "GSM1672376", "GSM1672377", "GSM1672378", "GSM1672379", "GSM1672380", "GSM1672381", "GSM1672382", "GSM1672383", "GSM1672384", "GSM1672385", "GSM1672386", "GSM1672387", "GSM1672388", "GSM1672389", "GSM1672390", "GSM1672391", "GSM1672392", "GSM1672393", "GSM1672394", "GSM1672395", "GSM1672396", "GSM1672397", "GSM1672398", "GSM1672399", "GSM1672400", "GSM1672401", "GSM1672402", "GSM1672403", "GSM1672404", "GSM1672405", "GSM1672406", "GSM1672407", "GSM1672408", "GSM1672409", "GSM1672410", "GSM1672411", "GSM1672412", "GSM1672413", "GSM1672414", "GSM1672415", "GSM1672416", "GSM1672417", "GSM1672418", "GSM1672419", "GSM1672420", "GSM1672421", "GSM1672422", "GSM1672423", "GSM1672424", "GSM1672425", "GSM1672426", "GSM1672427", "GSM1672428", "GSM1672429", "GSM1672430", "GSM1672431", "GSM1672432", "GSM1672433", "GSM1672434", "GSM1672435", "GSM1672436", "GSM1672437", "GSM1672438", "GSM1672439", "GSM1672440", "GSM1672441", "GSM1672442", "GSM1672443", "GSM1672444", "GSM1672445", "GSM1672446", "GSM1672447", "GSM1672448", "GSM1672449", "GSM1672450", "GSM1672451", "GSM1672452", "GSM1672453", "GSM1672454", "GSM1672455", "GSM1672456", "GSM1672457", "GSM1672458", "GSM1672459", "GSM1672460", "GSM1672461", "GSM1672462", "GSM1672463", "GSM1672464", "GSM1672465", "GSM1672466", "GSM1672467", "GSM1672468", "GSM1672469", "GSM1672470", "GSM1672471", "GSM1672472", "GSM1672473", "GSM1672474", "GSM1672475", "GSM1672476", "GSM1672477", "GSM1672478", "GSM1672479", "GSM1672480", "GSM1672481", "GSM1672482", "GSM1672483", "GSM1672484", "GSM1672485", "GSM1672486", "GSM1672487", "GSM1672488", "GSM1672489", "GSM1672490", "GSM1672491", "GSM1672492", "GSM1672493", "GSM1672494", "GSM1672495", "GSM1672496", "GSM1672497", "GSM1672498", "GSM1672499", "GSM1672500", "GSM1672501", "GSM1672502", "GSM1672503", "GSM1672504", "GSM1672505", "GSM1672506", "GSM1672507", "GSM1672508", "GSM1672509", "GSM1672510", "GSM1672511", "GSM1672512", "GSM1672513", "GSM1672514", "GSM1672515", "GSM1672516", "GSM1672517", "GSM1672518", "GSM1672519", "GSM1672520", "GSM1672521", "GSM1672522", "GSM1672523", "GSM1672524", "GSM1672525", "GSM1672526", "GSM1672527", "GSM1672528", "GSM1672529", "GSM1672530", "GSM1672531", "GSM1672532", "GSM1672533", "GSM1672534", "GSM1672535", "GSM1672536", "GSM1672537", "GSM1672538", "GSM1672539", "GSM1672540", "GSM1672541", "GSM1672542", "GSM1672543", "GSM1672544", "GSM1672545", "GSM1672546", "GSM1672547", "GSM1672548", "GSM1672549", "GSM1672550", "GSM1672551", "GSM1672552", "GSM1672553", "GSM1672554", "GSM1672555", "GSM1672556", "GSM1672557", "GSM1672558", "GSM1672559", "GSM1672560", "GSM1672561", "GSM1672562", "GSM1672563", "GSM1672564", "GSM1672565", "GSM1672566", "GSM1672567", "GSM1672568", "GSM1672569", "GSM1672570", "GSM1672571", "GSM1672572", "GSM1672573", "GSM1672574", "GSM1672575", "GSM1672576", "GSM1672577", "GSM1672578", "GSM1672579", "GSM1672580", "GSM1672581", "GSM1672582", "GSM1672583", "GSM1672584", "GSM1672585", "GSM1672586", "GSM1672587", "GSM1672588", "GSM1672589", "GSM1672590", "GSM1672591", "GSM1672592", "GSM1672593", "GSM1672594", "GSM1672595", "GSM1672596", "GSM1672597", "GSM1672598", "GSM1672599", "GSM1672600", "GSM1672601", "GSM1672602", "GSM1672603", "GSM1672604", "GSM1672605", "GSM1672606", "GSM1672607", "GSM1672608", "GSM1672609", "GSM1672610", "GSM1672611", "GSM1672612", "GSM1672613", "GSM1672614", "GSM1672615", "GSM1672616", "GSM1672617", "GSM1672618", "GSM1672619", "GSM1672620", "GSM1672621", "GSM1672622", "GSM1672623", "GSM1672624", "GSM1672625", "GSM1672626", "GSM1672627", "GSM1672628", "GSM1672629