← All .science files
pmid:33767977
A 15-Gene Signature and Prognostic Nomogram for Predicting Overall Survival in Non-Distant Metastatic Oral Tongue Squamous Cell Carcinoma.
Muyuan Liu · Litian Tong · Bin Liang · Xuhong Song · Lingzhu Xie · Hanwei Peng · Dongyang Huang
Frontiers in oncology · 2021 doi:10.3389/fonc.2021.587548
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 · 7 items
claims array · 1 item
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 · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 43 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 15 items
[0] array · 3 items
[1] array · 3 items
[2] array · 3 items
[3] array · 3 items
[4] array · 3 items
[5] array · 3 items
[6] array · 3 items
[7] array · 3 items
[8] array · 3 items
[9] array · 3 items
[10] array · 3 items
[11] array · 3 items
[12] array · 3 items
[13] array · 3 items
[14] array · 3 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 43 items
[0] array · 4 items
[1] array · 4 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 6 items
[23] array · 6 items
[24] array · 6 items
[25] array · 6 items
[26] array · 6 items
[27] array · 6 items
[28] array · 6 items
[29] array · 6 items
[30] array · 6 items
[31] array · 6 items
[32] array · 6 items
[33] array · 6 items
[34] array · 6 items
[35] array · 6 items
[36] array · 6 items
[37] array · 6 items
[38] array · 6 items
[39] array · 6 items
[40] array · 6 items
[41] array · 6 items
[42] array · 6 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 16 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[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
gaps array · 2 items
analysis object · 4 fields
methods array · 4 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
[3] object · 10 fields
dsl_operations array · 6 items
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 · 5 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 · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] 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:33767977", "kind": "science-record", "revision": 7, "content_hash": "sha256:966a2d6520f93e848192d519501f379f15228d88669cc727dc4aa2500e498c90", "created_at": "2026-11-01T15:41:30Z", "updated_at": "2026-11-01T22:03:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A 15-Gene Signature and Prognostic Nomogram for Predicting Overall Survival in Non-Distant Metastatic Oral Tongue Squamous Cell Carcinoma.", "doi": "10.3389/fonc.2021.587548", "pmid": "33767977", "authors": ["Muyuan Liu", "Litian Tong", "Bin Liang", "Xuhong Song", "Lingzhu Xie", "Hanwei Peng", "Dongyang Huang"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "BACKGROUND: Oral tongue squamous cell carcinoma (OTSCC) is a devastating tumor with poor prognosis. There is an urgent need for reliable biomarkers to help predict prognosis and guide treatment for OTSCC. In the current study, we aimed to develop a robust multi-gene signature and prognostic nomogram to predict the prognosis of patients with non-distant metastatic OTSCC.\nMETHODS: OTSCC-related differentially-expressed genes were screened from The Cancer Genome Atlas (TCGA) database. Univariate Cox regression based on 1,000 bootstrap replicates, LASSO regression and stepwise multivariate Cox regression were utilized to develop a novel multi-mRNA signature for predicting overall survival in OTSCC. The concordance index, area under receiver operating characteristic (ROC AUC) and calibration curve were employed to assess the prediction capacity of the novel multi-gene model. In addition, a prognostic nomogram was constructed to facilitate the clinical use of the fitted model. The Kaplan-Meier with log-rank test was employed to assess differences in overall survival.