Identification of a molecular subtyping system associated with the prognosis of Asian hepatocellular carcinoma patients receiving liver resection.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31068611", "kind": "science-record", "revision": 6, "content_hash": "sha256:43d51a9d90579f6fdeac6bc36b10f2a4519280c91f3d8cc8220a22ad9813a47d", "created_at": "2026-11-01T15:40:44Z", "updated_at": "2026-11-01T21:22:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a molecular subtyping system associated with the prognosis of Asian hepatocellular carcinoma patients receiving liver resection.", "doi": "10.1038/s41598-019-43548-1", "pmid": "31068611", "authors": ["Xiaohua Ma", "Jingxian Gu", "Kun Wang", "Xing Zhang", "Juan Bai", "Jingyao Zhang", "Chang Liu", "Qiang Qiu", "Kai Qu"], "journal": "Scientific reports", "year": 2019, "abstract": "Hepatocellular carcinoma (HCC) remains a severe health issue worldwide, especially in Asia. To date, molecular classifications proposed for the overall survival (OS) or recurrence-free survival (RFS) prediction of Asian HCC patients after hepatectomy are quite few and limited in clinical practice. Here, we established a molecular subtyping system for Asian HCC to facilitate prognosis evaluation. Firstly, differentially expressed genes (DEGs) (FDR [false discovery rate] <0.05) between different types of liver cancer and non-tumor tissue were screened. Among the DEGs solely between HCC and non-tumor samples, 185 genes simultaneously significantly associated with the OS and RFS were identified as HCC-characteristic genes. The molecular subtypes were developed based on the expression profiles of the 185 genes in the training dataset (TCGA [The Cancer Genome Atlas] dataset) using non-negative matrix factorization (NMF) clustering method. Patients were then classified into Subtype1 and Subtype2 groups denoting unfavorable and favorable clinical outcome respectively. The robustness and effectiveness of the molecular subtype was confirmed in another independent dataset (GSE14520) by the same clustering approach and Kaplan-Meier analyses. Moreover, functional prediction analysis revealed that the identified molecular signature was involved in chemotaxis, apoptosis and cell development associated pathways. Besides, the molecular signature was closely related to the clinical characteristics including TNM stage, preoperative alpha-fetoprotein (AFP) level and TP53 mutation. Furthermore, integration of the molecular subtype and TNM stage was demonstrated to improve risk stratification. Taken together, our molecular subtyping system exhibited great utility and potential in prognosis prediction and therapeutic decision making of Asian HCC patients.", "claims": [{"id": "claim-data-access", "statement": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31068611", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31068611"], "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:GSE14520"], "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:GSE14520"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31068611", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-019-43548-1", "sha256": "sha256:dcf797b0cd0c6351504d5ef14f0ad4c9ddc233a89a9b0a932cc2126664d72a53", "bytes": 