", "GSM1672630", "GSM1672631", "GSM1672632", "GSM1672633", "GSM1672634", "GSM1672635", "GSM1672636", "GSM1672637", "GSM1672638", "GSM1672639", "GSM1672640", "GSM1672641", "GSM1672642", "GSM1672643", "GSM1672644", "GSM1672645", "GSM1672646", "GSM1672647", "GSM1672648", "GSM1672649", "GSM1672650", "GSM1672651", "GSM1672652", "GSM1672653", "GSM1672654", "GSM1672655", "GSM1672656", "GSM1672657", "GSM1672658", "GSM1672659", "GSM1672660", "GSM1672661", "GSM1672662", "GSM1672663", "GSM1672664", "GSM1672665", "GSM1672666", "GSM1672667", "GSM1672668", "GSM1672669", "GSM1672670", "GSM1672671", "GSM1672672", "GSM1672673", "GSM1672674", "GSM1672675", "GSM1672676", "GSM1672677", "GSM1672678", "GSM1672679", "GSM1672680", "GSM1672681", "GSM1672682", "GSM1672683", "GSM1672684", "GSM1672685", "GSM1672686", "GSM1672687", "GSM1672688", "GSM1672689", "GSM1672690", "GSM1672691", "GSM1672692", "GSM1672693", "GSM1672694", "GSM1672695", "GSM1672696", "GSM1672697", "GSM1672698", "GSM1672699", "GSM1672700", "GSM1672701", "GSM1672702", "GSM1672703", "GSM1672704", "GSM1672705", "GSM1672706", "GSM1672707", "GSM1672708", "GSM1672709", "GSM1672710", "GSM1672711", "GSM1672712", "GSM1672713", "GSM1672714", "GSM1672715", "GSM1672716", "GSM1672717", "GSM1672718", "GSM1672719", "GSM1672720", "GSM1672721", "GSM1672722", "GSM1672723", "GSM1672724", "GSM1672725", "GSM1672726", "GSM1672727", "GSM1672728", "GSM1672729", "GSM1672730", "GSM1672731", "GSM1672732", "GSM1672733", "GSM1672734", "GSM1672735", "GSM1672736", "GSM1672737", "GSM1672738", "GSM1672739", "GSM1672740", "GSM1672741", "GSM1672742"], "sample_count": 462, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "caArray_jacob-00182: Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE72094", "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=GSE72094", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE72094", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1854797", "GSM1854798", "GSM1854799", "GSM1854800", "GSM1854801", "GSM1854802", "GSM1854803", "GSM1854804", "GSM1854805", "GSM1854806", "GSM1854807", "GSM1854808", "GSM1854809", "GSM1854810", "GSM1854811", "GSM1854812", "GSM1854813", "GSM1854814", "GSM1854815", "GSM1854816", "GSM1854817", "GSM1854818", "GSM1854819", "GSM1854820", "GSM1854821", "GSM1854822", "GSM1854823", "GSM1854824", "GSM1854825", "GSM1854826", "GSM1854827", "GSM1854828", "GSM1854829", "GSM1854830", "GSM1854831", "GSM1854832", "GSM1854833", "GSM1854834", "GSM1854835", "GSM1854836", "GSM1854837", "GSM1854838", "GSM1854839", "GSM1854840", "GSM1854841", "GSM1854842", "GSM1854843", "GSM1854844", "GSM1854845", "GSM1854846", "GSM1854847", "GSM1854848", "GSM1854849", "GSM1854850", "GSM1854851", "GSM1854852", "GSM1854853", "GSM1854854", "GSM1854855", "GSM1854856", "GSM1854857", "GSM1854858", "GSM1854859", "GSM1854860", "GSM1854861", "GSM1854862", "GSM1854863", "GSM1854864", "GSM1854865", "GSM1854866", "GSM1854867", "GSM1854868", "GSM1854869", "GSM1854870", "GSM1854871", "GSM1854872", "GSM1854873", "GSM1854874", "GSM1854875", "GSM1854876", "GSM1854877", "GSM1854878", "GSM1854879", "GSM1854880", "GSM1854881", "GSM1854882", "GSM1854883", "GSM1854884", "GSM1854885", "GSM1854886", "GSM1854887", "GSM1854888", "GSM1854889", "GSM1854890", "GSM1854891", "GSM1854892", "GSM1854893", "GSM1854894", "GSM1854895", "GSM1854896", "GSM1854897", "GSM1854898", "GSM1854899", "GSM1854900", "GSM1854901", "GSM1854902", "GSM1854903", "GSM1854904", "GSM1854905", "GSM1854906", "GSM1854907", "GSM1854908", "GSM1854909", "GSM1854910", "GSM1854911", "GSM1854912", "GSM1854913", "GSM1854914", "GSM1854915", "GSM1854916", "GSM1854917", "GSM1854918", "GSM1854919", "GSM1854920", "GSM1854921", "GSM1854922", "GSM1854923", "GSM1854924", "GSM1854925", "GSM1854926", "GSM1854927", "GSM1854928", "GSM1854929", "GSM1854930", "GSM1854931", "GSM1854932", "GSM1854933", "GSM1854934", "GSM1854935", "GSM1854936", "GSM1854937", "GSM1854938", "GSM1854939", "GSM1854940", "GSM1854941", "GSM1854942", "GSM1854943", "GSM1854944", "GSM1854945", "GSM1854946", "GSM1854947", "GSM1854948", "GSM1854949", "GSM1854950", "GSM1854951", "GSM1854952", "GSM1854953", "GSM1854954", "GSM1854955", "GSM1854956", "GSM1854957", "GSM1854958", "GSM1854959", "GSM1854960", "GSM1854961", "GSM1854962", "GSM1854963", "GSM1854964", "GSM1854965", "GSM1854966", "GSM1854967", "GSM1854968", "GSM1854969", "GSM1854970", "GSM1854971", "GSM1854972", "GSM1854973", "GSM1854974", "GSM1854975", "GSM1854976", "GSM1854977", "GSM1854978", "GSM1854979", "GSM1854980", "GSM1854981", "GSM1854982", "GSM1854983", "GSM1854984", "GSM1854985", "GSM1854986", "GSM1854987", "GSM1854988", "GSM1854989", "GSM1854990", "GSM1854991", "GSM1854992", "GSM1854993", "GSM1854994", "GSM1854995", "GSM1854996", "GSM1854997", "GSM1854998", "GSM1854999", "GSM1855000", "GSM1855001", "GSM1855002", "GSM1855003", "GSM1855004", "GSM1855005", "GSM1855006", "GSM1855007", "GSM1855008", "GSM1855009", "GSM1855010", "GSM1855011", "GSM1855012", "GSM1855013", "GSM1855014", "GSM1855015", "GSM1855016", "GSM1855017", "GSM1855018", "GSM1855019", "GSM1855020", "GSM1855021", "GSM1855022", "GSM1855023", "GSM1855024", "GSM1855025", "GSM1855026", "GSM1855027", "GSM1855028", "GSM1855029", "GSM1855030", "GSM1855031", "GSM1855032", "GSM1855033", "GSM1855034", "GSM1855035", "GSM1855036", "GSM1855037", "GSM1855038", "GSM1855039", "GSM1855040", "GSM1855041", "GSM1855042", "GSM1855043", "GSM1855044", "GSM1855045", "GSM1855046", "GSM1855047", "GSM1855048", "GSM1855049", "GSM1855050", "GSM1855051", "GSM1855052", "GSM1855053", "GSM1855054", "GSM1855055", "GSM1855056", "GSM1855057", "GSM1855058", "GSM1855059", "GSM1855060", "GSM1855061", "GSM1855062", "GSM1855063", "GSM1855064", "GSM1855065", "GSM1855066", "GSM1855067", "GSM1855068", "GSM1855069", "GSM1855070", "GSM1855071", "GSM1855072", "GSM1855073", "GSM1855074", "GSM1855075", "GSM1855076", "GSM1855077", "GSM1855078", "GSM1855079", "GSM1855080", "GSM1855081", "GSM1855082", "GSM1855083", "GSM1855084", "GSM1855085", "GSM1855086", "GSM1855087", "GSM1855088", "GSM1855089", "GSM1855090", "GSM1855091", "GSM1855092", "GSM1855093", "GSM1855094", "GSM1855095", "GSM1855096", "GSM1855097", "GSM1855098", "GSM1855099", "GSM1855100", "GSM1855101", "GSM1855102", "GSM1855103", "GSM1855104", "GSM1855105", "GSM1855106", "GSM1855107", "GSM1855108", "GSM1855109", "GSM1855110", "GSM1855111", "GSM1855112", "GSM1855113", "GSM1855114", "GSM1855115", "GSM1855116", "GSM1855117", "GSM1855118", "GSM1855119", "GSM1855120", "GSM1855121", "GSM1855122", "GSM1855123", "GSM1855124", "GSM1855125", "GSM1855126", "GSM1855127", "GSM1855128", "GSM1855129", "GSM1855130", "GSM1855131", "GSM1855132", "GSM1855133", "GSM1855134", "GSM1855135", "GSM1855136", "GSM1855137", "GSM1855138", "GSM1855139", "GSM1855140", "GSM1855141", "GSM1855142", "GSM1855143", "GSM1855144", "GSM1855145", "GSM1855146", "GSM1855147", "GSM1855148", "GSM1855149", "GSM1855150", "GSM1855151", "GSM1855152", "GSM1855153", "GSM1855154", "GSM1855155", "GSM1855156", "GSM1855157", "GSM1855158", "GSM1855159", "GSM1855160", "GSM1855161", "GSM1855162", "GSM1855163", "GSM1855164", "GSM1855165", "GSM1855166", "GSM1855167