\nRESULTS: We successfully established a novel 15-mRNA prognostic model for predicting overall survival of non-distant metastatic OTSCC, involving ADTRP, ITGA3, RFC4, CCDC96, CYP2J2, NELL2, SPHK1, SPAG16, HBEGF, S100A9, EGFL6, ADGRG6, PDE4D, ABCA4, and CTTN. The prediction ability of this 15-gene signature was independent of other clinicopathological factors, with an HR of 11.5 (95% CI: 4.70-28.3). Moreover, internal validation by bootstrap analysis yielded a C-index of 0.849, with a 3-year AUC of 0.907 and 5-year AUC of 0.944, which implied excellent prediction accuracy of the fitted model. In addition, external validation by using the GEO dataset (GSE41116) yielded a C-index of 0.804, with a 3-year AUC of 0.868 and 5-year AUC of 0.855, which also indicated good prediction ability of the 15-gene model. Finally, a prognostic nomogram integrating risk group, grade, T stage and N stage was established.\nCONCLUSION: Our results demonstrate our 15-gene signature was independently associated with overall survival in non-distant metastatic OTSCC. Moreover, the prognostic nomogram integrating the 15-gene signature and clinicopathological factors has potential to be developed as a prognostic tool.", "claims": [{"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33767977", "locator": "sections[17] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author."}], "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:33767977"], "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:GSE41116"], "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:GSE41116"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33767977", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2021.587548", "sha256": "sha256:b551d43206d25330cd9faa7f3410c828f874e1c8b1f7cbf210f7d7829a5f7145", "bytes": 32760, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2021.587548", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7985252", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE41116", "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=GSE41116", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41116", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1008824", "GSM1008825", "GSM1008826", "GSM1008827", "GSM1008828", "GSM1008829", "GSM1008830", "GSM1008831", "GSM1008832", "GSM1008833", "GSM1008834", "GSM1008835", "GSM1008836", "GSM1008837", "GSM1008838", "GSM1008839", "GSM1008840", "GSM1008841", "GSM1008842", "GSM1008843", "GSM1008844", "GSM1008845", "GSM1008846", "GSM1008847", "GSM1008848", "GSM1008849", "GSM1008850", "GSM1008851", "GSM1008852", "GSM1008853", "GSM1008854", "GSM1008855", "GSM1008856", "GSM1008857", "GSM1008858", "GSM1008859", "GSM1008860", "GSM1008861", "GSM1008862", "GSM1008863", "GSM1008864", "GSM1008865", "GSM1008866"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers (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": "asset:table:pmid:33767977:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5803f2c3d18a07f19fa8def60b288966cd33552b2779e6466c1536967f8a2769", "bytes": 783, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T1", "version": null, "note": "Clinicopathological characteristics of the patients included in the training set and validating set.", "structure": {"pmcid": "PMC7985252", "section_index": 7, "section_title": "Clinical Characteristics of Oral Tongue Squamous Cell Carcinoma Patient Cohorts in The Cancer Genome Atlas and GEO", "row_count": 15, "column_count": 3}, "table": {"label": "Table 1", "caption": "Clinicopathological characteristics of the patients included in the training set and validating set.", "rows": [["Clinicopathological parameters", "Training Set (TCGA dataset, n = 127)", "Validating Set (GEO dataset, n = 28)"], ["Sex", "", ""], ["Male", "83 (65.4%)", "18 (64.3%)"], ["Female", "44 (34.6%)", "10 (35.7%)"], ["Age", "57 (y, median)", "60 (y, median)"], ["T Stage", "", ""], ["T1-2", "67 (52.7%)", "6 (21.4%)"], ["T3-4", "60 (47.3%)", "22 (78.6%)"], ["N Stage", "", ""], ["N−", "57 (44.9%)", "9 (32.1%)"], ["N+", "70 (55.1%)", "19 (67.9%)"], ["Grade", "", ""], ["Well", "17 (13.4%)", "2 (7.1%)"], ["Moderate", "86 (67.7%)", "19 (67.9%)"], ["Poor", "24 (18.9%)", "7 (25.0%)"]], "row_count": 15, "column_count": 3, "numeric_cells": 24, "header_rows": 1, "locator": "section[7]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33767977:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f02aaca9b8873be53557caa6af7638817b02ce2c2490b90800d524cc6390ed2a", "bytes": 