{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36650426", "kind": "science-record", "revision": 3, "content_hash": "sha256:3da818188f2906be9da23aaf1b5453a62f9fd5fbf8c6a9a2ba831be33744cd01", "created_at": "2026-11-01T19:01:12Z", "updated_at": "2026-11-01T22:08:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genomic and immunogenomic analysis of three prognostic signature genes in LUAD.", "doi": "10.1186/s12859-023-05137-y", "pmid": "36650426", "authors": ["Hai-Ming Feng", "Ye Zhao", "Wei-Jian Yan", "Bin Li"], "journal": "BMC bioinformatics", "year": 2023, "abstract": "BACKGROUND: Searching for immunotherapy-related markers is an important research content to screen for target populations suitable for immunotherapy. Prognosis-related genes in early stage lung cancer may also affect the tumor immune microenvironment, which in turn affects immunotherapy.\nRESULTS: We analyzed the differential genes affecting lung cancer patients receiving immunotherapy through the Cancer Treatment Response gene signature DataBase (CTR-DB), and set a threshold to obtain a total of 176 differential genes between response and non-response to immunotherapy. Functional enrichment analysis found that these differential genes were mainly involved in immune regulation-related pathways. The early-stage lung adenocarcinoma (LUAD) prognostic model was constructed through the cancer genome atlas (TCGA) database, and three target genes (MMP12, NFE2, HOXC8) were screened to calculate the risk score of early-stage LUAD. The receiver operating characteristic (ROC) curve indicated that the model had good prognostic value, and the validation set (GSE50081, GSE11969 and GSE42127) from the gene expression omnibus (GEO) analysis indicated that the model had good stability, and the risk score was correlated with immune infiltrations to varying degrees. Multi-type survival analysis and immune infiltration analysis revealed that the transcriptome, methylation and the copy number variation (CNV) levels of the three genes were correlated with patient prognosis and some tumor microenvironment (TME) components. Drug sensitivity analysis found that the three genes may affect some anti-tumor drugs. The mRNA expression of immune checkpoint-related genes showed significant differences between the high and low group of the three genes, and there may be a mutual regulatory network between immune checkpoint-related genes and target genes. Tumor immune dysfunction and exclusion (TIDE) analysis found that three genes were associated with immunotherapy response and maybe the potential predictors to immunotherapy, consistent with the CTR-DB database analysis.\nCONCLUSIONS: From the perspective of data mining, this study suggests that MMP12, NFE2, and HOXC8 may be involved in tumor immune regulation and affect immunotherapy. They are expected to become markers of immunotherapy and are worthy of further experimental research.", "claims": [{"id": "claim-method", "statement": "Differential genes were screened by setting the threshold adjusted P value < = 0.05 and |logFC|> = 2, and the target genes were determined according to the AUC (Area under roc Curve) value > = 0.7.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36650426", "locator": "sections[3] \"Immunotherapy response differential genes (ImTRDG)\" paragraph 4", "quote": "Differential genes were screened by setting the threshold adjusted P value < = 0.05 and |logFC|> = 2, and the target genes were determined according to the AUC (Area under roc Curve) value > = 0.7."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36650426", "locator": "sections[35] \"Availability of data and materials\" paragraph 2", "quote": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 176 immunotherapy-response differential genes and constructed an early-stage LUAD prognostic risk score using MMP12, NFE2, and HOXC8.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36650426", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We analyzed the differential genes affecting lung cancer patients receiving immunotherapy through the Cancer Treatment Response gene signature DataBase (CTR-DB), and set a threshold to obtain a total of 176 differential genes between response and non-response to immunotherapy."