", "GSM1855168", "GSM1855169", "GSM1855170", "GSM1855171", "GSM1855172", "GSM1855173", "GSM1855174", "GSM1855175", "GSM1855176", "GSM1855177", "GSM1855178", "GSM1855179", "GSM1855180", "GSM1855181", "GSM1855182", "GSM1855183", "GSM1855184", "GSM1855185", "GSM1855186", "GSM1855187", "GSM1855188", "GSM1855189", "GSM1855190", "GSM1855191", "GSM1855192", "GSM1855193", "GSM1855194", "GSM1855195", "GSM1855196", "GSM1855197", "GSM1855198", "GSM1855199", "GSM1855200", "GSM1855201", "GSM1855202", "GSM1855203", "GSM1855204", "GSM1855205", "GSM1855206", "GSM1855207", "GSM1855208", "GSM1855209", "GSM1855210", "GSM1855211", "GSM1855212", "GSM1855213", "GSM1855214", "GSM1855215", "GSM1855216", "GSM1855217", "GSM1855218", "GSM1855219", "GSM1855220", "GSM1855221", "GSM1855222", "GSM1855223", "GSM1855224", "GSM1855225", "GSM1855226", "GSM1855227", "GSM1855228", "GSM1855229", "GSM1855230", "GSM1855231", "GSM1855232", "GSM1855233", "GSM1855234", "GSM1855235", "GSM1855236", "GSM1855237", "GSM1855238"], "sample_count": 442, "group_sizes": null, "group_sizes_basis": null, "platform": "15048", "taxon": "Homo sapiens", "title": "KRAS mutation-associated gene expression, p53 and STK11 mutations, proliferation and immune surveillance in lung adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE7670", "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=GSE7670", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7670", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM185811", "GSM185812", "GSM185813", "GSM185814", "GSM185815", "GSM185816", "GSM185817", "GSM185818", "GSM185819", "GSM185820", "GSM185821", "GSM185822", "GSM185823", "GSM185824", "GSM185825", "GSM185826", "GSM185827", "GSM185828", "GSM185829", "GSM185830", "GSM185831", "GSM185832", "GSM185833", "GSM185834", "GSM185835", "GSM185836", "GSM185837", "GSM185838", "GSM185839", "GSM185840", "GSM185841", "GSM185842", "GSM185843", "GSM185844", "GSM185845", "GSM185846", "GSM185847", "GSM185848", "GSM185849", "GSM185850", "GSM185851", "GSM185852", "GSM185853", "GSM185854", "GSM185855", "GSM185856", "GSM185857", "GSM185858", "GSM185859", "GSM185860", "GSM185861", "GSM185862", "GSM185863", "GSM185864", "GSM185865", "GSM185866", "GSM185867", "GSM185868", "GSM185869", "GSM185870", "GSM185871", "GSM185872", "GSM185873", "GSM185874", "GSM185875", "GSM185876"], "sample_count": 66, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from Lung cancer", "resolution_checked_at": "2026-11-01T15:14:33Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE10072 not downloaded", "asset:data:geo:GSE10072 licence not read", "asset:data:geo:GSE18842 not downloaded", "asset:data:geo:GSE18842 licence not read", "asset:data:geo:GSE27262 not downloaded", "asset:data:geo:GSE27262 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE32863 not downloaded", "asset:data:geo:GSE32863 licence not read", "asset:data:geo:GSE42127 not downloaded", "asset:data:geo:GSE42127 licence not read", "asset:data:geo:GSE50081 not downloaded", "asset:data:geo:GSE50081 licence not read", "asset:data:geo:GSE68465 not downloaded", "asset:data:geo:GSE68465 licence not read", "asset:data:geo:GSE72094 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:GSE7670 not downloaded", "asset:data:geo:GSE7670 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The overall survival of LUAD patients in each sub‐consensus was determined by the Kaplan–Meier survival analysis which was performed using “survival” package (version 3.1‐8) in R statistics software. The prognostic values of TPX2 and SELENBP1 on the relapse‐free survival or overall survival were also determined using “survival” package. P values were calculated by the log‐rank test."