3002, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T2", "version": null, "note": "Forty-one significantly differentially-expressed cancer-related genes selected by univariate Cox regression analysis.", "structure": {"pmcid": "PMC7985252", "section_index": 10, "section_title": "Univariate Cox Regression Based on 1,000 Bootstrap Replicates", "row_count": 43, "column_count": 6}, "table": {"label": "Table 2", "caption": "Forty-one significantly differentially-expressed cancer-related genes selected by univariate Cox regression analysis.", "rows": [["Gene", "HR", "Perc", "BCa"], ["95% CI_lower", "95% CI_upper", "95% CI_lower", "95% CI_upper"], ["KLF7", "2.051967", "1.181178", "4.013881", "1.169583", "4.006894"], ["TPTEP1", "0.489758", "0.254359", "0.833391", "0.282388", "0.892341"], ["ADTRP", "2.185642", "1.280026", "4.108594", "1.101236", "3.597496"], ["MAGIX", "0.395979", "0.196065", "0.691413", "0.211579", "0.735964"], ["ITGA3", "2.003327", "1.103321", "3.727782", "1.025672", "3.542512"], ["RFC4", "1.887744", "1.034734", "3.317223", "1.078374", "3.395053"], ["CCDC96", "0.430815", "0.241363", "0.775666", "0.24291", "0.776434"], ["SLC16A1", "2.302277", "1.254623", "4.446845", "1.143051", "3.997884"], ["BUB1", "1.883744", "1.068125", "3.44771", "1.082299", "3.56022"], ["ECT2", "2.064229", "1.193709", "3.845979", "1.167009", "3.664635"], ["MYO10", "1.872354", "1.074121", "3.459864", "1.077746", "3.487003"], ["STARD4", "1.97469", "1.129966", "3.52473", "1.120917", "3.502698"], ["ADAM8", "1.91557", "1.077973", "3.428193", "1.054494", "3.28236"], ["CYP2J2", "0.492253", "0.27153", "0.903332", "0.262146", "0.885367"], ["ANKRD6", "0.527813", "0.283685", "0.905571", "0.28838", "0.91253"], ["ZNF43", "0.418219", "0.215498", "0.759636", "0.227062", "0.774721"], ["NELL2", "1.942154", "1.131742", "3.661527", "1.131149", "3.648482"], ["HMMR", "2.0045", "1.141503", "3.624981", "1.086084", "3.533556"], ["CENPE", "1.8295", "1.033575", "3.431939", "1.050664", "3.445997"], ["SPHK1", "0.49007", "0.25464", "0.873303", "0.253429", "0.867494"], ["GMNN", "1.931726", "1.095112", "3.652783", "1.102352", "3.672541"], ["DPT", "0.519485", "0.281145", "0.896171", "0.291404", "0.945245"], ["FOXF2", "0.403354", "0.207124", "0.688939", "0.204161", "0.680017"], ["SPAG16", "0.484103", "0.250436", "0.877999", "0.247645", "0.86013"], ["PRC1", "1.782683", "1.061899", "3.250286", "1.029389", "3.162917"], ["BTBD19", "0.537572", "0.287423", "0.970207", "0.292695", "0.981974"], ["HBEGF", "1.844453", "1.055062", "3.368863", "1.035218", "3.279491"], ["LIMD2", "0.431411", "0.227756", "0.752626", "0.255372", "0.821784"], ["MAD2L1", "1.831203", "1.083429", "3.399503", "1.010933", "3.212912"], ["S100A9", "0.505054", "0.269118", "0.879279", "0.266268", "0.876931"], ["ZSCAN18", "0.540076", "0.280863", "0.949427", "0.292462", "0.972441"], ["F2RL1", "1.912172", "1.074282", "3.692009", "1.054937", "3.623047"], ["EGFL6", "0.463106", "0.235597", "0.83433", "0.23606", "0.841956"], ["ADGRG6", "2.712558", "1.593227", "5.241306", "1.474584", "4.89997"], ["COL8A2", "0.508989", "0.271427", "0.83458", "0.282756", "0.855419"], ["PDE4D", "2.122275", "1.220449", "4.164362", "1.133518", "4.039384"], ["EGFR", "1.794727", "1.041885", "3.212464", "1.008335", "3.136975"], ["ABCA4", "0.526956", "0.278465", "0.94388", "0.27772", "0.943084"], ["SPRR2B", "0.570465", "0.306516", "0.999423", "0.297087", "0.996577"], ["ATF3", "1.861422", "1.097457", "3.510935", "1.081672", "3.393476"], ["CTTN", "2.273275", "1.307902", "4.512247", "1.175267", "4.237856"]], "row_count": 43, "column_count": 6, "numeric_cells": 217, "header_rows": 2, "locator": "section[10]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:33767977:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:91b5624bf42f5d260247d64144290b45d0897821a500a02488f58ea4d63e3d4a", "bytes": 1485, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T3", "version": null, "note": "15-gene signature selected by stepwise multivariate Cox regression.", "structure": {"pmcid": "PMC7985252", "section_index": 11, "section_title": "Establishment of a 15-Gene