}, {"asset": "source:pmid:36650426", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The early-stage lung adenocarcinoma (LUAD) prognostic model was constructed through the cancer genome atlas (TCGA) database, and three target genes (MMP12, NFE2, HOXC8) were screened to calculate the risk score of early-stage LUAD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 176 immunotherapy-response differential genes and constructed an early-stage LUAD prognostic risk score using MMP12, NFE2, and HOXC8.", "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:36650426"], "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:GSE11969"], "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": {"hazard_ratio": "lues and hazard ratios (HR) with 95% confidence in"}, "inputs": ["data:geo:GSE11969"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36650426", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12859-023-05137-y", "sha256": "sha256:61d787e1bd7e2c5aef9713264000accde6ded795f309ff3399df9d0f726e8896", "bytes": 87375, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12859-023-05137-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9843910", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE11969", "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=GSE11969", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE11969", "version": null, "note": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM302996", "GSM302997", "GSM302998", "GSM302999", "GSM303000", "GSM303001", "GSM303002", "GSM303003", "GSM303004", "GSM303005", "GSM303006", "GSM303007", "GSM303008", "GSM303009", "GSM303010", "GSM303011", "GSM303012", "GSM303013", "GSM303014", "GSM303015", "GSM303016", "GSM303017", "GSM303018", "GSM303019", "GSM303020", "GSM303021", "GSM303022", "GSM303023", "GSM303024", "GSM303025", "GSM303026", "GSM303027", "GSM303028", "GSM303029", "GSM303030", "GSM303031", "GSM303032", "GSM303033", "GSM303034", "GSM303035", "GSM303036", "GSM303037", "GSM303038", "GSM303039", "GSM303040", "GSM303041", "GSM303042", "GSM303043", "GSM303044", "GSM303045", "GSM303046", "GSM303047", "GSM303048", "GSM303049", "GSM303050", "GSM303051", "GSM303052", "GSM303053", "GSM303054", "GSM303055", "GSM303056", "GSM303057", "GSM303058", "GSM303059", "GSM303060", "GSM303061", "GSM303062", "GSM303063", "GSM303064", "GSM303065", "GSM303066", "GSM303067", "GSM303068", "GSM303069", "GSM303070", "GSM303071", "GSM303072", "GSM303073", "GSM303074", "GSM303075", "GSM303076", "GSM303077", "GSM303078", "GSM303079", "GSM303080", "GSM303081", "GSM303082", "GSM303083", "GSM303084", "GSM303085", "GSM303086", "GSM303087", "GSM303088", "GSM303089", "GSM303090", "GSM303091", "GSM303092", "GSM303093", "GSM303094", "GSM303095", "GSM303096", "GSM303097", "GSM303098", "GSM303099", "GSM303100", "GSM303101", "GSM303102", "GSM303103", "GSM303104", "GSM303105", "GSM303106", "GSM303107", "GSM303108", "GSM303109", "GSM303110", "GSM303111", "GSM303112", "GSM303113", "GSM303114", "GSM303115", "GSM303116", "GSM303117", "GSM303118", "GSM303119", "GSM303120", "GSM303121", "GSM303122", "GSM303123", "GSM303124", "GSM303125", "GSM303126", "GSM303127", "GSM303128", "GSM303129", "GSM303130", "GSM303131", "GSM303132", "GSM303133", "GSM303134", "GSM303135", "GSM303136", "GSM303137", "GSM303138", "GSM303139", "GSM303140", "GSM303141", "GSM303142", "GSM303143", "GSM303144", "GSM303145", "GSM303146", "GSM303147", "GSM303148", "GSM303149", "GSM303150", "GSM303151", "GSM303152", "GSM303153", "GSM303154", "GSM303155", "GSM303156", "GSM303157", "GSM303158"], "sample_count": 163, "group_sizes": null, "group_sizes_basis": null, "platform": "7015", "taxon": "Homo sapiens", "title": "Expression Profile-Defined Classification of Lung Adenocarcinoma", "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:GSE126044", "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=GSE126044", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE126044", "version": null, "note": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3589673", "GSM3589674", "GSM3589675", "GSM3589676", "GSM3589677", "GSM3589678", "GSM3589679", "GSM3589680", "GSM3589681", "GSM3589682", "GSM3589683", "GSM3589684", "GSM3589685", "GSM3589686", "GSM3589687", "GSM3589688"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in 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:GSE135222", "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=GSE135222", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE135222", "version": null, "note": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3995402", "GSM3995403", "GSM3995404", "GSM3995405", "GSM3995406", "GSM3995407", "GSM3995408", "GSM3995409", "GSM3995410", "GSM3995411", "GSM3995412", "GSM3995413", "GSM3995414", "GSM3995415", "GSM3995416", "GSM3995417", "GSM3995418", "GSM3995419", "GSM3995420", "GSM3995421", "GSM3995422", "GSM3995423", "GSM3995424", "GSM3995425", "GSM3995426", "GSM3995427", "GSM3995428"], "sample_count": 27, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "DNA methylation loss coupled with mitotic cell division promotes immune evasion of tumours with high mutation load [RNA-seq]", "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 (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. 