← All .science files
pmid:34526012
TNFAIP3 mutation may be associated with favorable overall survival for patients with T-cell lymphoma.
Cunte Chen · Zheng Chen · Ling Huang · Lingling Zhou · Lihua Zhu · Sichu Liu · Gengxin Luo · Wenyu Li · Chengwu Zeng · Yangqiu Li
Cancer cell international · 2021 doi:10.1186/s12935-021-02191-5
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 10 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 4 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 67 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 31 items
[0] array · 5 items
[1] array · 5 items
[2] array · 3 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 1 item
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 1 item
[20] array · 5 items
[21] array · 5 items
[22] array · 5 items
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 5 items
[27] array · 5 items
[28] array · 5 items
[29] array · 5 items
[30] array · 5 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 24 items
[0] array · 9 items
[1] array · 1 item
[2] array · 9 items
[3] array · 9 items
[4] array · 9 items
[5] array · 9 items
[6] array · 9 items
[7] array · 9 items
[8] array · 9 items
[9] array · 9 items
[10] array · 9 items
[11] array · 9 items
[12] array · 9 items
[13] array · 9 items
[14] array · 1 item
[15] array · 9 items
[16] array · 9 items
[17] array · 1 item
[18] array · 9 items
[19] array · 9 items
[20] array · 9 items
[21] array · 9 items
[22] array · 9 items
[23] array · 9 items
gaps array · 2 items
analysis object · 4 fields
methods array · 3 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 4 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34526012", "kind": "science-record", "revision": 7, "content_hash": "sha256:e4819dd21de51bcda84709b5c7d0e336d3424990afe83592d46e8aa1fed52c8f", "created_at": "2026-11-01T15:41:52Z", "updated_at": "2026-11-01T22:47:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "TNFAIP3 mutation may be associated with favorable overall survival for patients with T-cell lymphoma.", "doi": "10.1186/s12935-021-02191-5", "pmid": "34526012", "authors": ["Cunte Chen", "Zheng Chen", "Ling Huang", "Lingling Zhou", "Lihua Zhu", "Sichu Liu", "Gengxin Luo", "Wenyu Li", "Chengwu Zeng", "Yangqiu Li"], "journal": "Cancer cell international", "year": 2021, "abstract": "BACKGROUND: T-cell lymphoma (TCL) is highly aggressive and has a poor prognosis; thus, it is worth exploring biomarkers that may predict clinical outcomes and investigate their potential role in developing targeted therapies. In this study, we characterized the mutation pattern of tumor necrosis factor-alpha-inducing protein 3 (TNFAIP3) and its role in the prognosis of TCL patients.\nMETHODS: Coding sequence (CDS) mutations in TNFAIP3 in TCL patients was explored using exome-sequencing data from 79 patients in our center (Guangdong Provincial People's Hospital, GDPH) and 544 samples from the Catalogue of Somatic Mutations in Cancer (COSMIC) database. Additionally, non-CDS mutations in TNFAIP3 in 41 TCL patients from our center (JNU) were investigated by polymerase chain reaction (PCR) and Sanger sequencing. Furthermore, non-CDS mutations in TNFAIP3 in 47 TCL patients from Gene Expression Omnibus (GEO) dataset were explored.\nRESULTS: In the COSMIC database, TNFAIP3 mutations in TCL patients were located in the CDS, and the overall mutation frequency was 2.2%. However, TNFAIP3 mutations were not detected in the CDS of any of the samples in our center's datasets. Interestingly, non-CDS TNFAIP3 mutations were found in 14.6% and 4.3% of TCL patients in the JNU and GSE15842 dataset, respectively. Importantly, there was a clear trend showing that TCL patients with a TNFAIP3 mutation were associated with a longer 5-year restricted mean survival time (RMST) and favorable OS rate compared with those without a TNFAIP3 mutation in the JNU dataset [hazard ratio (HR) = 0.29, 95% confidence interval (CI) 0.07 to 1.31, P = 0.089]. Furthermore, TNFAIP3 mutations significantly correlated with T-cell large granular lymphocytic leukemia (T-LGLL) with a favorable prognosis in the JNU dataset (P = 0.002). Notably, the different mutation patterns of TNFAIP3 when comparing our center and the COSMIC datasets might be due to different ethnic and genetic backgrounds.