Signature by Least Absolute Shrinkage and Selection Operator Regression and Stepwise Multivariate Cox Hazard Ratio Regression Modeling", "row_count": 16, "column_count": 5}, "table": {"label": "Table 3", "caption": "15-gene signature selected by stepwise multivariate Cox regression.", "rows": [["Gene Symbol", "Description", "Entrez ID", "HR (95% CI)", "p"], ["NELL2", "Neural Epidermal Growth Factor-Like 2", "4753", "3.46 (1.72–6.96)", "<0.001"], ["PDE4D", "Phosphodiesterase 4D", "5144", "2.80 (1.35–5.82)", "0.006"], ["CCDC96", "Coiled-Coil Domain-Containing Protein 96", "257236", "0.43 (0.23–0.82)", "0.01"], ["ADGRG6", "Adhesion G Protein-Coupled Receptor G6", "57211", "2.06 (1.01–4.17)", "0.046"], ["CTTN", "Cortactin", "2017", "2.47 (1.15–5.29)", "0.02"], ["HBEGF", "Heparin Binding EGF Like Growth Factor", "1839", "2.39 (1.20–4.78)", "0.013"], ["S100A9", "S100 Calcium Binding Protein A9", "6280", "0.49 (0.23–1.04)", "0.064"], ["ADTRP", "Androgen Dependent TFPI Regulating Protein", "84830", "2.15 (1.06–4.35)", "0.034"], ["CYP2J2", "Cytochrome P450 Family 2 Subfamily J Member 2", "1573", "0.43 (0.21–0.87)", "0.019"], ["RFC4", "Replication Factor C Subunit 4", "5984", "2.16 (1.07–4.36)", "0.032"], ["SPAG16", "Sperm Associated Antigen 16", "79582", "0.46 (0.24–0.90)", "0.023"], ["SPHK1", "Sphingosine Kinase 1", "8877", "0.50 (0.25–1.01)", "0.055"], ["ABCA4", "ATP Binding Cassette Subfamily A Member 4", "24", "0.48 (0.25–0.92)", "0.028"], ["EGFL6", "EGF Like Domain Multiple 6", "25975", "0.57 (0.30–1.08)", "0.085"], ["ITGA3", "Integrin Subunit Alpha 3", "3675", "1.93 (1.00–3.70)", "0.049"]], "row_count": 16, "column_count": 5, "numeric_cells": 60, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:GSE41116 not downloaded", "asset:data:geo:GSE41116 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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"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": 0.7, "band": "medium", "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": 0.7, "band": "medium", "quote": "log-rank"}}, {"id": "method-4", "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"}}], "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": ["GSE41116"], "resolved_accessions": ["GSE41116"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE41116 in 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:33767977", "data:geo:GSE41116", "asset:table:pmid:33767977:1", "asset:table:pmid:33767977:2", "asset:table:pmid:33767977:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE41116"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:29:18Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25004, "completion_tokens": 1755, "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:33767977", "type": "paper", "label": "pmid:33767977"}, {"id": "source:pmid:33767977", "type": "manuscript", "label": "PMID 33767977 full text"}, {"id": "data:geo:GSE41116", "type": "dataset", "label": "GEO GSE41116"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33767977", "type": "paper", "label": "pmid:33767977"}, {"id": "source:pmid:33767977", "type": "manuscript", "label": "PMID 33767977 full text"}, {"id": "data:geo:GSE41116", "type": "dataset", "label": "GEO GSE41116"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33767977", "type": "extraction", "used": ["source:pmid:33767977"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE41116", "type": "accession_resolution", "used": ["data:geo:GSE41116"], "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:33767977", "parent_hash": "sha256:9708982bb4b2886e28c9f225979bf17b74a62cb8f442d1bd4337a08cd2f274e8", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE41116 licence not read", "asset:data:geo:GSE41116 not downloaded", "execution.not_run", "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": 0.93, "evidence": ["nd GEO For the training cohort, clinical and RNA sequencing data of 13 normal tongue tissues and 127 OTS"], "order_basis": "paper_text_order:3664", "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": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}