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The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online.", "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", 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"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}}], "gaps": ["asset:data:geo:GSE11969 not downloaded", "asset:data:geo:GSE11969 licence not read", "asset:data:geo:GSE126044 not downloaded", "asset:data:geo:GSE126044 licence not read", "asset:data:geo:GSE135222 not downloaded", "asset:data:geo:GSE135222 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"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "lues and hazard ratios (HR) with 95% confidence in"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "KM"}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Cox regression"}}, {"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": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-5", "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"}}, {"id": "method-6", "family": null, "specific": null, "label": "Differential-expression screening using adjusted P value and absolute log-fold-change thresholds, followed by selection according to AUC.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differential genes were screened by setting the threshold adjusted P value < = 0.05 and |logFC|> = 2, and the target genes were determined according to the AUC (Area under roc Curve) value > = 0.7."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE135222", "GSE126044", "GSE50081", "GSE11969", "GSE42127"], "resolved_accessions": ["GSE135222", "GSE126044", "GSE50081", "GSE11969", "GSE42127"], "statements": ["The datasets (GSE135222, GSE126044, GSE50081, GSE11969 and GSE42127) generated and analysed during the current study are available in the GEO dataset repository. https://www.ncbi.nlm.nih.gov/gds. The original contributions presented in the study are included in the article/Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. Further inquiries can be directed to the corresponding authors. The Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 for this article can be found online."], "basis": "The paper names GSE135222, GSE126044, GSE50081, GSE11969, GSE42127 in Cancer Treatment Response gene signature DataBase (CTR-DB) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:36650426", "data:geo:GSE11969"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE11969"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:23:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 23730, "completion_tokens": 2994, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36650426", "type": "paper", "label": "pmid:36650426"}, {"id": "source:pmid:36650426", "type": "manuscript", "label": "PMID 36650426 full text"}, {"id": "data:geo:GSE11969", "type": "dataset", "label": "GEO GSE11969"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36650426", "type": "paper", "label": "pmid:36650426"}, {"id": "source:pmid:36650426", "type": "manuscript", "label": "PMID 36650426 full text"}, {"id": "data:geo:GSE11969", "type": "dataset", "label": "GEO GSE11969"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36650426", "type": "extraction", "used": ["source:pmid:36650426"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE11969", "type": "accession_resolution", "used": ["data:geo:GSE11969"], "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:36650426", "parent_hash": "sha256:36353e7e0515bac3700a7569d5e224005627af6be2766e67c900fe98767edadc", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE11969 licence not read", "asset:data:geo:GSE11969 not downloaded", "asset:data:geo:GSE126044 licence not read", "asset:data:geo:GSE126044 not downloaded", "asset:data:geo:GSE135222 licence not read", "asset:data:geo:GSE135222 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", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["mune infiltration analysis revealed that the transcriptome, methylation and the copy number variation (", "Univariate Cox regression analysis of ImTRDG RNAseq data (FPKM; Fragments Per Kilobase of transc"], "order_basis": "paper_text_order:1382", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["KM"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T00:35:22+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}}}