\nCONCLUSIONS: To the best of our knowledge, we for the first time describe that TNFAIP3 mutations in non-CDS regions are associated with favorable OS for TCL patients, which might be a potential biomarker for the prognostic stratification of Chinese TCL patients.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier curves were plotted by the R package “survival’’, which was compared using the log-rank test [25, 26]. The R package “survRM2’’ was also used to determine the restricted mean survival time (RMST) [27].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34526012", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Kaplan–Meier curves were plotted by the R package “survival’’, which was compared using the log-rank test [25, 26]. The R package “survRM2’’ was also used to determine the restricted mean survival time (RMST) [27]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The COSMIC data used in this study were acquired from the COSMIC database (https://cancer.sanger.ac.uk/cosmic). The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34526012", "locator": "sections[19] \"Availability of data and materials\" paragraph 2", "quote": "The COSMIC data used in this study were acquired from the COSMIC database (https://cancer.sanger.ac.uk/cosmic). The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "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:34526012"], "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:GSE15842"], "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:GSE15842"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34526012", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-021-02191-5", "sha256": "sha256:cf5b07e8a947d2f623846972fb7d6d2f65a83fc5058a47684f27c808cc25ea7a", "bytes": 33788, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-021-02191-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8444556", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15842", "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=GSE15842", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15842", "version": null, "note": "The COSMIC data used in this study were acquired from the COSMIC database (https://cancer.sanger.ac.uk/cosmic). The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The COSMIC data used in this study were acquired from the COSMIC database (https://cancer.sanger.ac.uk/cosmic). The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM397926", "GSM397927", "GSM397928", "GSM397929", "GSM397930", "GSM397931", "GSM397932", "GSM397933", "GSM397934", "GSM397935", "GSM397936", "GSM397937", "GSM397938", "GSM397939", "GSM397940", "GSM397941", "GSM397942", "GSM397943", "GSM397944", "GSM397945", "GSM397946", "GSM397947", "GSM397948", "GSM397949", "GSM397950", "GSM397951", "GSM397952", "GSM397953", "GSM397954", "GSM397955", "GSM397956", "GSM397957", "GSM397958", "GSM397959", "GSM397960", "GSM397961", "GSM397962", "GSM397963", "GSM397964", "GSM397965", "GSM397966", "GSM397967", "GSM397968", "GSM397969", "GSM397970", "GSM397971", "GSM397972", "GSM397973", "GSM397974", "GSM397975", "GSM397976", "GSM397977", "GSM397978", "GSM397979", "GSM397980", "GSM397981", "GSM397982", "GSM397983", "GSM397984", "GSM397985", "GSM397986", "GSM397987", "GSM397988", "GSM397989", "GSM397990", "GSM397991", "GSM397992"], "sample_count": 67, "group_sizes": null, "group_sizes_basis": null, "platform": "3720", "taxon": "Homo sapiens", "title": "SNP array genomic profiling of PTCL