22967, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-019-43548-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6506502", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM362947", "GSM362948", "GSM362949", "GSM362950", "GSM362951", "GSM362952", "GSM362953", "GSM362954", "GSM362955", "GSM362956", "GSM362957", "GSM362958", "GSM362959", "GSM362960", "GSM362961", "GSM362962", "GSM362963", "GSM362964", "GSM362965", "GSM362966", "GSM362967", "GSM362968", "GSM362969", "GSM362970", "GSM362971", "GSM362972", "GSM362973", "GSM362974", "GSM362975", "GSM362976", "GSM362977", "GSM362978", "GSM362979", "GSM362980", "GSM362981", "GSM362982", "GSM362983", "GSM362984", "GSM362985", "GSM362986", "GSM362987", "GSM362988", "GSM362989", "GSM362990", "GSM362991", "GSM362992", "GSM362993", "GSM362994", "GSM362995", "GSM362996", "GSM362997", "GSM362998", "GSM362999", "GSM363000", "GSM363001", "GSM363002", "GSM363003", "GSM363004", "GSM363005", "GSM363006", "GSM363007", "GSM363008", "GSM363009", "GSM363010", "GSM363011", "GSM363012", "GSM363013", "GSM363014", "GSM363015", "GSM363016", "GSM363017", "GSM363018", "GSM363019", "GSM363020", "GSM363021", "GSM363022", "GSM363023", "GSM363024", "GSM363025", "GSM363026", "GSM363027", "GSM363028", "GSM363029", "GSM363030", "GSM363031", "GSM363032", "GSM363033", "GSM363034", "GSM363035", "GSM363036", "GSM363037", "GSM363038", "GSM363039", "GSM363040", "GSM363041", "GSM363042", "GSM363043", "GSM363044", "GSM363045", "GSM363046", "GSM363047", "GSM363048", "GSM363049", "GSM363050", "GSM363051", "GSM363052", "GSM363053", "GSM363054", "GSM363055", "GSM363056", "GSM363057", "GSM363058", "GSM363059", "GSM363060", "GSM363061", "GSM363062", "GSM363063", "GSM363064", "GSM363065", "GSM363066", "GSM363067", "GSM363068", "GSM363069", "GSM363070", "GSM363071", "GSM363072", "GSM363073", "GSM363074", "GSM363075", "GSM363076", "GSM363077", "GSM363078", "GSM363079", "GSM363080", "GSM363081", "GSM363082", "GSM363083", "GSM363084", "GSM363085", "GSM363086", "GSM363087", "GSM363088", "GSM363089", "GSM363090", "GSM363091", "GSM363092", "GSM363093", "GSM363094", "GSM363095", "GSM363096", "GSM363097", "GSM363098", "GSM363099", "GSM363100", "GSM363101", "GSM363102", "GSM363103", "GSM363104", "GSM363105", "GSM363106", "GSM363107", "GSM363108", "GSM363109", "GSM363110", "GSM363111", "GSM363112", "GSM363113", "GSM363114", "GSM363115", "GSM363116", "GSM363117", "GSM363118", "GSM363119", "GSM363120", "GSM363121", "GSM363122", "GSM363123", "GSM363124", "GSM363125", "GSM363126", "GSM363127", "GSM363128", "GSM363129", "GSM363130", "GSM363131", "GSM363132", "GSM363133", "GSM363134", "GSM363135", "GSM363136", "GSM363137", "GSM363138", "GSM363139", "GSM363140", "GSM363141", "GSM363142", "GSM363143", "GSM363144", "GSM363145", "GSM363146", "GSM363147", "GSM363148", "GSM363149", "GSM363150", "GSM363151", "GSM363152", "GSM363153", "GSM363154", "GSM363155", "GSM363156", "GSM363157", "GSM363158", "GSM363159", "GSM363160", "GSM363161", "GSM363162", "GSM363163", "GSM363164", "GSM363165", "GSM363166", "GSM363167", "GSM363168", "GSM363169", "GSM363170", "GSM363171", "GSM363172", "GSM363173", "GSM363174", "GSM363175", "GSM363176", "GSM363177", "GSM363178", "GSM363179", "GSM363180", "GSM363181", "GSM363182", "GSM363183", "GSM363184", "GSM363185", "GSM363186", "GSM363187", "GSM363188", "GSM363189", "GSM363190", "GSM363191", "GSM363192", "GSM363193", "GSM363194", "GSM363195", "GSM363196", "GSM363197", "GSM363198", "GSM363199", "GSM363200", "GSM363201", "GSM363202", "GSM363203", "GSM363204", "GSM363205", "GSM363206", "GSM363207", "GSM363208", "GSM363209", "GSM363210", "GSM363211", "GSM363212", "GSM363213", "GSM363214", "GSM363215", "GSM363216", "GSM363217", "GSM363218", "GSM363219", "GSM363220", "GSM363221", "GSM363222", "GSM363223", "GSM363224", "GSM363225", "GSM363226", "GSM363227", "GSM363228", "GSM363229", "GSM363230", "GSM363231", "GSM363232", "GSM363233", "GSM363234", "GSM363235", "GSM363236", "GSM363237", "GSM363238", "GSM363239", "GSM363240", "GSM363241", "GSM363242", "GSM363