}}, {"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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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", "GSE42127", "GSE50081", "GSE68465", "GSE72094", "GSE7670", "GSE10072", "GSE18842", "GSE27262", "GSE32863"], "resolved_accessions": ["GSE30219", "GSE42127", "GSE50081", "GSE68465", "GSE72094", "GSE7670", "GSE10072", "GSE18842", "GSE27262", "GSE32863"], "statements": ["The datasets generated and/or analyzed during the current study are available in TCGA (tcga.xenahubs.net) and GEO (www.ncbi.nlm.nih.gov/geo) repositories."], "basis": "The paper names GSE30219, GSE42127, GSE50081, GSE68465, GSE72094, GSE7670, GSE10072, GSE18842, GSE27262, GSE32863 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": ["logrank_test"], "assets": ["source:pmid:34734491", "data:geo:GSE10072"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10072"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:05:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11915, "completion_tokens": 1793, "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:34734491", "type": "paper", "label": "pmid:34734491"}, {"id": "source:pmid:34734491", "type": "manuscript", "label": "PMID 34734491 full text"}, {"id": "data:geo:GSE10072", "type": "dataset", "label": "GEO GSE10072"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34734491", "type": "paper", "label": "pmid:34734491"}, {"id": "source:pmid:34734491", "type": "manuscript", "label": "PMID 34734491 full text"}, {"id": "data:geo:GSE10072", "type": "dataset", "label": "GEO GSE10072"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34734491", "type": "extraction", "used": ["source:pmid:34734491"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10072", "type": "accession_resolution", "used": ["data:geo:GSE10072"], "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:34734491", "parent_hash": "sha256:b45f9c2fdcaa1db3afad0bab07aa7e1215e76881d4f68a22241483a09e044e1a", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE10072 licence not read", "asset:data:geo:GSE10072 not downloaded", "asset:data:geo:GSE18842 licence not read", "asset:data:geo:GSE18842 not downloaded", "asset:data:geo:GSE27262 licence not read", "asset:data:geo:GSE27262 not downloaded", "asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE32863 licence not read", "asset:data:geo:GSE32863 not downloaded", "asset:data:geo:GSE42127 licence not read", "asset:data:geo:GSE42127 not downloaded", "asset:data:geo:GSE50081 licence not read", "asset:data:geo:GSE50081 not downloaded", "asset:data:geo:GSE68465 licence not read", "asset:data:geo:GSE68465 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:GSE72094 not downloaded", "asset:data:geo:GSE7670 licence not read", "asset:data:geo:GSE7670 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": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The overall survival of LUAD patients in each sub‐consensus was determined by the Kaplan–Meier survival analysis which was performed using “survival” package (version 3.1‐8) in R statistics software. The prognostic values of TPX2 and SELENBP1 on the relapse‐free survival or overall survival were also determined using “survival” package. P values were calculated by the log‐rank test."], "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":"2026-11-04T01:21:07+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}}}