NOS", "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:34526012:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9aad1ff229c2dbd056c08343f53b4ace0a13d4b148ea1c97a2ac3896dfe78edd", "bytes": 1776, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Clinical characteristics of TCL patients", "structure": {"pmcid": "PMC8444556", "section_index": 3, "section_title": "GDPH and JNU datasets", "row_count": 31, "column_count": 5}, "table": {"label": "Table 1", "caption": "Clinical characteristics of TCL patients", "rows": [["Variables", "JNU dataset", "GDPH dataset", "COSMIC dataset", "GSE15842 dataset"], ["Number", "41", "79", "544", "47"], ["Gender, n (%)", "–", "–"], ["Female", "19 (46.3)", "30 (38.0)", "–", "–"], ["Male", "22 (53.7)", "49 (62.0)", "–", "–"], ["Age, y, mean ± SD", "48 ± 19", "46 ± 19", "–", "–"], ["Subtype, n (%)a"], ["AITL", "5 (12.2)", "18 (22.8)", "101 (18.6)", "0 (0.0)"], ["ALCL", "1 (2.4)", "6 (7.6)", "19 (3.5)", "0 (0.0)"], ["ATLL", "0 (0.0)", "0 (0.0)", "292 (53.7)", "0 (0.0)"], ["CTCL", "1 (2.4)", "1 (1.3)", "73 (13.4)", "0 (0.0)"], ["EATL", "1 (2.4)", "0 (0.0)", "0 (0.0)", "0 (0.0)"], ["HSTCL", "0 (0.0)", "1 (1.3)", "3 (0.6)", "0 (0.0)"], ["MEITL", "0 (0.0)", "1 (1.3)", "0 (0.0)", "0 (0.0)"], ["NKTCL", "15 (36.6)", "15 (19.0)", "7 (1.3)", "0 (0.0)"], ["PTCL-NOS", "5 (12.2)", "18 (22.8)", "48 (8.8)", "47 (100%)"], ["SPTCL", "1 (2.4)", "1 (1.3)", "0 (0.0)", "0 (0.0)"], ["T-LBL", "9 (22.0)", "18 (22.8)", "0 (0.0)", "0 (0.0)"], ["T-LGLL", "3 (7.3)", "0 (0.0)", "1 (0.2)", "0 (0.0)"], ["Country, n (%)a"], ["China", "41 (100)", "79 (100)", "0 (0.0)", "0 (0.0)"], ["USA", "0 (0.0)", "0 (0.0)", "237 (43.6)", "0 (0.0)"], ["Japan", "0 (0.0)", "0 (0.0)", "291 (53.5)", "0 (0.0)"], ["Australia", "0 (0.0)", "0 (0.0)", "9 (1.7)", "0 (0.0)"], ["Italy", "0 (0.0)", "0 (0.0)", "5 (0.9)", "0 (0.0)"], ["Germany", "0 (0.0)", "0 (0.0)", "0 (0.0)", "47 (100%)"], ["Unknown", "0 (0.0)", "0 (0.0)", "4 (0.7)", "0 (0.0)"], ["Detection method", "PCR + sanger sequencing", "Exome sequencing", "–", "SNP array"], ["Covered area", "Non-CDS and CDS", "CDS", "CDS", "–"], ["Follow up, m, median (range)", "23.37 (0.23 to 157.83)", "–", "–", "–"], ["Status (alive/dead), n", "22/19", "–", "–", "–"]], "row_count": 31, "column_count": 5, "numeric_cells": 89, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:34526012:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a3dd475e234a0655009db5baa4ab38397341133f75a166fa30f962b236f5e474", "bytes": 2076, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#Tab2", "version": null, "note": "Clinical characteristics of T-cell lymphoma patients with a TNFAIP3 mutation", "structure": {"pmcid": "PMC8444556", "section_index": 9, "section_title": "Mutation pattern of TNFAIP3 in TCL", "row_count": 24, "column_count": 9}, "table": {"label": "Table 2", "caption": "Clinical characteristics of T-cell lymphoma patients with a TNFAIP3 mutation", "rows": [["Sample ID", "Histological subtype", "Age, y", "Gender", "Country", "Mutation sites", "TNFAIP3 mutation", "OS time (months)", "Clinical outcome"], ["COSMIC dataset"], ["Patient 1", "PTCL-NOS", "< 60", "Female", "USA", "CDS", "g.305 A>G", "–", "Not relapse"], ["Patient 2", "PTCL-NOS", "≥ 60", "Female", "USA", "CDS", "g.1939 A>C", "–", "Not relapse"], ["Patient 3", "PTCL-NOS", "–", "–", "USA", "CDS", "g.1939 A>C", "–", "Not relapse"], ["Patient 4", "CTCL", "≥ 60", "Male", "USA", "CDS", "g.1307G>A, g.796dup, and g.732 C>A", "–", "Alive"], ["Patient 5", "AITL", "–", "Female", "USA", "CDS", "g.811 C>T", "–", "Alive"], ["Patient 6", "CTCL", "67", "Male", "USA", "CDS", "g.