243", "GSM363244", "GSM363245", "GSM363246", "GSM363247", "GSM363248", "GSM363249", "GSM363250", "GSM363251", "GSM363252", "GSM363253", "GSM363254", "GSM363255", "GSM363256", "GSM363257", "GSM363258", "GSM363259", "GSM363260", "GSM363261", "GSM363262", "GSM363263", "GSM363264", "GSM363265", "GSM363266", "GSM363267", "GSM363268", "GSM363269", "GSM363270", "GSM363271", "GSM363272", "GSM363273", "GSM363274", "GSM363275", "GSM363276", "GSM363277", "GSM363278", "GSM363279", "GSM363280", "GSM363281", "GSM363282", "GSM363283", "GSM363284", "GSM363285", "GSM363286", "GSM363287", "GSM363288", "GSM363289", "GSM363290", "GSM363291", "GSM363292", "GSM363293", "GSM363294", "GSM363295", "GSM363296", "GSM363297", "GSM363298", "GSM363299", "GSM363300", "GSM363301", "GSM363302", "GSM363303", "GSM363304", "GSM363305", "GSM363306", "GSM363307", "GSM363308", "GSM363309", "GSM363310", "GSM363311", "GSM363312", "GSM363313", "GSM363314", "GSM363315", "GSM363316", "GSM363317", "GSM363318", "GSM363319", "GSM363320", "GSM363321", "GSM363322", "GSM363323", "GSM363324", "GSM363325", "GSM363326", "GSM363327", "GSM363328", "GSM363329", "GSM363330", "GSM363331", "GSM363332", "GSM363333", "GSM363334", "GSM363335", "GSM363336", "GSM363337", "GSM363338", "GSM363339", "GSM363340", "GSM363341", "GSM363342", "GSM363343", "GSM363344", "GSM363345", "GSM363346", "GSM363347", "GSM363348", "GSM363349", "GSM363350", "GSM363351", "GSM363352", "GSM363353", "GSM363354", "GSM363355", "GSM363356", "GSM363357", "GSM363358", "GSM363359", "GSM363360", "GSM363361", "GSM363362", "GSM363363", "GSM363364", "GSM363365", "GSM363366", "GSM363367", "GSM363368", "GSM363369", "GSM363370", "GSM363371", "GSM363372", "GSM363373", "GSM363374", "GSM363375", "GSM363376", "GSM363378", "GSM363380", "GSM363381", "GSM363382", "GSM363384", "GSM363386", "GSM363388", "GSM363391", "GSM363393", "GSM363397", "GSM363400", "GSM363402", "GSM363404", "GSM363407", "GSM363417", "GSM363420", "GSM363421", "GSM363422", "GSM363423", "GSM363424", "GSM363425", "GSM363426", "GSM363427", "GSM363428", "GSM363429", "GSM363430", "GSM363431", "GSM363432", "GSM363433", "GSM363434", "GSM363435", "GSM363436", "GSM363437", "GSM363438", "GSM363439", "GSM363440", "GSM363441", "GSM363442", "GSM363443", "GSM363444", "GSM363445", "GSM363446", "GSM363447", "GSM363448", "GSM363449", "GSM363450", "GSM363451", "GSM712532", "GSM712533", "GSM712534", "GSM712535", "GSM712536", "GSM712537", "GSM712538", "GSM712539", "GSM712540", "GSM712541", "GSM712542"], "sample_count": 488, "group_sizes": null, "group_sizes_basis": null, "platform": "3921;571", "taxon": "Homo sapiens", "title": "Gene expression data of human hepatocellular carcinoma (HCC)", "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:GSE15765", "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=GSE15765", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15765", "version": null, "note": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM395647", "GSM395648", "GSM395649", "GSM395650", "GSM395651", "GSM395652", "GSM395653", "GSM395654", "GSM395655", "GSM395656", "GSM395657", "GSM395658", "GSM395659", "GSM395660", "GSM395661", "GSM395662", "GSM395663", "GSM395664", "GSM395665", "GSM395666", "GSM395667", "GSM395669", "GSM395670", "GSM395671", "GSM395672", "GSM395673", "GSM395674", "GSM395675", "GSM395676", "GSM395677", "GSM395678", "GSM395679", "GSM395680", "GSM395681", "GSM395682", "GSM395683", "GSM395684", "GSM395685", "GSM395686", "GSM395687", "GSM395688", "GSM395689", "GSM395690", "GSM395691", "GSM395692", "GSM395693", "GSM395694", "GSM395695", "GSM395696", "GSM395697", "GSM395698", "GSM395699", "GSM395700", "GSM395701", "GSM395702", "GSM395703", "GSM395704", "GSM395705", "GSM395706", "GSM395707", "GSM395708", "GSM395709", "GSM395710", "GSM395711", "GSM395712", "GSM395713", "GSM395714", "GSM395715", "GSM395716", "GSM395717", "GSM395718", "GSM395719", "GSM395720", "GSM395721", "GSM395722", "GSM395723", "GSM395724", "GSM395725", "GSM395726", "GSM395727", "GSM395728", "GSM395729", "GSM395730", "GSM395731", "GSM395732", "GSM395733", "GSM395734", "GSM395735", "GSM395736", "GSM395737"], "sample_count": 90, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Identification of cholangiocarcinoma-like gene expression traits in hepatocellular carcinoma", "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:GSE28691", "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=GSE28691", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28691", "version": null, "note": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM710556", "GSM710557", "GSM710558", "GSM710559", "GSM710560", "GSM710561", "GSM710562", "GSM710563", "GSM710564", "GSM710565", "GSM710566", "GSM710567", "GSM710568", "GSM710569", "GSM710570", "GSM710572", "GSM710573", "GSM710574", "GSM710575", "GSM710576", "GSM710577", "GSM710578", "GSM710579", "GSM710580", "GSM710581", "GSM710582", "GSM710583", "GSM710584", "GSM710585", "GSM710586", "GSM710587", "GSM710588", "GSM710589", "GSM710590", "GSM710591", "GSM710592", "GSM710593", "GSM710594", "GSM710595", "GSM710596", "GSM710597", "GSM774389"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Characterization of an Oxaliplatin Sensitivity Predictor in a preclinical Murine Model of Colorectal 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:GSE32879", "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=GSE32879", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32879", "version": null, "note": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM813712", "GSM813713", "GSM813714", "GSM813715", "GSM813716", "GSM813717", "GSM813718", "GSM813719", "GSM813720", "GSM813721", "GSM813722", "GSM813723", "GSM813724", "GSM813725", "GSM813726", "GSM813727", "GSM813728", "GSM813729", "GSM813730", "GSM813731", "GSM813732", "GSM813733", "GSM813734", "GSM813735", "GSM813736", "GSM813737", "GSM813738", "GSM813739", "GSM813740", "GSM813741", "GSM813742", "GSM813743", "GSM813744", "GSM813745", "GSM813746", "GSM813747", "GSM813748"], "sample_count": 37, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Integrative Transcriptomic Profiling reveals Hepatic Stem-like Phenotype and Interplay of EMT and miR-200c in Intrahepatic Cholangiocarcinoma [mRNA]", "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:GSE5851", "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=GSE5851", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE5851", "version": null, "note": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM136578", "GSM136579", "GSM136580", "GSM136581", "GSM136582", "GSM136583", "GSM136584", "GSM136585", "GSM136586", "GSM136587", "GSM136588", "GSM136589", "GSM136590", "GSM136591", "GSM136592", "GSM136593", "GSM136594", "GSM136595", "GSM136596", "GSM136597", "GSM136598", "GSM136599", "GSM136600", "GSM136601", "GSM136602", "GSM136603", "GSM136604", "GSM136605", "GSM136606", "GSM136607", "GSM136608", "GSM136609", "GSM136610", "GSM136611", "GSM136612", "GSM136613", "GSM136614", "GSM136615", "GSM136616", "GSM136617", "GSM136618", "GSM136619", "GSM136620", "GSM136621", "GSM136622", "GSM136623", "GSM136624", "GSM136625", "GSM136626", "GSM136627", "GSM136628", "GSM136629", "GSM136630", "GSM136631", "GSM136632", "GSM136633", "GSM136634", "GSM136635", "GSM136636", "GSM136637", "GSM136638", "GSM136639", "GSM136640", "GSM136641", "GSM136642", "GSM136643", "GSM136644", "GSM136645", "GSM136646", "GSM136647", "GSM136648", "GSM136649", "GSM136650", "GSM136651", "GSM136652", "GSM136653", "GSM136654", "GSM136655", "GSM136656", "GSM136657"], "sample_count": 80, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Phase II exploratory pharmacogenomics study of cetuximab monotherapy in patients with advanced metastatic CRC", "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:GSE14520 not downloaded", "asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE15765 not downloaded", "asset:data:geo:GSE15765 licence not read", "asset:data:geo:GSE28691 not downloaded", "asset:data:geo:GSE28691 licence not read", "asset:data:geo:GSE32879 not downloaded", "asset:data:geo:GSE32879 licence not read", "asset:data:geo:GSE5851 not downloaded", "asset:data:geo:GSE5851 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "reordered", "quote": "“The Kaplan-Meier analysis were performed in GraphPad Prism version 7.0.” “The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.”"}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}, {"id": "method-3", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}], "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": ["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": ["GSE15765", "GSE5851", "GSE28691", "GSE32879", "GSE14520"], "resolved_accessions": ["GSE15765", "GSE5851", "GSE28691", "GSE32879", "GSE14520"], "statements": ["The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/."], "basis": "The paper names GSE15765, GSE5851, GSE28691, GSE32879, GSE14520 in Gene Expression Omnibus (GEO) database 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:31068611", "data:geo:GSE14520"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14520"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:14:47Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 17437, "completion_tokens": 2786, "cached_tokens": 784}}, "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:31068611", "type": "paper", "label": "pmid:31068611"}, {"id": "source:pmid:31068611", "type": "manuscript", "label": "PMID 31068611 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31068611", "type": "paper", "label": "pmid:31068611"}, {"id": "source:pmid:31068611", "type": "manuscript", "label": "PMID 31068611 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31068611", "type": "extraction", "used": ["source:pmid:31068611"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14520", "type": "accession_resolution", "used": ["data:geo:GSE14520"], "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:31068611", "parent_hash": "sha256:f7be1b45cda660f7b4a5fbb38b5ecfbcc4394d2155b1d6fc57d7f2e59946cf42", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE15765 licence not read", "asset:data:geo:GSE15765 not downloaded", "asset:data:geo:GSE28691 licence not read", "asset:data:geo:GSE28691 not downloaded", "asset:data:geo:GSE32879 licence not read", "asset:data:geo:GSE32879 not downloaded", "asset:data:geo:GSE5851 licence not read", "asset:data:geo:GSE5851 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ecular signature was involved in chemotaxis, apoptosis and cell development associated pathways. Be"], "order_basis": "paper_text_order:1470", "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": 1.0, "evidence": ["“The Kaplan-Meier analysis were performed in GraphPad Prism version 7.0.” “The datasets used in this manuscript could be accessible through https://www.ncbi.nlm.nih.gov/geo/ and https://portal.gdc.cancer.gov/.”"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}