Identification of a novel four-lncRNA signature as a prognostic indicator in cirrhotic hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31396449", "kind": "science-record", "revision": 4, "content_hash": "sha256:ec8f2318bf221e44e809c1263171d70c869d18f41d35165efc6f4da9fcb4c044", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T21:22:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a novel four-lncRNA signature as a prognostic indicator in cirrhotic hepatocellular carcinoma.", "doi": "10.7717/peerj.7413", "pmid": "31396449", "authors": ["Linkun Ma", "Cunliang Deng"], "journal": "PeerJ", "year": 2019, "abstract": "BACKGROUND: Many studies have shown that long noncoding RNAs (lncRNA) are closely associated with the occurrence and development of various tumors and have the potential to be prognostic markers. Moreover, cirrhosis is an important prognostic risk factors in patients with liver cancer. Some studies have reported that lncRNA-related prognostic models have been used to predict overall survival (OS) and recurrence-free survival (RFS) in patients with hepatocellular carcinoma (HCC). However, no one has constructed a prognostic lncRNA model only in patients with cirrhotic HCC. Thus, it is necessary to screen novel potential lncRNA markers for improve the prognosis of cirrhotic HCC patients.\nMETHODS: The probe expression profile dataset (GSE14520-GPL3921) from the Gene Expression Omnibus (GEO), which included 204 cirrhotic HCC samples, was reannotated and the lncRNA and mRNA expression dataset was obtained. The patients were randomly assigned to either the training set (n = 103) and testing set (n = 100). Univariate cox regression and the least absolute shrinkage and selection operator (LASSO) model were applied to screen lncRNAs linked to the OS of cirrhotic HCC in the training set. The lncRNAs having significant correlation with OS were then selected and the multivariate Cox regression model was implemented to construct the prognostic score model. Whether or not this model was related to RFS in the training set was simultaneously determined. The testing set was used to validate the lncRNA risk score model. A risk score based on the lncRNA signature was used for stratified analysis of different clinical features to test their prognostic performance. The prognostic lncRNA-related protein genes were identified by the co-expression matrix of lncRNA-mRNA, and the function of these lncRNAs was predicted through the enrichment of these co-expression genes.\nRESULTS: The signature consisted of four lncRNAs:AC093797.1,POLR2J4,AL121748.1 and AL162231.4. The risk model was closely correlated with the OS of cirrhotic HCC in the training cohort, with a hazard ratio (HR) of 3.650 (95% CI [1.761-7.566]) and log-rank P value of 0.0002. Moreover, this model also showed favorable prognostic significance for RFS in the training set (HR: 2.392, 95% CI [1.374-4.164], log-rank P = 0.0015). The predictive performance of the four-lncRNA model for OS and RFS was verified in the testing set. Furthermore, the results of stratified analysis revealed that the four-lncRNA model was an independent factor in the prediction of OS and RFS of patients with clinical characteristics such as TNM (Tumor, Node, Metastasis system) stages I-II, Barcelona Clinic Liver Cancer (BCLC) stages 0-A, and solitary tumors in both the training set and testing set. The results of functional prediction showed that four lncRNAs may be potentially involve in multiple metabolic processes, such as amino acid, lipid, and glucose metabolism in cirrhotic HCC.", "claims": [{"id": "claim-method", "statement": "Candidate prognostic lncRNAs were further reduced by least absolute shrinkage and selection operator (LASSO) regression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31396449", "locator": "sections[6] \"Construction of lncRNA expression-based prognostic signature\" paragraph 2", "quote": "Candidate prognostic lncRNAs were further reduced by least absolute shrinkage and selection operator (LASSO) regression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability: Raw data were generated in the study. All original data in this study were downloaded from the public databases GEO (https://www.ncbi.nlm.nih.gov/geo/). For the four-lncRNA signature identification, we used GSE14520.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31396449", "locator": "sections[3] \"Data availability statement\" paragraph 2", "quote": "The following information was supplied regarding data availability: Raw data were generated in the study. All original data in this study were downloaded from the public databases GEO (https://www.ncbi.nlm.nih.gov/geo/). For the four-lncRNA signature identification, we used GSE14520."}], "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:31396449"], "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:31396449", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.7413", "sha256": "sha256:c4a96b1d6b20f93be818f62712e90307ee57b0bcbf9d4ecc0fae577c4f92bfec", "bytes": 33809, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.7413", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6679908", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "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 following information was supplied regarding data availability: Raw data were generated in the study. All original data in this study were downloaded from the public databases GEO (https://www.ncbi.nlm.nih.gov/geo/). For the four-lncRNA signature identification, we used GSE14520.