-15-1829_-15-1814del", "–", "–"], ["Patient 7", "ATLL", "56", "Male", "Japan", "CDS", "g.318dup", "–", "–"], ["Patient 8", "CTCL", "–", "Female", "USA", "CDS", "g.380T>G", "–", "–"], ["Patient 9", "ATLL", "–", "–", "Japan", "CDS", "g.1616_1617insT", "–", "–"], ["Patient 10", "ATLL", "–", "–", "Japan", "CDS", "g.1439_1440dup", "–", "–"], ["Patient 11", "ATLL", "79", "Female", "Japan", "CDS", "g.1667dup", "–", "–"], ["Patient 12", "ATLL", "–", "–", "Japan", "CDS", "g.1166 C>T", "–", "–"], ["GSE15842 dataset"], ["Patient 13", "PTCL-NOS", "–", "–", "Germany", "Intron", "rs582757", "–", "–"], ["Patient 14", "PTCL-NOS", "–", "–", "Germany", "Intron", "rs582757", "–", "–"], ["JNU dataset"], ["Patient 15", "T-LBL", "69", "Female", "China", "Promoter", "g.3918 C>T", "98.9", "Death"], ["Patient 16", "CTCL", "36", "Male", "China", "Promoter", "g.3918 C>T and g.3637 T>A", "58.8", "Death"], ["Patient 17", "T-LBL", "19", "Male", "China", "3’UTR", "g.3869 C>G", "94.3", "Alive"], ["Patient 18", "T-LGLL", "27", "Male", "China", "Intron", "g.13751 A>C", "97.1", "Alive"], ["Patient 19", "T-LGLL", "40", "Female", "China", "Intron", "g.13751 A>C", "118.5", "Alive"], ["Patient 20", "T-LGLL", "50", "Female", "China", "Intron", "g.13751 A>C, g.14244 C>T, and g.11822T>C", "102.4", "Alive"]], "row_count": 24, "column_count": 9, "numeric_cells": 60, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:GSE15842 not downloaded", "asset:data:geo:GSE15842 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "restricted_mean_survival", "label": "Survival analysis", "dsl_operations": ["restricted_mean_survival"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Kaplan–Meier curves were plotted by the R package “survival’’, which was compared using the log-rank test [25, 26]. The R package “survRM2’’ was also used to determine the restricted mean survival time (RMST) [27]."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}], "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": ["restricted_mean_survival"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: restricted_mean_survival."}, "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": ["GSE15842"], "resolved_accessions": ["GSE15842"], "statements": ["The COSMIC data used in this study were acquired from the COSMIC database (https://cancer.sanger.ac.uk/cosmic). The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE15842 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": ["restricted_mean_survival"], "assets": ["source:pmid:34526012", "data:geo:GSE15842", "asset:table:pmid:34526012:1", "asset:table:pmid:34526012:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15842"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:40Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 29519, "completion_tokens": 1413, "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:34526012", "type": "paper", "label": "pmid:34526012"}, {"id": "source:pmid:34526012", "type": "manuscript", "label": "PMID 34526012 full text"}, {"id": "data:geo:GSE15842", "type": "dataset", "label": "GEO GSE15842"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34526012", "type": "paper", "label": "pmid:34526012"}, {"id": "source:pmid:34526012", "type": "manuscript", "label": "PMID 34526012 full text"}, {"id": "data:geo:GSE15842", "type": "dataset", "label": "GEO GSE15842"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34526012", "type": "extraction", "used": ["source:pmid:34526012"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15842", "type": "accession_resolution", "used": ["data:geo:GSE15842"], "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:34526012", "parent_hash": "sha256:38f115ea7b56b3d9e963d580c9fabdb45e969defbf9e17065775264337a432b4", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE15842 licence not read", "asset:data:geo:GSE15842 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["restricted_mean_survival"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan–Meier curves were plotted by the R package “survival’’, which was compared using the log-rank test [25, 26]. The R package “survRM2’’ was also used to determine the restricted mean survival time (RMST) [27]."], "order_basis": "analysis_only", "id": "assay:1"}]}