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability: Raw data were generated in the study. All original data in this study were downloaded from the public databases GEO (https://www.ncbi.nlm.nih.gov/geo/). For the four-lncRNA signature identification, we used GSE14520.", "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": "asset:table:pmid:31396449:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:98a002375beac068b6f2f0874f9ae4247f3bea03d43c58dcc9f7720327d0e4cf", "bytes": 220, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#table-1", "version": null, "note": "Clinical parameters of patients in the training set and testing set.", "structure": {"pmcid": "PMC6679908", "section_index": 5, "section_title": "Data and clinical characteristics", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Clinical parameters of patients in the training set and testing set.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[5]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:31396449:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bc82f005f49affff023c2a71b5847454f357bd8cdd57cd2cd10df90af551e8ed", "bytes": 387, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#table-2", "version": null, "note": "Five candidate lncRNAs screened by LASSO regression were inserted in multivariate COX regression.Four lncRNAs with independent prognostic significance for overall survival were screened out. Details of the four lncRNAs are as follows.", "structure": {"pmcid": "PMC6679908", "section_index": 10, "section_title": "Construction of risk prognostic scoring system in the training set", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Five candidate lncRNAs screened by LASSO regression were inserted in multivariate COX regression.Four lncRNAs with independent prognostic significance for overall survival were screened out. Details of the four lncRNAs are as follows.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:31396449:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4b88cfa8d36979c036dabf2c320afd15fa49be6292ec505c023e3738524d7723", "bytes": 258, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#table-3", "version": null, "note": "Stratified analysis of the overall survival of four-lncRNA signature in the training set and testing set.", "structure": {"pmcid": "PMC6679908", "section_index": 12, "section_title": "Stratification analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "Stratified analysis of the overall survival of four-lncRNA signature in the training set and testing set.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[12]/table-wrap[1]#table-3"}}, {"id": "asset:table:pmid:31396449:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7f326bd93f5e452865a7858c2c5c8d1884d7523d08bc5b309f858eb4670433cf", "bytes": 266, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#table-4", "version": null, "note": "Stratified analysis of the recurrence-free survival of four-lncRNA signature in the training set and testing set.", "structure": {"pmcid": "PMC6679908", "section_index": 12, "section_title": "Stratification analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 4", "caption": "Stratified analysis of the recurrence-free survival of four-lncRNA signature in the training set and testing set.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[12]/table-wrap[2]#table-4"}}], "gaps": ["asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE14520 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "cox regression"}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"p_value": "566]) and log-rank P value of 0"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "log-rank"}}, {"id": "method-3", "family": null, "specific": null, "label": "least absolute shrinkage and selection operator (LASSO) regression", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Candidate prognostic lncRNAs were further reduced by least absolute shrinkage and selection operator (LASSO) regression."}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE14520"], "resolved_accessions": ["GSE14520"], "statements": ["The following information was supplied regarding data availability: Raw data were generated in the study. All original data in this study were downloaded from the public databases GEO (https://www.ncbi.nlm.nih.gov/geo/). For the four-lncRNA signature identification, we used GSE14520."], "basis": "The paper names GSE14520 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:31396449", "data:geo:GSE14520", "asset:table:pmid:31396449:1", "asset:table:pmid:31396449:2", "asset:table:pmid:31396449:3", "asset:table:pmid:31396449:4"], "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": "2026-10-31T18:15:44Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25134, "completion_tokens": 913, "cached_tokens": 656}}, "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:31396449", "type": "paper", "label": "pmid:31396449"}, {"id": "source:pmid:31396449", "type": "manuscript", "label": "PMID 31396449 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31396449", "type": "paper", "label": "pmid:31396449"}, {"id": "source:pmid:31396449", "type": "manuscript", "label": "PMID 31396449 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31396449", "type": "extraction", "used": ["source:pmid:31396449"], "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:31396449", "parent_hash": "sha256:c31cd8a2824d0252ecc114136c4d2033fdcc07725fa89cf84073ebac2b35d057", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "clinical_trial", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["nd mRNA expression dataset was obtained. The patients were randomly assigned to either the training set (n = 103) and tes"], "order_basis": "paper_text_order:987", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["cox regression"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}